Abstract:
The invention relates to a new method of determining in a sample the presence or absence of one or more analyte members of a group of two or more analytes. The invention therefore relates to a multiplex assay for determining the presence or absence of each analyte in a group of multiple analytes. The assay uses aptamers and transmembrane pores.
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Notices, Deadlines & Correspondence
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
Inventors
1. TURNER Daniel John
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
2. FORDHAM Daniel George
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
3. GILL Roger Charles
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
4. BROWN Clive Gavin
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
5. REID Stuart
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
6. CLARKE James Anthony
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
7. WHITE James
Oxford Nanopore Technologies Limited
Edmund Cartwright House
4 Robert Robinson Avenue
Oxford Science Park
Oxford Oxfordshire OX4 4GA
Specification
Field of the invention
The invention relates to a new method of determining in a sample the presence or
absence of one or more analyte members of a group of two or more analytes. The invention
therefore relates to a multiplex assay for determining the presence or absence of each analyte in a
group of multiple analytes. The assay uses aptamers and transmembrane pores.
Background of the invention
Transmembrane pores (nanopores) have great potential as direct, electrical biosensors for
a variety of analytes, such as polymers and small molecules. When a potential is applied across
a nanopore, there is a change in the current flow when a molecule, such as a nucleotide or a
polynucleotide, resides transiently in the barrel or channel of the nanopore for a certain period of
time. Specific molecules, such as specific nucleotides and specific polynucleotides, give current
changes of known signature and duration. Such current changes can be used to identify the
nucleotide or polynucleotide present in the pore.
Summary of the invention
The inventors have demonstrated that a transmembrane pore can be used in a multiplex
assay to determine the presence or absence of each analyte in a group of two or more analytes.
More specifically, the inventors have demonstrated that the presence or absence of analytes can
be determined using a transmembrane pore and panel of aptamer-containing probes. Each of the
analytes of interest is recognised by at least one probe in the panel. Each probe also includes a
tail that is capable of entering the pore and affecting the current flowing through the pore. Each
tail affects the current flowing through the pore in different and distinctive ways depending on
whether or not the probe is bound to one of the analytes of interest. The effect each probe in the
panel has on the current flowing through the pore is also distinctive so that the identity of each
probe can be detected. This combination of aptamers and tails is such that it is surprisingly
possible to identify the binding of one or more of, or even all of, the probes in the panel to the
analytes of interest by analyzing the effect of the probe tails on the current flowing through the
pore.
Accordingly, the invention provides a method of determining in a sample the presence or
absence of one or more analyte members of a group of two or more analytes, the method
comprising:
(a) contacting the sample with a transmembrane pore and a panel of two or more probes,
wherein each probe recognises one or more of the analyte members and comprises (i) an
aptamer that binds to one or more of the analyte members and (ii) a tail which is capable of
entering the pore and has different effects on the current flowing through the pore depending on
whether or not the aptamer in the probe is bound to one of the analyte members,
wherein each probe affects the current flowing through the pore in a distinctive manner,
and
wherein each analyte member in the group of two or more analytes is recognised by at
least one probe in the panel; and
(b) measuring the current flowing through the pore to determine which probes in the
panel, if any, have bound to an analyte member and thereby determining the presence or absence
of one or more analyte members in the sample.
The invention also provides:
a method of determining in a sample the concentration of one or more analyte members
of a group of two or more analytes, the method comprising:
(i) carrying out a method of the invention; and
(ii) for one or more analyte members shown to be present in the sample comparing
the current flowing through the pore in step (b) with control or reference data for each analyte
member and thereby determining the concentration of the one or more analyte members in the
sample;
- a panel of probes for determining in a sample the presence, concentration or absence of
one or more analyte members of a group of two or more analytes, the panel comprising two or
more probes,
wherein each probe recognises one or more of the analyte members and comprises (i) an
aptamer that binds to one or more of the analyte members and (ii) a tail which is capable of
entering a transmembrane pore and has different effects on the current flowing through the pore
depending on whether or not the aptamer in the probe is bound to one of the analyte members,
wherein each probe affects the current flowing through the pore in a distinctive manner,
and
wherein each analyte member in the group of two or more analytes is recognised by at
least one probe in the panel;
a kit for determining in a sample the presence, concentration or absence of one or more
analyte members of a group of two or more analytes, comprising (a) a panel of probes of the
invention and (b) a transmembrane pore; and
an analysis apparatus for determining in a sample the presence, concentration or absence
of one or more analyte members of a group of two or more analytes, comprising a plurality of
pores and a panel of probes of the invention.
Description of the Figures
Figure 1 shows a cartoon representation of the probe configuration within the nanopore in
the absence (a) and presence (b) of a bound analyte. The expected event traces corresponding to
the absence (c) and presence (d) of a bound analyte are shown below (the y-axis = current and
the x-axis = time for (c) and (d)). The dashed line represents a poly(dA) region and the cross
region represents an abasic region. In this embodiment, when the abasic region is held within
the b-barrel of the pore more current flows through the channel than when the poly(dA) region
resides within the b-barrel. Transitions from the upper to the lower current level indicate
dissociation of the aptamer-analyte complex.
Figure 2 illustrates the different block levels that are observed for aptamer sequence
5A15xl0A_TBA in the presence (b) and absence (a) of thrombin (the y-axis = current (pA) and
the x-axis = time (s) for (a) and (b)). a) Level 1 alone is observed when the aptamer (sequence
5A15xl0A_TBA) is present in solution in the absence of thrombin. b) Levels 1 and 2 are
detected when the aptamer (sequence 5A15xl0A_TBA) and thrombin are present in solution
(the difference between the levels is 30.5 pA). The appearance of level 2 indicates aptamer
bound to thrombin, and transitions from level 2 to level 1 indicate dissociation of the aptamerthrombin
complex.
Figure 3 illustrates the relationship between the thrombin concentration and the observed
event ratio (the number of thrombin bound events only compared to the number of thrombin
bound and unbound events combined). These two graphs show how the ratio between the
thrombin bound events and the total number of events (thrombin bound and unbound) vary with
the concentration of thrombin. The probe sequence used in this experiment was
5A15xl0A_TBA and the final concentration was 1250 nM. Using these calibration graphs it is
possible to determine the concentration of thrombin in a sample (graph (a) y-axis = ratio
(bound/unbound), x-axis = thrombin concentration (nM), graph (b) y-axis = ratio, x-axis = logio
thrombin concentration (nM)).
Figure 4 illustrates the different block levels that are observed for aptamer sequence
15X15A_TBA3'CholTEG (SEQ ID NO: 19 which has a cholesterol TEG at the 3' end) is the
presence (b) and absence (a) of thrombin (the y-axis = current (pA) and the x-axis = time (s) for
(a) and (b)). a) Level 1 alone is observed when the aptamer (sequence
15xl5A_TBA_3'CholTEG) is present in solution in the absence of thrombin. b) Levels 1 and 2
are detected when the aptamer has been pre-incubated in the presence of thrombin. The
appearance of level 2 indicates aptamer bound to thrombin, and transitions from level 2 to level 1
indicate dissociation of the aptamer-protein complex. This experiment was carried out with over
a magnitude lower concentration of aptamer than used in Example 2 .
Figure 5 illustrates how a number of different aptamers can be used to detect the presence
of thrombin, where each aptamer produces its own distinctive step level signal. The top figure
(a) shows the number of events detected for the free aptamer signals (labelled section A) and the
signals for each of the different aptamer tails when bound to thrombin (labelled section B). The
events for the bound aptamer 15xl5A to thrombin is labelled 1, the events for the bound aptamer
17xl3A to thrombin is labelled 2, the events for the bound aptamer 19x1 1A to thrombin is
labelled 3 and the events for the bound aptamer 5A15xl0A to thrombin is labelled 4 . The 'ratio'
shown on the x-axis is the current level obtained with the aptamer tail divided by the open pore
level (bin size = 0.0025) and the y-axis is the count. The lower figure (b, y-axis = current (pA)
and x-axis = time (s)) shows the four different block signals detected for each of the aptamer tail
sequences (1-4). A separate distinguishable signal is noted for each aptamer.
Figure 6 illustrates the different block levels that are observed for aptamer sequence
17x8A_PDGF in the presence (b) and absence (a) of PDGF (the y-axis = current (pA) and the xaxis
= time (s) for (a) and (b)). a) Level 1 alone is observed when the aptamer (sequence
17x8A_PDGF) is present in solution in the absence of PDGF. b) Levels 1 and 2 are detected
when the aptamer (sequence 17x8A_PDGF) and PDGF are present in solution. The appearance
of level 2 indicates aptamer bound to PDGF, and transitions from level 2 to level 1 indicate
dissociation of the aptamer-PDGF complex.
Figure 7 illustrates the different block levels that are observed for aptamer sequence
25x_PDGF in the presence (b) and absence (a) of PDGF (the y-axis = current (pA) and the x-axis
= time (s) for (a) and (b)). a) Level 1 alone is observed when the aptamer (sequence 25x_PDGF)
is present in solution in the absence of PDGF. b) Levels 1 and 3 are detected when the aptamer
(sequence 25x_PDGF) and PDGF are present in solution. The appearance of level 3 indicates
aptamer bound to PDGF, and transitions from level 3 to level 1 indicate dissociation of the
aptamer-PDGF complex.
Figure 8 illustrates the relationship between the PDGF concentration and the observed
event ratio (PDGF bound events only compared to PDFG bound and unbound events combined).
This graph (y-axis = logio event rate, x-axis = logio PDGF concentration (nM)) shows how the
ratio between the PDGF bound events and the total number of events (PDGF bound and unbound
events) vary with the concentration of PDGF. The probe sequence used in this experiment was
25x_PDGF. Using this calibration graph it is possible to determine the concentration of PDGF
in a sample.
Figure 9 illustrates the different block levels that are observed for aptamer sequence
25x_ATP in the presence (b) and absence (a) of ATP (the y-axis = current (pA) and the x-axis =
time (s) for (a) and (b)). a) Level 1 alone is observed when the aptamer (sequence 25x_ATP) is
present in solution in the absence of ATP. b) Levels 1 and 2 are detected when the aptamer
(sequence 25x_ATP) and ATP are present in solution. The appearance of level 2 indicates
aptamer bound to ATP, and transitions from level 2 to level 1 indicate dissociation of the
aptamer-ATP complex.
Figure 10 illustrates the different block levels that are observed for the aptamer sequence
and 17x8A_ATP in the presence (b) and absence (a) of ATP (the y-axis = current (pA) and the xaxis
= time (s) for (a) and (b)). a) Level 3 alone is observed when the aptamer (sequence
17x8A_ATP) is present in solution in the absence of ATP. b) Levels 2 and 3 are detected when
the aptamer (sequence 17x8A_ATP) and ATP are present in solution. The appearance of level 2
indicates aptamer bound to ATP, and transitions from level 2 to level 3 indicate dissociation of
the aptamer-ATP complex.
Figure 11 illustrates the relationship between the ATP concentration and the observed
event ratio (ATP bound events only compared to ATP bound and unbound events combined).
This graph (y-axis = event rate, x-axis = logioATP concentration (mM)) shows how the ratio
between the ATP bound events and the total number of events (ATP bound and unbound events),
varies with the concentration of ATP. The probe sequence used in this experiment was
17x8A_ATP. Using this calibration graph it is possible to determine the concentration of ATP in
a sample. Using aptamer 17x8A_ATP, a similar increase in event rate was observed, as the
concentration of ATP increased, as was observed previously for increasing thrombin
concentration. However, the Kd of ATP is in the micromolar range so a higher concentration of
ATP is needed to obtain a similar event rate.
Figure 12 highlights how an array of probes can be used to detect more than one analyte
in the same experiment. It is possible to observe both bound and unbound aptamer signals for all
three analytes - ATP (ATP aptamer alone = 1, ATP aptamer bound to ATP = 2), PDGF (PDGF
aptamer alone = 3, PDGF aptamer bound to PDGF = 4), expanded version shown in b) and
thrombin (thrombin aptamer alone = 5, thrombin aptamer bound to thrombin = 6). The different
analytes can be detected from their characteristic block levels and signal shapes. The y-axis =
current in pA for traces a) and b), the x-axis = time for traces a) and b) (total trace time for a) = 4
seconds and total trace time for b) = 0 .1 seconds).
Figure 13 shows a calibration plot (event ratio (y-axis) against thrombin concentration
(nM) (x-axis)) of the theoretically calculated (shown as a black line) and experimentally
observed values (shown as a grey bar chart). It is clear from the graph that the theoretical value
closely matches that which was determined experimentally.
Figure 14 illustrates the different block levels that are observed for aptamer sequence
strep probe 1 (SEQ ID NO: 24) in the presence (b) and absence (a) of streptavidin (the y-axis =
current (pA) and the x-axis = time (s) for (a) and (b)). a) Level 1 alone is observed when the
aptamer (strep probe 1) is present in solution in the absence of streptavidin. b) Level 2 is
detected when the aptamer (strep probe 1) and streptavidin are present in solution.
Figure 15 shows an expanded view of the different block levels that are observed for
aptamer sequence strep probe 1 (SEQ ID NO: 24) in the presence (2) and absence (1) of
streptavidin (the y-axis = current (pA) and the x-axis = time (s) for (a) and (b)). This data has
been Bessel filtered for presentation purposes.
Figure 16 illustrates an example block level observed for aptamer sequence 27x3A TBA
in the presence of thrombin (the y-axis = current (pA) and the x-axis = time (s)) in a solution of
20% whole rabbit blood in K2 EDTA (Harlan Scientific, code - S.B-0009) 80% buffer (625mM
KC1, lOOmM HEPES, 75mM potassium ferrocyanide, 25mM potassium ferricyanide pH8.0).
Levels 1 and 2 are detected when the aptamer (sequence 27x3A TBA) and thrombin are present
in solution. The appearance of level 2 indicates aptamer bound to thrombin, and transitions from
level 2 to level 1 indicate dissociation of the aptamer-thrombin complex.
Figure 17 illustrates an example block level observed for aptamer sequence
17x8A_PDGF in the presence of PDGF (the y-axis = current (pA) and the x-axis = time (s)) in a
solution of 20% whole rabbit blood in K2 EDTA (Harlan Scientific, code - S.B-0009) 80%
buffer (625mM KC1, lOOmM HEPES, 75mM potassium ferrocyanide, 25mM potassium
ferricyanide pH8.0). Levels 1 and 2 are detected when the aptamer (sequence 17x8A_PDGF)
and PDGF are present in solution. The appearance of level 2 indicates aptamer bound to PDGF,
and transitions from level 2 to level 1 indicate dissociation of the aptamer-PDGF complex.
Figure 18 illustrates an example block level observed for aptamer sequence 25x_ATP in
the presence of ATP (the y-axis = current (pA) and the x-axis = time (s)) in a solution of 20%
whole rabbit blood in K2 EDTA (Harlan Scientific, code - S.B-0009) 80% buffer (625mM KC1,
lOOmM HEPES, 75mM potassium ferrocyanide, 25mM potassium ferricyanide pH8.0). Levels
1 and 2 are detected when the aptamer (sequence 25x_ATP) and ATP are present in solution.
The appearance of level 2 indicates aptamer bound to ATP, and transitions from level 2 to level
1 indicate dissociation of the aptamer-ATP complex.
Description of the Sequence Listing
SEQ ID NO: 1 shows the polynucleotide sequence encoding one subunit of a-hemolysin-
E l 11N/K147N (a-HL-NN; (Stoddart, D. S., et al, (2009), Proceedings of the National Academy
of Sciences of the United States of America 106, p7702-7707).
SEQ ID NO: 2 shows the amino acid sequence of one subunit of a-HL-NN.
SEQ ID NO: 3 shows the polynucleotide sequence encoding the LukF subunit of g-
hemolysin.
SEQ ID NO: 4 shows the amino acid sequence of the LukF subunit of g-hemolysin.
SEQ ID NO: 5 shows the polynucleotide sequence encoding the Hlg2 subunit of g-
hemolysin.
SEQ ID NO: 6 shows the amino acid sequence of the Hlg2 subunit of g-hemolysin.
SEQ ID NOs: 7 to 24 show the sequences used in the Examples.
Detailed description of the invention
It is to be understood that different applications of the disclosed products and methods
may be tailored to the specific needs in the art. It is also to be understood that the terminology
used herein is for the purpose of describing particular embodiments of the invention only, and is
not intended to be limiting.
In addition as used in this specification and the appended claims, the singular forms "a",
"an", and "the" include plural referents unless the content clearly dictates otherwise. Thus, for
example, reference to "a pore" includes two or more such pores, reference to "a tail" includes
two or more such tails, reference to "a polynucleotide" includes two or more such
polynucleotides, and the like.
All publications, patents and patent applications cited herein, whether supra or infra, are
hereby incorporated by reference in their entirety.
Methods of the invention
The invention provides a method of determining in a sample the presence or absence of
one or more analyte members of a group of two or more analytes. The invention therefore
concerns a multiplex assay for each analyte member of a group of analytes. The two or more
analytes in the group are predetermined. The invention therefore concerns a multiplex assay for
each analyte member of a specific and predetermined group of analytes.
The method comprises contacting the sample with a transmembrane pore and a panel of
two or more probes. Each or every probe in the panel recognises one or more of the analyte
members and comprises (i) an aptamer that binds to the one or more analyte members and (ii) a
tail which is capable of entering the pore and has different effects on the current flowing through
the pore depending on whether or not the aptamer in the probe is bound to one of the analyte
members. In other words, the tail in each or every probe affects the current flowing through the
pore in one way when the aptamer is not bound to one of the analyte members and affects the
current flowing through the pore in a different way when the aptamer is bound to the analyte
member. This is discussed in more detail below. Each or every probe in the panel also affects
the current flowing through the pore in a distinctive manner. This allows a particular probe in
the panel to be identified. Since both the identity of a probe and its binding to an analyte
member can be measured, the presence of the analyte member can be determined. Each or every
analyte member of the group of two or more analytes is recognised by at least one probe in the
panel.
The method also comprises measuring the current flowing through the pore to determine
which probes in the panel, if any, have bound to an analyte member and thereby determining the
presence or absence of one or more analyte members in the sample. The current may be
measured using any method known in the art. Specific methods are discussed below.
Steps (a) and (b) are preferably carried out with a potential applied across the pore. The
applied potential may be a voltage potential. Alternatively, the applied potential may be a
chemical potential. An example of this is using a salt gradient across an amphiphilic layer. A
salt gradient is disclosed in Holden et al, J Am Chem Soc. 2007 Jul 11;129(27):8650-5.
The method has several advantages. The method is rapid and cheap compared to existing
protein assays, whilst still having high specificity. Probes containing aptamers are quick and
cheap to prepare in comparison to, for example, antibodies. The output from the assay is
analysed in real time, allowing the assay to be stopped when sufficient information has been
obtained. The method allows the detection of multiple analytes from a single sample with
minimal or no sample preparation, for example the sample can be blood straight from a patient,
thus allowing the method to be carried out by someone with minimal training or qualification.
The method can be used to detect many analytes from a single sample, thus obviating the need
for multiple tests on a single sample, the number of analytes being limited only by the diversity
and number of distinct tails of the probes which can be generated. The method is generally
carried out in the presence of unbound aptamers and unbound analyte without the need for
washing steps or removal of the unbound entities.
Sample
The sample may be any suitable sample. The invention is typically carried out on a
sample that is known to contain or suspected to contain the two or more analytes. The invention
may be carried out on a sample that contains two or more analytes whose identity is unknown.
Alternatively, the invention may be carried out on a sample to confirm the identity of two or
more analytes whose presence in the sample is known or expected.
The sample may be a biological sample. The invention may be carried out in vitro on a
sample obtained from or extracted from any organism or microorganism. The organism or
microorganism is typically archaean, prokaryotic or eukaryotic and typically belongs to one the
five kingdoms: plantae, animalia, fungi, monera and protista. The invention may be carried out
in vitro on a sample obtained from or extracted from any virus. The sample is preferably a fluid
sample. The sample typically comprises a body fluid of the patient. The sample may be urine,
lymph, saliva, mucus or amniotic fluid but is preferably blood, plasma or serum. Typically, the
sample is human in origin, but alternatively it may be from another mammal animal such as from
commercially farmed animals such as horses, cattle, sheep or pigs or may alternatively be pets
such as cats or dogs. Alternatively a sample of plant origin is typically obtained from a
commercial crop, such as a cereal, legume, fruit or vegetable, for example wheat, barley, oats,
canola, maize, soya, rice, bananas, apples, tomatoes, potatoes, grapes, tobacco, beans, lentils,
sugar cane, cocoa, cotton, tea, coffee.
The sample may be a non-biological sample. The non-biological sample is preferably a
fluid sample. Examples of a non-biological sample include surgical fluids, water such as
drinking water, sea water or river water, and reagents for laboratory tests.
The sample is typically processed prior to being assayed, for example by centrifugation
or by passage through a membrane that filters out unwanted molecules or cells, such as red blood
cells. The sample may be measured immediately upon being taken. The sample may also be
typically stored prior to assay, preferably below -70°C.
Analytes
The method of the invention is for determining in a sample the presence or absence of
one or more analyte members of a group of two or more analytes. The group of two or more
analytes may comprise any number of analytes such as 2, 5, 10, 15, 20, 30, 40, 50, 100 or more
analytes. The group preferably has from about 4 to about 100 analytes, such as from about 5 to
about 80 analytes, from about 10 to about 60 analytes or from about 20 to about 50 analytes.
The presence or absence of one or more of the analyte members is determined. In other
words, for a group of two or more analytes, the method determines whether each of the analyte
members in the group is present or absent. One or more, such as 2, 5, 10, 15, 20, 30, 40, 50, 100
or more, of the analyte members may be present and all of the other analyte members in the
group may be absent. All of the analyte members may be present. None of the analyte members
may be present (i.e. all of the analyte members may be absent). The number of analyte members
that are present and the number that are absent are determined using the method of the invention.
The two or more analytes are preferably independently selected from metal ions,
inorganic salts, polymers, amino acids, peptides, polypeptides, proteins, nucleotides,
oligonucleotides, polynucleotides, dyes, bleaches, pharmaceuticals, diagnostic agents,
recreational drugs, explosives and environmental pollutants. The group may comprise two or
more analytes of the same type, such as two or more proteins, two or more nucleotides or two or
more pharmaceuticals. Alternatively, the group may comprise two or more analytes of different
types, such as one or more proteins, one or more nucleotides and one or more pharmaceuticals.
The two or more analytes in the group can be analytes that are secreted from cells.
Alternatively, the two or more analytes can be analytes that are present inside cells such that the
analyte members must be extracted from the cells before the invention can be carried out.
The two or more analytes in the group are preferably selected from amino acids, peptides,
polypeptides and/or proteins. The amino acids, peptides, polypeptides or proteins can be
naturally-occurring or non-naturally-occurring. The polypeptides or proteins can include within
them synthetic or modified amino acids. A number of different types of modification to amino
acids are known in the art. Suitable amino acids and modifications thereof are discussed below
with reference to the transmembrane pore. For the purposes of the invention, it is to be
understood that the analytes can be modified by any method available in the art.
The proteins can be enzymes, antibodies, hormones, biomarkers, growth factors or
growth regulatory proteins, such as cytokines. The cytokines may be selected from interleukins,
preferably IFN-1, IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12 and IL-13, interferons, preferably IL-
g, and other cytokines such as TNF-a. The proteins may be bacterial proteins, fungal proteins,
virus proteins or parasite-derived proteins.
The two or more analytes are preferably selected from nucleotides, oligonucleotides
and/or polynucleotides. A nucleotide typically contains a nucleobase, a sugar and at least one
phosphate group. The nucleobase is typically heterocyclic. Nucleobases include, but are not
limited to, purines and pyrimidines and more specifically adenine, guanine, thymine, uracil and
cytosine. The sugar is typically a pentose sugar. Nucleotide sugars include, but are not limited
to, ribose and deoxyribose. The nucleotide is typically a ribonucleotide or deoxyribonucleotide.
The nucleotide typically contains a monophosphate, diphosphate or triphosphate. Phosphates
may be attached on the 5' or 3' side of a nucleotide.
Nucleotides include, but are not limited to, adenosine monophosphate (AMP), adenosine
diphosphate (ADP), adenosine triphosphate (ATP), guanosine monophosphate (GMP),
guanosine diphosphate (GDP), guanosine triphosphate (GTP), thymidine monophosphate (TMP),
thymidine diphosphate (TDP), thymidine triphosphate (TTP), uridine monophosphate (UMP),
uridine diphosphate (HDP), uridine triphosphate (UTP), cytidine monophosphate (CMP),
cytidine diphosphate (CDP), cytidine triphosphate (CTP), 5-methylcytidine monophosphate, 5-
methylcytidine diphosphate, 5-methylcytidine triphosphate, 5-hydroxymethylcytidine
monophosphate, 5-hydroxymethylcytidine diphosphate, 5-hydroxymethylcytidine triphosphate,
cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP),
deoxyadenosine monophosphate (dAMP), deoxyadenosine diphosphate (dADP),
deoxyadenosine triphosphate (dATP), deoxyguanosine monophosphate (dGMP),
deoxyguanosine diphosphate (dGDP), deoxyguanosine triphosphate (dGTP), deoxythymidine
monophosphate (dTMP), deoxythymidine diphosphate (dTDP), deoxythymidine triphosphate
(dTTP), deoxyuridine monophosphate (dUMP), deoxyuridine diphosphate (dUDP), deoxyuridine
triphosphate (dUTP), deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate
(dCDP) and deoxycytidine triphosphate (dCTP), 5-methyl-2' -deoxycytidine monophosphate, 5-
methyl-2' -deoxycytidine diphosphate, 5-methyl-2' -deoxycytidine triphosphate, 5-
hydroxymethyl-2' -deoxycytidine monophosphate, 5-hydroxymethyl-2' -deoxycytidine
diphosphate and 5-hydroxymethyl-2 '-deoxycytidine triphosphate. The nucleotides are
preferably selected from AMP, TMP, GMP, UMP, dAMP, dTMP, dGMP or dCMP. The
nucleotides may be abasic (i.e. lack a nucleobase). The nucleotides may contain additional
modifications. In particular, suitable modified nucleotides include, but are not limited to,
2'amino pyrimidines (such as 2'-amino cytidine and 2'-amino uridine), 2'-hyrdroxyl purines
(such as, 2'-fluoro pyrimidines (such as 2'-fluorocytidine and 2'fluoro uridine), hydroxyl
pyrimidines (such as 5'-a-P-borano uridine), 2'-0-methyl nucleotides (such as 2'-0-methyl
adenosine, 2'-0-methyl guanosine, 2'-0-methyl cytidine and 2'-0-methyl uridine), 4'-thio
pyrimidines (such as 4'-thio uridine and 4'-thio cytidine) and nucleotides have modifications of
the nucleobase (such as 5-pentynyl-2'-deoxy uridine, 5-(3-aminopropyl)-uridine and 1,6-
diaminohexyl-N-5-carbamoylmethyl uridine).
Oligonucleotides are short nucleotide polymers which typically have 50 or fewer
nucleotides, such 40 or fewer, 30 or fewer, 20 or fewer, 10 or fewer or 5 or fewer nucleotides.
The oligonucleotides may comprise any of the nucleotides discussed above, including the abasic
and modified nucleotides.
The polynucleotides may be single stranded or double stranded. At least a portion of the
polynucleotide may be double stranded. The polynucleotides can be nucleic acids, such as
deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The polynucleotides can comprise one
strand of RNA hybridized to one strand of DNA. The polynucleotides may be any synthetic
nucleic acid known in the art, such as peptide nucleic acid (PNA), glycerol nucleic acid (GNA),
threose nucleic acid (TNA), locked nucleic acid (LNA) or other synthetic polymers with
nucleotide side chains. The polynucleotides may comprise any of the nucleotides discussed
above, including the modified nucleotides.
The polynucleotides can be any length. For example, the polynucleotides can be at least
10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400 or at
least 500 nucleotides or nucleotide pairs in length. The polynucleotides can be 1000 or more
nucleotides or nucleotide pairs, 5000 or more nucleotides or nucleotide pairs in length or 100000
or more nucleotides or nucleotide pairs in length.
The group of two or more analytes may be any group of analytes. For instance, the group
may be associated with a particular phenotype. The group may be associated with a particular
type of cell. For instance, the group may be indicative of a bacterial cell. The group may be
indicative of a virus, a fungus or a parasite. The group may be a specific panel of recreational
drugs (such as the SAMHSA 5 panel test), of explosives or of environmental pollutants.
The group of two or more analytes is preferably a group of two or more biomarkers that
can be used to diagnose or prognose a disease or condition. The biomarkers may be any of the
analytes mentioned above, such as proteins or polynucleotides. Suitable panels of biomarkers
are known in the art, for example as described in Edwards, A.V.G. et al. (2008) Mol. Cell.
Proteomics 7, pi 824- 183 7; Jacquet, S. et al. (2009), Mol. Cell. Proteomics 8, p2687-2699;
Anderson N.L. et al (2010) Clin. Chem. 56, 177-185. The disease or condition is preferably
cancer, coronary heart disease, cardiovascular disease or sepsis.
As discussed in more detail below, the group may comprise two or more analytes in the
same class. Analytes are within the same class if they have structural similarity. If the analytes
are proteins, they are within the same class if they are in the same Structural Classification of
Proteins (SCOP) classification. Analytes are within the same class if they related functionally or
related phylogenetically. For instance, the opiates, such as heroin, codeine and morphine, may
be considered to be in the same class of analytes. Similarly, the different forms of interleukin 1,
such as IL-la, IL- I b and IL-IRA, may be considered to be in same class of analytes. In the
context of the invention, a class of analytes is typically two or more analytes that are different
structurally but can be bound by one aptamer. The method preferably comprises the use of at
least one probe which comprises an aptamer that binds to the analyte members in a class. For
instance, such an embodiment allows the determination of the presence or absence or one or
more IL-1 analytes in a sample. The ability to detect the presence or absence of one or more
analyte members in a particular class has its advantages. For instance, an initial multiplex assay
may be carried out for a variety of classes of analytes. Once the presence of one more classes
has been determined, more specific multiplex assays relating to those classes may be carried out
to determine the presence or absence of one or more of the analyte members within each class.
Transmembranepore
The method of the invention comprises contacting the sample with a transmembrane
protein pore. A transmembrane pore is a structure that permits hydrated ions driven by an
applied potential to flow from one side of the membrane to the other side of the membrane.
Any membrane may be used in accordance with the invention. Suitable membranes are
well-known in the art. The membrane is preferably an amphiphilic layer. An amphiphilic layer
is a layer formed from amphiphilic molecules, such as phospholipids, which have both at least
one hydrophilic portion and at least one lipophilic or hydrophobic portion. The amphiphilic
molecules may be synthetic or naturally occurring. Non-naturally occurring amphiphiles and
amphiphiles which form a monolayer are known in the art and include, for example, block
copolymers (Gonzalez-Perez et al., Langmuir, 2009, 25, 10447-10450). Block copolymers are
polymeric materials in which two or more monomer sub-units are polymerized together to create
a single polymer chain. Block copolymers typically have properties that are contributed by each
monomer sub-unit. However, a block copolymer may have unique properties that polymers
formed from the individual sub-units do not possess. Block copolymers can be engineered such
that one of the monomer sub-units is hydrophobic (i.e. lipophilic), whilst the other sub-unit(s) are
hydrophilic whilst in aqueous media. In this case, the block copolymer may possess amphiphilic
properties and may form a structure that mimics a biological membrane. The block copolymer
may be a diblock (consisting of two monomer sub-units), but may also be constructed from more
than two monomer sub-units to form more complex arrangements that behave as amphipiles.
The copolymer may be a triblock, tetrablock or pentablock copolymer.
The amphiphilic layer may be a monolayer or a bilayer. The amphiphilic layer is
typically a planar lipid bilayer or a supported bilayer.
The amphiphilic layer is typically a lipid bilayer. Lipid bilayers are models of cell
membranes and serve as excellent platforms for a range of experimental studies. For example,
lipid bilayers can be used for in vitro investigation of membrane proteins by single-channel
recording. Alternatively, lipid bilayers can be used as biosensors to detect the presence of a
range of substances. The lipid bilayer may be any lipid bilayer. Suitable lipid bilayers include,
but are not limited to, a planar lipid bilayer, a supported bilayer or a liposome. The lipid bilayer
is preferably a planar lipid bilayer. Suitable lipid bilayers are disclosed in International
Application No. PCT/GB08/000563 (published asWO 2008/102121), International Application
No. PCT/GB08/004127 (published asWO 2009/077734) and International Application No.
PCT/GB2006/001057 (published asWO 2006/100484).
Methods for forming lipid bilayers are known in the art. Suitable methods are disclosed
in the Examples. Lipid bilayers are commonly formed by the method of Montal and Mueller
(Proc. Natl. Acad. Sci. USA., 1972; 69: 3561-3566), in which a lipid monolayer is carried on
aqueous solution/air interface past either side of an aperture which is perpendicular to that
interface.
The method of Montal & Mueller is popular because it is a cost-effective and relatively
straightforward method of forming good quality lipid bilayers that are suitable for protein pore
insertion. Other common methods of bilayer formation include tip-dipping, painting bilayers and
patch-clamping of liposome bilayers.
In a preferred embodiment, the lipid bilayer is formed as described in International
Application No. PCT/GB08/004127 (published asWO 2009/077734).
In another preferred embodiment, the membrane is a solid state layer. A solid-state layer
is not of biological origin. In other words, a solid state layer is not derived from or isolated from
a biological environment such as an organism or cell, or a synthetically manufactured version of
a biologically available structure. Solid state layers can be formed from both organic and
inorganic materials including, but not limited to, microelectronic materials, insulating materials
such as Si3N4, A 120 3, and SiO, organic and inorganic polymers such as polyamide, plastics such
as Teflon® or elastomers such as two-component addition-cure silicone rubber, and glasses. The
solid state layer may be formed from monatomic layers, such as graphene, or layers that are only
a few atoms thick. Suitable graphene layers are disclosed in International Application No.
PCT/US2008/010637 (published asWO 2009/035647). An amphiphilic layer may be formed
across a solid state pore. This may be described in the art as hybrid pore formation (Hall et al,
Nat Nanotechnol, 2010, 5, 874-877). The method is typically carried out using (i) an artificial
amphiphilic layer comprising a pore, (ii) an isolated, naturally-occurring lipid bilayer comprising
a pore, or (iii) a cell having a pore inserted therein. The method is typically carried out using an
artificial amphiphilic layer, such as an artificial lipid bilayer. The layer may comprise other
transmembrane and/or intramembrane proteins as well as other molecules in addition to the pore.
Suitable apparatus and conditions are discussed below. The method of the invention is typically
carried out in vitro.
One or more of the probes in the panel are preferably coupled to the membrane. Each
probe in the panel is more preferably coupled to the membrane. This may be done using any
known method. If the membrane is an amphiphilic layer, such as a lipid bilayer (as discussed in
detail above), a probe is preferably coupled to the membrane via a polypeptide present in the
membrane or a hydrophobic anchor present in the membrane. The hydrophobic anchor is
preferably a lipid, fatty acid, sterol, carbon nanotube or amino acid.
A probe may be coupled directly to the membrane. A probe is preferably coupled to the
membrane via a linker. Preferred linkers include, but are not limited to, polymers, such as
polynucleotides, polyethylene glycols (PEGs) and polypeptides.
The coupling may be stable or transient. For certain applications, the transient nature of
the coupling is preferred. Transient coupling minimises permanent blocking allowing data to be
accumulated more quickly as time is not lost in manually unblocking the pore. When permanent
coupling is used the amphiphilic layer may be destabilized or it could cause the build up of
tethered aptamers on the cis side, thus altering the experimental equilibrium. Theses effects can
be minimised by coupling transiently. Chemical groups that form stable or transient links with
the membrane are discussed in more detail below. A probe may be transiently coupled to an
amphiphilic layer, such as a lipid bilayer using cholesterol or a fatty acyl chain. Any fatty acyl
chain having a length of from about 6 to about 30 carbon atoms, such as hexadecanoic acid, may
be used.
In preferred embodiments, one or more probes are or each probe is coupled to an
amphiphilic layer. Coupling to synthetic lipid bilayers has been carried out previously with
various different tethering strategies. These are summarised in Table 1 below.
Table 1
Probes may be functionalized using a modified phosphoramidite in the synthesis reaction,
which is easily compatible for the addition of reactive groups, such as thiol, cholesterol, lipid and
biotin groups. These different attachment chemistries give a suite of attachment options for
probes. Each different modification group tethers the probe in a slightly different way and
coupling is not always permanent so giving different dwell times for the probe to the bilayer.
Coupling of probes can also be achieved by a number of other means provided that a
reactive group can be added to the probe. The addition of reactive groups to either end of DNA
has been reported previously. A thiol group can be added to the 5' of ssDNA using
polynucleotide kinase and ATPyS (Grant, G. P. and P. Z. Qin (2007). "A facile method for
attaching nitroxide spin labels at the 5' terminus of nucleic acids." Nucleic Acids Res 35(10):
ell). A more diverse selection of chemical groups, such as biotin, thiols and fluorophores, can
be added using terminal transferase to incorporate modified oligonucleotides to the 3' of ssDNA
(Kumar, A., P. Tchen, et al. (1988). "Nonradioactive labeling of synthetic oligonucleotide probes
with terminal deoxynucleotidyl transferase." Anal Biochem 169(2) : 376-82).
Alternatively, the reactive group could be considered to be the addition of a short piece of
DNA complementary to one already coupled to the bilayer, so that attachment can be achieved
via hybridisation. Ligation of short pieces of ssDNA have been reported using T4 RNA ligase I
(Troutt, A. B., M. G. McHeyzer-Williams, et al. (1992). "Ligation-anchored PCR: a simple
amplification technique with single-sided specificity." Proc Natl Acad Sci U S A 89(20): 9823-
5). Alternatively either ssDNA or dsDNA could be ligated to native dsDNA and then the two
strands separated by thermal or chemical denaturation. To native dsDNA, it is possible to add
either a piece of ssDNA to one or both of the ends of the duplex, or dsDNA to one or both ends.
Then, when the duplex is melted, each single strand will have either a 5' or 3' modification if
ssDNA was used for ligation or a modification at the 5' end, the 3' end or both if dsDNA was
used for ligation. If the probe contains a synthetic polynucleotide, the coupling chemistry can be
incorporated during the chemical synthesis of the probe. For instance, the probe can be
synthesized using a primer with a reactive group attached to it.
A common technique for the amplification of sections of genomic DNA is using
polymerase chain reaction (PCR). In this technique, using two synthetic oligonucleotide
primers, a number of copies of the same section of DNA can be generated, where for each copy
the 5' end of each strand in the duplex will be a synthetic polynucleotide. By using an antisense
primer that has a reactive group, such as a cholesterol, thiol, biotin or lipid, each copy of the
target DNA amplified will contain a reactive group for coupling.
If the transmembrane pore is a transmembrane protein pore as discussed below, the
probes in the panel are preferably not coupled to the pore. If the pore is a protein pore, the
probes in the panel are more preferably not covalently attached to the pore.
The transmembrane pore generally comprises a vestibule and a barrel or channel. The
barrel or channel is typically a substantially cylindrical passage through which hydrated ions can
flow across the membrane. The vestibule typically forms an entrance to the barrel or channel
and has a different cross-sectional area from the barrel or channel. Typically the vestibule has a
greater cross-sectional area than the barrel. A good example of a pore with a vestibule and a
barrel or channel is a-hemolysin (a-HL), which is discussed in more detail below. A pore
comprising a vestibule and a barrel or channel can be formed in a solid state layer. The presence
of a vestibule is preferred because it facilitates the method of the invention as discussed in more
detail below.
The barrel or channel may have any width. Typically, the barrel or channel is sufficiently
wide that the tail of each probe can enter the barrel or channel and affect the current flowing
through the pore. As discussed in more detail below, the tail preferably comprises a polymer.
The barrel or channel is preferably sufficiently wide that the polymer can enter the barrel or
channel and affect the current flowing through the pore. In some instances, the tail can comprise
a polynucleotide. The barrel or channel is preferably sufficiently narrow that a single stranded
polynucleotide can enter and pass through the pore, but a double-stranded polynucleotide cannot
enter and pass through the pore.
For the reasons discussed in more detail below, the vestibule is typically wide enough to
allow each aptamer in the panel of probes to enter, but narrow enough to prevent each
aptamer/analyte member complex from entering. The vestibule and barrel or channel are each
typically long enough to contain at least two nucleotides, such at least 5, at least 10, at least 20
nucleotides in total, for example at least 8 in the vestibule and at least 12 in the barrel.
The transmembrane pore is preferably a transmembrane protein pore. A transmembrane
protein pore is a polypeptide or a collection of polypeptides that permits hydrated ions, such as
analyte, to flow from one side of a membrane to the other side of the membrane. In the present
invention, the transmembrane protein pore is capable of forming a pore that permits hydrated
ions driven by an applied potential to flow from one side of the membrane to the other. The
transmembrane protein pore permits the probes to flow from one side of the membrane, such as a
lipid bilayer, to the other as discussed below. The transmembrane protein pore preferably allows
a single-stranded polynucleotide, such as ssDNA or RNA, to be moved through the pore.
The transmembrane protein pore may be a monomer or an oligomer. The pore is
preferably made up of several repeating subunits, such as 6, 7, 8 or 9 subunits. The pore is
preferably a hexameric, heptameric, octameric or nonameric pore.
The transmembrane protein pore typically comprises a barrel or channel through which
the ions may flow. The subunits of the pore typically surround a central axis and contribute
strands to a transmembrane b barrel or channel or a transmembrane a-helix bundle or channel.
The barrel or channel of the transmembrane protein pore typically comprises amino acids
that facilitate interaction with the tail, such as polymer units in the tail. These amino acids are
preferably located near a constriction of the barrel or channel. The transmembrane protein pore
typically comprises one or more positively charged amino acids, such as arginine, lysine or
histidine, or aromatic amino acids, such as tyrosine or tryptophan. These amino acids typically
facilitate the interaction between the pore and negatively-charged polymer units, such as
nucleotides, in the tail.
Transmembrane protein pores for use in accordance with the invention can be derived
from b-barrel pores or a-helix bundle pores b-barrel pores comprise a barrel or channel that is
formed from b-strands. Suitable b-barrel pores include, but are not limited to, b-toxins, such as
a-hemolysin, anthrax toxin and leukocidins, and outer membrane proteins/porins of bacteria,
such as Mycobacterium smegmatis porin (Msp), for example MspA, outer membrane
phospholipase A and Neisseria autotransporter lipoprotein (NalP). a-helix bundle pores
comprise a barrel or channel that is formed from a-helices. Suitable a-helix bundle pores
include, but are not limited to, inner membrane proteins and a outer membrane proteins, such as
WZA and ClyA toxin. The transmembrane pore is preferably derived from a-hemolysin (a-HL)
or leukocidin.
The pore may be a homo-oligomer (all monomer units identical) or a hetero-oligomer
(two or more different types of monomer). The pore may comprise linked monomers, for
example dimers.
The pore may comprise at least one dimer and 1, 2, 3, 4, 5, 6, 7 or 8 monomers. The pore
may comprise two, three, four or more dimers. Such pores further comprise sufficient monomers
to form the pore. A further pore comprises only dimers, for example a pore may comprise 4, 5,
6, 7 or 8 dimers. A specific pore according to the inventions comprises four dimers. The dimers
may oligomerise into a pore with a structure such that only one monomer of a dimer contributes
to the barrel or vestibule of the pore. Typically the other monomers of the construct will be on
the outside of the barrel or vestibule of the pore. For example, a pore may comprise 5, 6, 7 or 8
dimers where the barrel or vestibule comprises 8 monomers.
The transmembrane protein pore is preferably derived from a-hemolysin (a-HL). The
wild type a-HL pore is formed of seven identical monomers or subunits (i.e. it is heptameric).
The transmembrane protein pore preferably comprises seven monomers derived from a-HL. The
sequence of one monomer or subunit of a-hemolysin-NN (i.e. a pore derived from a-HL) is
shown in SEQ ID NO: 2 . a-hemolysin-NN contains the substitutions El 1IN and K147N. The
transmembrane protein pore preferably comprises seven monomers each comprising the
sequence shown in SEQ ID NO: 2 or a variant thereof. Amino acids 1, 7 to 21, 31 to 34, 45 to
51, 63 to 66, 72, 92 to 97, 104 to 111, 124 to 136, 149 to 153, 160 to 164, 173 to 206, 210 to 213,
217, 218, 223 to 228, 236 to 242, 262 to 265, 272 to 274, 287 to 290 and 294 of SEQ ID NO: 4
form loop regions. Residues 113 and 147 of SEQ ID NO: 2 form part of a constriction of the
barrel or channel of a-HL.
The pore preferably comprises seven proteins or monomers each comprising the
sequence shown in SEQ ID NO: 2 or a variant thereof. The transmembrane protein is preferably
(a) formed of seven identical subunits as shown in SEQ ID NO: 2 or (b) a variant thereof in
which one or more of, or all of, the seven subunits is a variant of SEQ ID NO: 2 and which
retains pore activity. The seven proteins may be the same (homoheptamer) or different
(heteroheptamer) .
A variant of SEQ ID NO: 2 is a protein that has an amino acid sequence which varies
from that of SEQ ID NO: 2 and which retains its pore forming ability. The ability of a variant to
form a pore can be assayed using any method known in the art. For instance, the variant may be
inserted into an amphiphilic layer, such as a lipid bilayer, along with other appropriate subunits
and its ability to oligomerise to form a pore may be determined. Methods are known in the art
for inserting subunits into amphiphilic layers, such as lipid bilayers. For example, subunits may
be suspended in a purified form in a solution containing a lipid bilayer such that it diffuses to the
lipid bilayer and is inserted by binding to the lipid bilayer and assembling into a functional state.
Alternatively, subunits may be directly inserted into the membrane using the "pick and place"
method described in M.A. Holden, H. Bayley. J . Am. Chem. Soc. 2005, 127, 6502-6503 and
International Application No. PCT/GB2006/001057 (published asWO 2006/100484).
One preferred variant of SEQ ID NO: 2 is the wild-type subunit, i.e. a subunit in which E
has been replaced at position 111 and K has been replaced at position 147.
The variant may include modifications that facilitate covalent attachment to or interaction
with another molecule. The variant preferably comprises one or more reactive cysteine residues
that facilitate attachment. For instance, the variant may include a cysteine at one or more of
positions 8, 9, 17, 18, 19, 44, 45, 50, 51, 237, 239 and 287 and/or on the amino or carboxy
terminus of SEQ ID NO: 2 . Preferred variants comprise a substitution of the residue at position
8, 9, 17, 237, 239 and 287 of SEQ ID NO: 2 with cysteine (A8C, T9C, N17C, K237C, S239C or
E287C). The variant is preferably any one of the variants described in International Application
No. PCT/GB09/001690 (published asWO 2010/004273), PCT/GB09/001679 (published asWO
2010/004265) or PCT/GB 10/000 133 (published asWO 2010/086603).
The variant may also include modifications that facilitate any interaction with polymer
units in the tail, such as nucleotides, amino acids or ethylene oxide.
The variant may be a naturally occurring variant which is expressed naturally by an
organism, for instance by a Staphylococcus bacterium. Alternatively, the variant may be
expressed in vitro or recombinantly by a bacterium such as Escherichia coli. Variants also
include non-naturally occurring variants produced by recombinant technology.
Over the entire length of the amino acid sequence of SEQ ID NO: 2, a variant will
preferably be at least 50% homologous to that sequence based on amino acid identity. More
preferably, the variant may be at least 55%, at least 60%>, at least 65%>, at least 70%, at least 75%,
at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99%
homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the
entire sequence. There may be at least 80%>, for example at least 85%>, 90% or 95%, amino acid
identity over a stretch of 200 or more, for example 230, 250, 270 or 280 or more, contiguous
amino acids ("hard homology").
Standard methods in the art may be used to determine homology. For example the
UWGCG Package provides the BESTFIT program which can be used to calculate homology, for
example used on its default settings (Devereux et al (1984) Nucleic Acids Research 12, p387-
395). The PILEUP and BLAST algorithms can be used to calculate homology or line up
sequences (such as identifying equivalent residues or corresponding sequences (typically on their
default settings)), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300;
Altschul, S.F et al (1990) J Mol Biol 215:403-10. Software for performing BLAST analyses is
publicly available through the National Center for Biotechnology Information
(http://www.ncbi.nlm.nih.gov/).
Amino acid substitutions may be made to the amino acid sequence of SEQ ID NO: 2 in
addition to those discussed above, for example up to 1, 2, 3, 4, 5, 10, 20 or 30 substitutions.
Conservative substitutions replace amino acids with other amino acids of similar chemical
structure, similar chemical properties or similar side-chain volume. The amino acids introduced
may have similar polarity, hydrophilicity, hydrophobicity, basicity, acidity, neutrality or charge
to the amino acids they replace. Alternatively, the conservative substitution may introduce
another amino acid that is aromatic or aliphatic in the place of a pre-existing aromatic or
aliphatic amino acid. Conservative amino acid changes are well-known in the art and may be
selected in accordance with the properties of the 20 main amino acids as defined in Table 2
below. Where amino acids have similar polarity, this can also be determined by reference to the
hydropathy scale for amino acid side chains in Table 3 .
Table 2 - Chemical properties of amino acids
Table 3 - Hydropathy scale
Side Chain Hydrc
e 4.5
Val 4.2
Leu 3.8
Phe 2.8
Cys 2.5
Met 1.9
Ala 1.8
Gly -0.4
Thr -0.7
Ser -0.8
Trp -0.9
Tyr -1.3
Pro -1.6
His -3.2
Glu -3.5
Gin -3.5
Asp -3.5
Asn -3.5
Lys -3.9
Arg -4.5
One or more amino acid residues of the amino acid sequence of SEQ ID NO: 2 may
additionally be deleted from the polypeptides described above. Up to 1, 2, 3, 4, 5, 10, 20 or 30
residues may be deleted, or more.
Variants may include fragments of SEQ ID NO: 2 . Such fragments retain pore forming
activity. Fragments may be at least 50, 100, 200 or 250 amino acids in length. Such fragments
may be used to produce the pores. A fragment preferably comprises the pore forming domain of
SEQ ID NO: 2 . Fragments typically include residues 119, 121, 135. 113 and 139 of SEQ ID
NO: 2 .
One or more amino acids may be alternatively or additionally added to the polypeptides
described above. An extension may be provided at the amino terminal or carboxy terminal of the
amino acid sequence of SEQ ID NO: 2 or polypeptide variant or fragment thereof. The
extension may be quite short, for example from about 1 to about 10 amino acids in length.
Alternatively, the extension may be longer, for example up to about 50 or about 100 amino acids.
A carrier protein may be fused to an amino acid sequence according to the invention.
As discussed above, a variant is a polypeptide that has an amino acid sequence which
varies from that of SEQ ID NO: 2 and which retains its ability to form a pore. A variant
typically contains the regions of SEQ ID NO: 2 that are responsible for pore formation. The
pore forming ability of a-HL, which contains a b-barrel, is provided by b-strands in each
subunit. A variant of SEQ ID NO: 2 typically comprises the regions in SEQ ID NO: 2 that form
b-strands. The amino acids of SEQ ID NO: 2 that form b-strands are discussed above. One or
more modifications can be made to the regions of SEQ ID NO: 2 that form b-strands as long as
the resulting variant retains its ability to form a pore. Specific modifications that can be made to
the b-strand regions of SEQ ID NO: 2 are discussed above.
A variant of SEQ ID NO: 2 preferably includes one or more modifications, such as
substitutions, additions or deletions, within its a-helices and/or loop regions. Amino acids that
form a-helices and loops are discussed above.
The transmembrane protein pore is also preferably derived from leukocidin. A
leukocidin is a hetero-oligomeric pore with two different subunits, one class S subunit and one
class F subunit. Suitable leukocidins include, but are not limited to, gamma hemolysin (g-HL)
comprising LukF (HlgB) and Hlg2 (HlgA), leukocidin comprising LukF (HlgB) and
LukS(HlgC), leukocidin PV comprising LukF-PV and LukS-PV, LukE/LukD pore comprising
LukE and LukD and LukS-I/LukF-I comprising LukF-I and LukS-I.
When the transmembrane protein pore is a leukocidin, it is preferably derived from
gamma hemolysin (g-HL). The wild type g-HL pore is formed of eight subunits (i.e. it is
octameric) and contains four subunits of LukF and four subunits of Hlg2. The sequence of one
monomer or subunit of LukF is shown in shown in SEQ ID NO: 4 . The sequence of one
monomer or subunit of Hlg2 is shown in SEQ ID NO: 6 . The transmembrane protein pore
preferably comprises four monomers each comprising the sequence shown in SEQ ID NO: 4 or a
variant thereof and four monomers each comprising the sequence shown in SEQ ID NO: 6 or a
variant thereof. Amino acids 109-147 of SEQ ID NO: 4 and 103-139 of SEQ ID NO: 6 form
loop regions.
The g-hemolysin pore is preferably (a) g-hemolysin formed of four identical subunits as
shown in SEQ ID NO: 4 and four identical subunits as shown in SEQ ID NO: 6 or (b) a variant
thereof in which one or more of, or all of, the subunits is a variant of SEQ ID NO: 4 and/or one
or more of, or all of, the subunits is a variant of SEQ ID NO: 6 and the pore retains pore activity.
Such pores are hetero-octamers.
A variant of SEQ ID NO: 4 or 6 is a protein that has an amino acid sequence which varies
from that of SEQ ID NO: 4 or 6 and which retains its pore forming ability. The ability of a
variant to form a pore can be assayed using any method known in the art. For instance, the
variant may be inserted into an amphiphilic layer, such as a lipid bilayer, along with other
appropriate subunits and its ability to oligomerise to form a pore may be determined. Methods
are known in the art for inserting subunits into amphiphilic layers, such as lipid bilayers.
Suitable methods are discussed above.
The variant may include modifications that facilitate covalent attachment to or interaction
with another molecule. The variant preferably comprises one or more reactive cysteine residues
that facilitate attachment. The variant may also include modifications that facilitate any
interaction with polymer units in the tail, such as nucleotides, amino acids or ethylene oxide.
The variant may be a naturally occurring variant which is expressed naturally by an
organism, for instance by a Staphylococcus bacterium. Alternatively, the variant may be
expressed in vitro or recombinantly by a bacterium such as Escherichia coli. Variants also
include non-naturally occurring variants produced by recombinant technology. Over the entire
length of the amino acid sequence of SEQ ID NO: 4 or 6, a variant will preferably be at least
50% homologous to that sequence based on amino acid identity. More preferably, the variant
polypeptide may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least
80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous
based on amino acid identity to the amino acid sequence of SEQ ID NO: 4 or 6 over the entire
sequence. There may be at least 80%, for example at least 85%, 90% or 95%, amino acid
identity over a stretch of 200 or more, for example 230, 250, 270 or 280 or more, contiguous
amino acids ("hard homology"). Homology can be determined as discussed above.
Amino acid substitutions may be made to the amino acid sequence of SEQ ID NO: 4 or 6
in addition to those discussed above, for example up to 1, 2, 3, 4, 5, 10, 20 or 30 substitutions.
Conservative substitutions may be made as discussed above.
One or more amino acid residues of the amino acid sequence of SEQ ID NO: 4 or 6 may
additionally be deleted from the polypeptides described above. Up to 1, 2, 3, 4, 5, 10, 20 or 30
residues may be deleted, or more.
Variants may be fragments of SEQ ID NO: 4 or 6 . Such fragments retain pore-forming
activity. Fragments may be at least 50, 100, 200 or 250 amino acids in length. A fragment
preferably comprises the pore-forming domain of SEQ ID NO: 4 or 6 .
One or more amino acids may be alternatively or additionally added to the polypeptides
described above. An extension may be provided at the amino terminus or carboxy terminus of
the amino acid sequence of SEQ ID NO: 4 or 6 or a variant or fragment thereof. The extension
may be quite short, for example from about 1 to about 10 amino acids in length. Alternatively,
the extension may be longer, for example up to about 50 or about 100 amino acids. A carrier
protein may be fused to a pore or variant.
As discussed above, a variant of SEQ ID NO: 4 or 6 is a subunit that has an amino acid
sequence which varies from that of SEQ ID NO: 4 or 6 and which retains its ability to form a
pore. A variant typically contains the regions of SEQ ID NO: 4 or 6 that are responsible for pore
formation. The pore forming ability of g-HL, which contains a b-barrel, is provided by b-strands
in each subunit. A variant of SEQ ID NO: 4 or 6 typically comprises the regions in SEQ ID NO:
4 or 6 that form b-strands. The amino acids of SEQ ID NO: 4 or 6 that form b-strands are
discussed above. One or more modifications can be made to the regions of SEQ ID NO: 4 or 6
that form b-strands as long as the resulting variant retains its ability to form a pore. Specific
modifications that can be made to the b-strand regions of SEQ ID NO: 4 or 6 are discussed
above.
A variant of SEQ ID NO: 4 or 6 preferably includes one or more modifications, such as
substitutions, additions or deletions, within its a-helices and/or loop regions. Amino acids that
form a-helices and loops are discussed above.
In some embodiments, the transmembrane protein pore is chemically modified. The
monomers derived from a-HL (i.e. SEQ ID NO: 2 or a variant thereof) or g-HL (i.e. SEQ ID NO:
4 or 6 or a variant thereof) may be modified to assist their identification or purification, for
example by the addition of histidine residues (a hist tag), aspartic acid residues (an asp tag), a
streptavidin tag or a flag tag, or by the addition of a signal sequence to promote their secretion
from a cell where the polypeptide does not naturally contain such a sequence. An alternative to
introducing a genetic tag is to chemically react a tag onto a native or engineered position on the
pore. An example of this would be to react a gel-shift reagent to a cysteine engineered on the
outside of the pore. This has been demonstrated as a method for separating a-HL heterooligomers
(Chem Biol. 1997 Jul; 4(7):497-505).
The monomer derived from a-HL or g-HL may be labelled with a revealing label. The
revealing label may be any suitable label which allows the pore to be detected. Suitable labels
include, but are not limited to, fluorescent molecules, radioisotopes, e.g. 1251, S, enzymes,
antibodies, antigens, polynucleotides and ligands such as biotin.
The monomer derived from a-HL or g-HL may also be produced using D-amino acids.
For instance, the monomer derived from a-HL or g-HL may comprise a mixture of L-amino
acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.
The monomer derived from a-HL or g-HL may contain one or more specific
modifications to facilitate interactions with the tails. The monomer derived from a-HL or g-HL
may also contain other non-specific modifications as long as they do not interfere with pore
formation. A number of non-specific side chain modifications are known in the art and may be
made to the side chains of the monomer derived from a-HL or g-HL. Such modifications
include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed
by reduction with NaBH4, amidination with methylacetimidate or acylation with acetic
anhydride.
The monomer derived from a-HL or g-HL can be produced using standard methods
known in the art. The monomer derived from a-HL may be made synthetically or by
recombinant means. For example, the pore may be synthesized by in vitro translation and
transcription (IVTT). Suitable methods for producing pores are discussed in International
Application Nos. PCT/GB09/001690 (published asWO 2010/004273), PCT/GB09/001679
(published asWO 2010/004265) or PCT/GB 10/000 133 (published asWO 2010/086603).
Methods for inserting pores into membranes are discussed.
The pore can be produced using standard methods known in the art. Polynucleotide
sequences encoding a pore may be derived and replicated using standard methods in the art.
Polynucleotide sequences encoding a pore may be expressed in a bacterial host cell using
standard techniques in the art. The pore may be produced in a cell by in situ expression of the
polypeptide from a recombinant expression vector. The expression vector optionally carries an
inducible promoter to control the expression of the polypeptide. These methods are described in
described in Sambrook, J . and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd
Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
The pore may be produced in large scale following purification by any protein liquid
chromatography system from protein producing organisms or after recombinant expression.
Typical protein liquid chromatography systems include FPLC, AKTA systems, the Bio-Cad
system, the Bio-Rad BioLogic system and the Gilson HPLC system.
Panel of probes
The method of the invention comprises contacting the sample with a panel of two or
more probes. In other words, the method of the invention comprises contacting the sample with
a panel of two or more types of probe. The panel may comprise any number of two or more
probes, such as 2, 5, 10, 15, 20, 30, 40, 50, 100 or more probes. The panel preferably has from
about 4 to about 100 probes, such as from about 5 to about 80 probes, from about 10 to about 60
probes or from about 20 to about 50 probes.
The method uses multiple instances of each or every probe in the panel because, if an
analyte is present in the sample, there will almost certainly be multiple instances of the analyte in
the same. In other words, the method uses multiple instances of each or every type of probe in
the panel.
Each or every analyte member of the group of two or more analytes is recognised by at
least one probe (i.e. at least one type of probe) in the panel. A probe recognises an analyte
member if it provides a positive signal in the method of the invention when the analyte is present
in the sample. In other words, a probe recognises an analyte member if it affects the current in a
distinctive manner when the analyte is present in the sample. A probe typically recognises an
analyte member because it comprises an aptamer that binds the analyte member. The fact that
each analyte member is recognised by at least one probe allows the presence or absence of each
analyte member in the group to be determined using the method of the invention. The way in
which a probe recognises an analyte member is discussed in more detail below.
At least one probe (i.e. at least one type of probe) in the panel preferably recognises a
class of analyte members within the group of two or more analytes and comprises an aptamer
that binds to the analyte members in the class. The advantages associated with determining the
presence or absence of a class of analyte members within the group is discussed above. The
production of an aptamer that binds to more than one analyte members is discussed below.
At least one probe in the panel (i.e. at least one type of probe) preferably specifically
recognises one of the analyte members and comprises an aptamer that specifically binds to the
analyte member. A probe specifically recognises one of the analyte members if it only provides
a positive signal in the method of the invention when the analyte is present in the sample. In
other words, a probe specifically recognises an analyte member if it only affects the current in a
distinctive manner when the analyte is present in the sample. A probe typically specifically
recognises an analyte member because it comprises an aptamer that specifically binds the analyte
member. Specific binding of aptamers is discussed in more detail below. In this embodiment, at
least one probe is targeted to only one analyte member. Each probe (i.e. each type of probe) in
the panel more preferably specifically recognises one of the analyte members and comprises an
aptamer that specifically binds to the analyte member. In this embodiment, each probe is
targeted to only one analyte member. The multiplex assay of the invention is simpler if only one
probe is used to detect an analyte member. In particular, it is more straightforward to determine
the presence or absence of an analyte member by measuring the distinctive effect of one probe
on the current flowing through the pore.
Each probe (i.e. each type of probe) in the panel preferably comprises a different
aptamer. In other words, no two probes (i.e. no two types of probe) in the panel comprise the
same aptamer. As discussed in more detail below, differences between different aptamers can
contribute to the distinctiveness of effect each probe has on the current flowing through the pore.
Different aptamers typically bind to different analyte members, but may bind to the same analyte
member. In a preferred embodiment, two or more probes in the panel comprise different
aptamers that specifically bind to the same analyte member. Two or more probes in the panel
preferably comprise different aptamers and the same polynucleotide tail. In this embodiment,
the distinctiveness of the effects each probe has on the current flowing through pore is typically
provided by the differences between the aptamers.
Each probe (i.e. each type of probe) in the panel preferably comprises a different tail. As
discussed in more detail below, the differences between different tails can also contribute to the
distinctiveness of the effects each probe has on the current flowing through the pore. Two or
more probes in the panel preferably comprise the same aptamer and different tails. In this
embodiment, the distinctiveness of the effects each probe has on the current flowing through
pore is typically provided by the differences between the tails. In this embodiment, two or more
probes are targeted to the same one or more analyte members because they share the same
aptamer. This can provide an internal control because positive signals from both probes will be
required to conclude that one of the one or more analyte members is present in the sample.
Each probe (i.e. each type of probe) in the panel may comprise a different aptamer and a
different polynucleotide tail. In other words, In other words, no two probes (i.e. no two types of
probe) in the panel comprise the same aptamer and the same tail. In the embodiment, the
different aptamers and different tails typically both contribute to the distinctiveness of the effects
each of the two or more probes has on the current flowing through pore.
The number of probes (i.e. types of probes) in the panel is typically the same as or greater
than number of analyte members of the group. There may be fewer probes in the panel than the
number of analyte members of the group because each probe can recognise one or more analyte
members. If the number of probes in the panel is greater than the number of analyte members of
the group, two or more probes are targeted to the same one or more analyte members and the
method of the invention comprises an internal control as discussed above. The number of probes
in the panel is preferably the same as the number of analyte members of the group of two or
more analytes. This is the simplest embodiment of the invention, but it does not include an
internal control.
Aptamer
Each probe (i.e. each type of probe) in the panel recognises one or more of the analyte
members and comprises an aptamer that binds to one or more analyte members. Recognition of
analyte members by probes is discussed above.
Aptamers are small molecules that bind to one or more analyte members. Aptamers can
be produced using SELEX (Stoltenburg, R. et al, (2007), Biomolecular Engineering 24, p38 1-
403; Tuerk, C. et al., Science 249, p505-510; Bock, L. C. etal., (1992), Nature 355, p564-566)
or NON-SELEX (Berezovski, M. et al. (2006), Journal of the American Chemical Society 128,
pl410-141 1).
The aptamer may be capable of binding to one or more analyte members. In this
embodiment, a probe comprising the aptamer is capable of recognising the one or more analyte
members. Aptamers that bind to more than one analyte member can be produced using Toggle
SELEX (White, R. et al, (2001), Molecular Therapy 4, p567-573). Although an aptamer may
be capable of binding to one or more analytes, each aptamer typically binds to only one analyte
in the method of the invention. This is discussed in more detail below.
The aptamer preferably binds to a class of analyte members within the group of two or
more analytes. A class of analyte members is discussed above. Aptamers that bind to a class of
analyte members can be produced using Toggle SELEX.
The aptamer is preferably a peptide aptamer or an oligonucleotide aptamer. The peptide
aptamer may comprise any amino acids. The amino acids may be any of those discussed above.
The oligonucleotide aptamer may comprise any nucleotides. The nucleotides may be any of
those discussed above.
The aptamer can be any length. The aptamer is typically at least 15 amino acids or
nucleotides in length, such as from about 15 to about 50, from about 20 to about 40 or from
about 25 to about 30 amino acids or nucleotides in length.
Tail
Each probe (i.e. each type of probe) in the panel comprises a tail which is capable of
entering the pore. The tail is typically a linear molecule that is capable of entering and passing
through the barrel or channel of the pore. Suitable molecules for forming the tail are discussed
below. When the tail enters the pore, it affects the current flowing through the pore in a manner
that is specific for the part of the tail that is present in the barrel or channel.
The tail has different effects on the current flowing through the pore depending on
whether or not the aptamer in the probe is bound to one of the analyte members. The tail in each
probe affects the current flowing through the pore in one way when the aptamer is not bound to
the analyte member and affects the current flowing through the pore in a different way when the
aptamer is bound to the analyte member. This is important because it allows the presence or
absence of each analyte member in the group to be determined using the method.
The different effects of the tail on the current flowing through the pore depending on
whether or not the aptamer in the probe is bound to one of the analyte members can be measured
based on the time it takes for the probe to move through the pore. In other words, the different
effects of the tail on the current flowing through the pore depending on whether or not the
aptamer in the probe is bound to one of the analyte members can be measured based on the time
for which the probe affects the current flowing through the pore. Without wishing to be bound
by theory, the tail of each probe enters the barrel or channel of a pore when the panel is
contacted with the pore and affects the current flowing through the pore. Multiple instances of
the pore are used in the method of the invention. For a short while, the movement of the entire
probe through the pore is prevented (i.e. delayed) by the aptamer. Aptamers are typically folded
into a three-dimensional structure and so are typically too large to move through the barrel or
channel of the pore. After a short while, the aptamer unfolds under the influence of the potential
and the entire probe moves through the pore along the potential. Once the probe has passed
through the pore, the current flowing through the pore returns to the level seen in the absence of
the panel of probes. If the probe's target analyte member is present, the aptamer binds to the
analyte member and the aptamer/analyte complex further delays the probe moving through the
pore. In this embodiment, the probe moves through the pore more slowly in the presence of the
analyte member than in the absence of the analyte member. In other words, the probe affects the
current flowing through the pore for more time in the presence of the analyte member than in the
absence of the analyte member. In this embodiment, the distinctiveness between probes (i.e.
between different types of probes) may be due to one or more, or all, of (1) the different lengths
of the probes, (2) the presence or absence of one or more double stranded polynucleotide regions
in the tails of each probe and (3) the different binding affinities of the different aptamers in each
probe. All three of these can be altered such that each probe affects the current flowing through
the pore for a specific amount of time ("dwell time"). The presence of one or more double
stranded polynucleotide region may also be used to hold a specific tail region that is indicative of
the probe in the barrel or channel as discussed below.
The tail preferably comprises at least two regions that affect the current flowing through
the pore in different ways and one region is situated in the pore when the aptamer is not bound to
one of the analyte members and a different region is situated in the pore when the aptamer is
bound to the analyte member. The at least two regions have different compositions and so affect
the current flowing through the pore in different ways. For instance, one region could be a
polypeptide and the other could be a polynucleotide or the at least two regions could be
polynucleotides having different nucleotide sequences. This is discussed in more detail below.
Control experiments may be carried out to determine the effect the different regions in a
tail have on the current flowing through the pore when the probe is bound to one of the analyte
members or not. Results from carrying out the method of the invention on a test sample can then
be compared with those derived from such control experiments in order to determine whether a
particular analyte is present or absent in the test sample.
Again without wishing to be bound by theory, the tail of each probe enters the barrel or
channel of a pore when the panel is contacted with the pore and affects the current flowing
through the pore. Multiple instances of the pore are used in the method of the invention. For a
short while, the movement of the entire probe through the pore is prevented by the aptamer
because, as discussed above, folded aptamers are typically too large to move through the barrel
or channel of the pore. If the probe's target analyte member is not present, the aptamer is not
bound to an analyte member and one region (the first region) of the tail is typically held in the
barrel or channel as the aptamer prevents the movement of the probe through the pore. This first
region affects the current flowing through the pore in a particular way based on the composition
of the region. After a short while, the aptamer unfolds under the influence of the potential and
the entire probe moves through the pore along the potential. Once the probe has passed through
the pore, the current flowing through the pore returns to the level seen in the absence of the panel
of probes.
If the probe's target analyte member is present in the sample, the tail of each probe still
enters the barrel or channel of the pore as discussed above, but the aptamer/analyte member
complex typically prevents the tail entering as far as if the analyte member was not present.
Hence, a different region of the tail (the second region) is held in the barrel or channel and
affects the current flowing through the pore in a different way from the first region. After a short
while, the aptamer unfolds under the influence of the potential, releases the analyte member and
the entire probe moves through pore. As the probe moves through the pore, the first region will
follow the second region through the barrel or channel and for a short while will affect the
current flowing through the pore as if the analyte member is not present. Once the probe has
passed through the pore, the current flowing through the pore returns to the level seen in the
absence of the panel of probes. An example of this is shown in cartoon form in Figure 1.
In this embodiment, the distinctiveness between probes (i.e. between different types of
probes) may be due to one or more, or all, of (1) the different lengths of the probes, (2) the
presence or absence of one or more double stranded polynucleotide regions in the tails of each
probe, (3) the different binding affinities of the different aptamers in each probe and (4)
differences between the at least two regions in each probe. 1 to 3 can be altered such that each
probe affects the current flowing through the pore for a specific amount of time ("dwell time").
The presence of one or more double stranded polynucleotide region may also be used to hold a
specific tail region that is indicative of the probe in the barrel or channel as discussed below.
The at least two regions in each probe can be designed such that it is straightforward to
distinguish between each (or every) probe used in the method.
As discussed above, the pore preferably comprises a vestibule. This is advantageous
because the vestibule typically allows the aptamer to enter, but does not allow the
aptamer/analyte member complex to enter. This means that the tail can enter the barrel or
channel of the pore to differing extents depending on whether or not the aptamer is bound to one
of the analyte members. It also means that different regions of the tail are present in the barrel or
channel of the pore depending on whether or not the aptamer is bound to one of the analyte
members. For a particular pore, it is straightforward to design tails that are suitable for use in the
panel of probes. For instance, it is straightforward to design probe tails if the lengths of the
vestibule and the barrel or channel of the pore are known.
Each aptamer molecule binds only one of the analyte member molecules in the method of
the invention even though it may be capable of binding to more than one analyte member. As
discussed above, the entire probe typically moves through the pore along the potential shortly
after being contacted with the pore. There is enough time for the aptamer to bind to one analyte
member before it moves through the pore. If the probe' s target analyte member is not present,
the probe moves through the pore without the aptamer binding to an analyte member. If the
probe's target analyte is present, the movement of the probe through the pore may be delayed
slightly, but is unlikely to be prevented. This is discussed in more detail below.
The tail preferably comprises a polymer. The polymer is capable of entering the pore and
affecting the current flowing through the pore. The polymer is preferably a polynucleotide, a
polypeptide or a polyethylene glycol (PEG).
The polynucleotide may comprise any of the nucleotides discussed above. However, the
polynucleotide in the tail typically comprises nucleotides selected from adenosine
monophosphate (AMP), guanosine monophosphate (GMP), thymidine monophosphate (TMP),
uridine monophosphate (UMP), cytidine monophosphate (CMP), cyclic adenosine
monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine
monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxythymidine
monophosphate (dTMP), deoxyuridine monophosphate (dUMP), deoxycytidine monophosphate
(dCMP) and any of the modified nucleotides discussed above. The polynucleotide preferably
comprises nucleotides selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP or
dCMP. The polynucleotide preferably comprises one or more abasic nucleotides. The
polynucleotide in the tail may be single stranded or double stranded. The polynucleotide can be
a nucleic acid, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The
polynucleotide in the tail can comprise one strand of RNA hybridized to one strand of DNA.
The polynucleotide in the tail may be any synthetic nucleic acid known in the art, such as peptide
nucleic acid (PNA), glycerol nucleic acid (GNA), threose nucleic acid (TNA), locked nucleic
acid (LNA) or other synthetic polymers with nucleotide side chains.
Typically the tail has an abasic leader sequence, which leader sequence is the first region
of the tail to pass into the pore. Preferably the tail comprises at least 2 adjacent abasic residues,
for example 3, 4, 5, 6, 7 or more adjacent abasic residues.
Although double stranded polynucleotides in the tail typically cannot pass through the
pore, they can be useful in the method of the invention. For instance, the tail may comprise one
or more double stranded polynucleotides or polynucleotide regions. The presence of such a
double stranded region does not prevent the probe from moving through the pore, but instead
simply delays the movement of the probe through the pore as one of the strands in the region is
stripped from the probe under the influence of the potential. Such a delay can be seen as the
current flowing through the pore is measured. An embodiment in which binding to an analyte
delays the movement of the probe through the pore is discussed above. Hence, including one or
more double stranded polynucleotide regions in each tail increases the number of possible
signals that can be obtained from a population of tails and hence increases the number of analyte
members that can be assayed using the method of the invention. A double stranded
polynucleotide region may also be used to hold a specific region of the tail, such as a barcode,
that is indicative of the probe in the barrel or channel of the pore so that it may be read in
accordance with the invention. The one or more double stranded regions may be located on the
tail such that they enter the pore before or after the at least two regions that indicate the presence
or absence of the analyte member as discussed above. Hence, in a preferred embodiment, the tail
comprises a double stranded polynucleotide region and a specific tail region that is indicative of
the probe such that the double stranded polynucleotide delays the movement of the probe
through the pore and holds the specific tail region in the barrel or channel of the pore. Different
specific tail regions between probes (i.e. between different types of probes) typically have
different effects on the current flowing through the pore and so can be distinguished from one
another. The specific tail region is preferably a polymer. The polymer may be any of those
discussed above or below. In such an embodiment, the specific tail region enters the pore and is
held in the barrel or channel by the double stranded polynucleotide region. This allows the
specific tail region to be identified by its specific effects on the current flowing through the pore.
After a short while, one of the strands in the double stranded region is stripped and the probe
moves through the pore under the influence of the potential. The binding of the probe to an
analyte member may then be measured by (a) a delay in the movement of the probe through the
pore and/or (b) the use of at least two specific regions in the tail as discussed above.
The tail preferably comprises at least one single stranded polynucleotide or
polynucleotide region. Single stranded polynucleotides are useful in the tail because they can
pass through the pore and can easily be divided into different regions that affect the current
flowing through the pore in different ways. For instance, different regions of a polynucleotide
having different sequences typically affect the current flowing through the pore in different
ways. The tail preferably comprises at least two regions of single-stranded polynucleotide with
different nucleotide sequences that affect the current flowing through the pore in different ways
and one region is situated in the pore when the aptamer is not bound to the one or more analyte
members and a different region is situated in the pore when the aptamer is bound to the analyte
member. The at least two regions preferably correspond to at least two stretches of different
nucleotides. For instance, the polynucleotide may comprise a stretch of adenine nucleotides and
a stretch of abasic nucleotides. Each stretch will affect the current flowing through the pore in a
different way. Alternatively, the at least two stretches of different nucleotides are different
polynucleotide barcodes. Polynucleotide barcodes are well-known in the art (Kozarewa, I . et al,
(201 1), Methods Mol. Biol. 733, p279-298). A barcode is a specific sequence of polynucleotide
that affects the current flowing through the pore in a specific and known manner.
The polypeptide in the tail may comprise any amino acids, including any of those
discussed above. Different amino acid sequences will affect the current flowing through the pore
in different ways and so specific tails may be designed as discussed above for polynucleotides.
Any of the embodiments discussed above for polynucleotides apply to polypeptides (with the
substitution of nucleotides with amino acids).
The tail may comprise PEG. PEG will affect the current flowing through the pore in a
specific manner. PEG may be used to form one region in the tail that is present in the barrel or
channel of the pore when the aptamer is bound or not bound to one of the analyte members.
Something other than PEG may be used in the other region in the tail that is present in the barrel
or channel of the pore when the aptamer is not bound or bound to the analyte member
respectively.
The tail may comprise different combinations of polymers. The tail preferably comprises
at least two regions of different polymers that affect the current flowing through the pore in
different ways and one region is situated in the pore when the aptamer is not bound to one of the
analyte members and a different region is situated in the pore when the aptamer is bound to the
analyte member. Table 4 below summarises some preferred combinations.
The tail may be any length. The tail preferably comprises a polynucleotide from about 7
to about 70 nucleotides in length, such as from about 10 to about 60, from about 20 to about 50
or from about 30 to about 40 nucleotides in length.
The tail may comprise any of the polynucleotides used in the Examples. In particular, the
tail preferably comprises residues 1 to 30 of any of SEQ ID NOs: 7 to 23. The panel of probes
preferably comprises a population of tails that correspond to residues 1 to 30 of SEQ ID NOs: 7
to 23.
Distinctive currents
Each probe (i.e. each type of probe) affects the current flowing through the pore in a
distinctive manner. In other words, a probe affects the current flowing through the pore in a
manner that can be distinguished or differentiated from the way in which a different probe
affects the current flowing through the pore. This allows the identity of each probe (i.e. each
type of probe) to be measured in accordance with the invention. The binding of the probe to an
analyte member can then be measured as discussed above. Since the identity of each probe and
the binding of each probe to an analyte member can be measured, the presence or absence of
each analyte member can be determined.
Each probe (i.e. each type of probe) preferably affects the current flowing through the
pore in a distinctive manner when it binds to one of the analyte members. In other words, the
binding of an analyte member to a probe preferably affects the current flowing through the pore
in a manner that can be distinguished or differentiated from the way in which a different probe
affects the current flowing through the pore when it binds an analyte member. The different
probes may bind to the same analyte member.
The distinctive manner may concern the extent to which the current flowing through the
pore is affected, i.e. a change in amount of current that flows through the pore as the probe binds,
and/or the time for which the current is affected by binding of the probe (the "dwell time"). The
value of the current disruption is of greater value than the dwell time as the former provides
more distinct signatures, whereas dwell times have broader distribution. The distinctive manner
may concern the extent to which the variance of the current flowing the through the pore is
affected. The variance may increase or decrease as a result of the binding of an analyte member
to a probe. Control experiments may be carried out to ensure that different probes have different
effects on the current flowing through the pore when the probe binds to one of the analyte
members. Such control experiments can also help to determine the effect a particular probe has
on the current flowing through the pore when the probe is bound to the analyte member. Results
from carrying out the method of the invention on a test sample can then be compared with those
derived from such control experiments in order to determine whether a particular analyte is
present or absent in the test sample.
The distinctiveness between probes can be achieved via differences in their lengths.
Longer probes will affect the current flowing through a pore for more time, i.e. longer dwell
time. Shorter probes will affect the current flowing through the pore for less time, i.e. shorter
dwell time.
The distinctiveness between probes can be achieved via differences in their aptamers
and/or tails. For instance, different aptamers bind to analytes to different degrees, i.e. have
different binding constants. An aptamer that binds more strongly to an analyte member will
prevent the probe from moving through the pore for longer and this can be identified by
measuring the current flowing through the pore. The opposite is also true, i.e. an aptamer that
binds less strongly to an analyte member will prevent the probe from moving through the pore
for less time and this can be identified by measuring the current flowing through the pore.
In preferred embodiments discussed above, a specific region of the tail is briefly held in
the barrel or channel of the pore when an aptamer binds to one of the analyte members or when a
double stranded polynucleotide region in the tail enters the pore. Differences in such specific
regions between different probes, such as the presence of different polymers. For example, single
stranded and double stranded DNA, or different sequences of the same type of polymer, for
example where one sequence is two or more adjacent abasic residues, can also account for the
distinctiveness between the probes. It is straightforward to design a panel of probes that have the
required distinctiveness.
Each probe (i.e. each type of probe) also preferably affects the current flowing through
the pore in a distinctive manner when its aptamer is not bound to one of the analyte members. In
other words, in the absence of the analyte member, the probe affects the current flowing through
the pore in a manner that can be distinguished or differentiated from the way in which a different
probe affects the current flowing through the pore when its analyte member is absent. Different
probes may bind to the same analyte member. This "absence" distinctiveness can further add to
the ability to distinguish between different probes and thus analytes, especially if different
probes bind to the same analyte member, and therefore enhance the multiplex nature of the
assay. This preferred distinctiveness can also be determined using control experiments as
described above.
This preferred "absence" distinctiveness between probes can be achieved via differences
in the probes' length and/or tails. As discussed above, the entire probe moves through the pore
in the absence of the analyte member and affects the current flowing through the pore as it does.
Different probes (i.e. different types of probes) will affect the current flowing through the pores
for different amounts of time, i.e. will have different dwell times. As discussed above, when the
aptamer is not bound to an analyte member or a double stranded polynucleotide region enters the
pore, a specific region of the tail is briefly held in the barrel or channel of the pore. Differences
in such specific regions between different probes, such as the presence of different polymers or
different sequences of the same type of polymer, can account for the distinctiveness between the
probes. As discussed above, tails can include one or more regions of double stranded
polynucleotide. These allow different probes to be distinguished. For example, different tails
can comprise different numbers of such regions and/or such regions of different lengths.
Apparatus and conditions
Electrical measurements may be made using standard single channel recording
equipment as describe in Stoddart, D. S., et al., (2009), Proceedings of the National Academy of
Sciences of the United States of America 106, p7702-7707, Lieberman KR et al, J Am Chem
Soc. 2010;132(50):17961-72, and International ApplicationWO-2000/28312. Alternatively,
electrical measurements may be made using a multi-channel system, for example as described in
International Application WO-2009/077734 and International Application WO-201 1/067559.
The methods may be carried out using any apparatus that is suitable for investigating a
membrane/pore system in which a pore is inserted into a membrane. The method may be carried
out using any apparatus that is suitable for transmembrane pore sensing. For example, the
apparatus comprises a chamber comprising an aqueous solution and a barrier that separates the
chamber into two sections. The barrier has an aperture in which the membrane containing the
pore is formed.
The methods may be carried out using the apparatus described in International
Application No. PCT/GB08/000562 (WO 2008/102120).
The methods involve measuring the current flowing through the pore. Therefore the
apparatus may also comprise an electrical circuit capable of applying a potential and measuring
an electrical signal across the membrane and pore. The methods may be carried out using a
patch clamp or a voltage clamp. The methods preferably involve the use of a voltage clamp.
The methods may be carried out on a silicon-based array of wells where each array
comprises 128, 256, 512, 1024 or more wells.
The methods of the invention may involve the measuring of a current flowing through the
pore. Suitable conditions for measuring ionic currents through transmembrane pores are known
in the art and disclosed in the Examples. The method is typically carried out with a voltage
applied across the membrane and pore. The voltage used is typically from +2 V to -2 V,
typically -400 mV to +400 mV. The voltage used is preferably in a range having a lower limit
selected from -400 mV, -300 mV, -200 mV, -150 mV, -100 mV, -50 mV, -20 mV and 0 mV and
an upper limit independently selected from +10 mV, + 20 mV, +50 mV, +100 mV, +150 mV,
+200 mV, +300 mV and +400 mV. The voltage used is more preferably in the range 100 mV to
240 mV and most preferably in the range of 120 mV to 220 mV. It is possible to increase
discrimination between different nucleotides by a pore by using an increased applied potential.
The methods are typically carried out in the presence of any charge carriers, such as
metal salts, for example alkali metal salt, halide salts, for example chloride salts, such as alkali
metal chloride salt. Charge carriers may include ionic liquids or organic salts, for example
tetramethyl ammonium chloride, trimethylphenyl ammonium chloride, phenyltrimethyl
ammonium chloride, or l-ethyl-3 -methyl imidazolium chloride. In the exemplary apparatus
discussed above, the salt is present in the aqueous solution in the chamber. Potassium chloride
(KC1), sodium chloride (NaCl) or caesium chloride (CsCl) is typically used. KC1 is preferred.
The salt concentration may be at saturation. The salt concentration may be 3M or lower and is
typically from 0.1 to 2.5 M, from 0.3 to 1.9 M, from 0.5 to 1.8 M, from 0.7 to 1.7 M, from 0.9 to
1.6 M or from 1M to 1.4 M. The salt concentration is preferably from 150 mM to 1M. The
method is preferably carried out using a salt concentration of at least 0.3 M, such as at least 0.4
M, at least 0.5 M, at least 0.6 M, at least 0.8 M, at least 1.0 M, at least 1.5 M, at least 2.0 M, at
least 2.5 M or at least 3.0 M. High salt concentrations provide a high signal to noise ratio and
allow for currents indicative of binding/no binding to be identified against the background of
normal current fluctuations.
The methods are typically carried out in the presence of a buffer. In the exemplary
apparatus discussed above, the buffer is present in the aqueous solution in the chamber. Any
buffer may be used in the method of the invention. Typically, the buffer is HEPES. Another
suitable buffer is Tris-HCl buffer. The methods are typically carried out at a pH of from 4.0 to
12.0, from 4.5 to 10.0, from 5.0 to 9.0, from 5.5 to 8.8, from 6.0 to 8.7 or from 7.0 to 8.8 or 7.5
to 8.5. The pH used is preferably about 7.5.
The methods may be carried out at from 0 °C to 100 °C, from 15 °C to 95 °C, from 16 °C
to 90 °C, from 17 °C to 85 °C, from 18 °C to 80 °C, 19 °C to 70 °C, or from 20 °C to 60 °C. The
methods are typically carried out at room temperature. The methods are optionally carried out at
a temperature that supports enzyme function, such as about 37 °C.
The sample and panel of probes may be contacted with the pore on either side of the
membrane. The sample and panel of probes are typically contacted with the pore on the same
side of the membrane.
The sample and the panel of probes may be contacted the pore in any order. It is
preferred that the sample is contacted with the pore before the panel or at the same time as the
panel. If the panel is contacted with the pore before the sample is contacted with the pore, it is
essential to ensure that sufficient probes remain available for binding to the analyte members
(and have not all crossed the membrane through the pore).
Methods of measuring concentration
The method of the invention preferably further comprises, for those probes that bind the
one or more analyte members, comparing the different currents flowing through the pore when
each probe is bound and unbound. This helps to determine the concentration of the analyte
members present in the sample, generally by reference to a calibration curve, use of equilibrium
constants or reference to control data. Methods for calculating the concentration are well known
in the art.
The invention also provides a method of determining in a sample the concentration of
one or more analyte members of a group of two or more analytes, the method comprising:
(i) carrying out a method of the invention as described above; and
(ii) for one or more analyte members shown to be present in the sample comparing
the current flowing through the pore in step (b) with control or reference data for each analyte
member and thereby determining the concentration of the one or more analyte members in the
sample. Step (i) preferably comprises, for those probes that bind the one or more analyte
members, comparing the different currents flowing through the pore when each probe is bound
and unbound. Control or reference data can be generated by conducting control experiments in
which known concentrations of an analyte member are used to calibrate the assay. This is
described in Example 2 .
Panels and Kits
The invention also provides a panel of probes for determining in a sample the presence,
concentration or absence of one or more analyte members of a group of two or more analytes.
The panel comprises two or more probes,
wherein each probe recognises one or more of the analyte members and comprises (i) an
aptamer that binds to one or more analyte members and (ii) a tail which is capable of entering a
transmembrane pore and has different effects on the current flowing through the pore depending
on whether or not the aptamer in the probe is bound to one of the analyte members,
wherein each probe affects the current flowing through the pore in a distinctive manner,
and
wherein each analyte member in the group of two or more analytes is recognised by at
least one probe in the panel. Any embodiments discussed above with reference to the method of
the invention equally apply to the panel of the invention. Each probe in the panel preferably
further comprises a chemical group that allows it to be coupled to a membrane. The chemical
group is preferably cholesterol.
The invention also provides a kit for determining in a sample the presence, concentration
or absence of one or more analyte members of a group of two or more analytes. The kit
comprises (a) a panel of probes of the invention and (b) a transmembrane pore. Any of the
embodiments discussed above with reference to the method of the invention equally apply to the
kits.
The kit may further comprise the components of a membrane, such as the phospholipids
needed to form an amphiphilic layer, such as a lipid bilayer.
The kits of the invention may additionally comprise one or more other reagents or
instruments which enable any of the embodiments mentioned above to be carried out. Such
reagents or instruments include one or more of the following: suitable buffer(s) (aqueous
solutions), means to obtain a sample from a subject (such as a vessel or an instrument comprising
a needle), means to amplify and/or express polynucleotides, a membrane as defined above or
voltage or patch clamp apparatus. Reagents may be present in the kit in a dry state such that a
fluid sample resuspends the reagents. The kit may also, optionally, comprise instructions to
enable the kit to be used in the method of the invention or details regarding which patients the
method may be used for. The kit may, optionally, comprise nucleotides.
Apparatus
The invention also provides an apparatus for determining in a sample the presence,
concentration or absence of one or more analyte members of a group of two or more analytes.
The apparatus comprises a plurality of pores and a panel of probes of the invention. The
apparatus preferably further comprises instructions for carrying out the method of the invention.
The apparatus may be any conventional apparatus for polynucleotide analysis, such as an array
or a chip. Any of the embodiments discussed above with reference to the methods of the
invention are equally applicable to the apparatus of the invention.
The apparatus is preferably set up to carry out the method of the invention.
The apparatus preferably comprises:
a sensor device that is capable of supporting the membrane and plurality of pores and
being operable to perform analyte member characterisation using the pores;
at least one reservoir for holding material for performing the characterising;
a fluidics system configured to controllably supply material from the at least one
reservoir to the sensor device; and
a plurality of containers for receiving respective samples, the fluidics system being
configured to supply the samples selectively from the containers to the sensor device. The
apparatus may be any of those described in International Application No. PCT/GB08/004127
(published asWO 2009/077734), PCT/GB 10/000789 (published asWO 2010/122293),
International Application No. PCT/GB 10/002206 (not yet published) or International
Application No. PCT/US99/25679 (published asWO 00/28312).
The following Examples illustrate the invention.
Example 1
This example illustrates how a nanopore can be used to detect the presence of the protein
thrombin.
Materials and Methods
Electrical measurements were acquired using the standard 128 well silicon chips (format
75 mih diameter, 20 mih depth and 250 mih pitch) which were silver plated (WO 2009/077734).
Chips were initially washed with 20 mL ethanol, then 20 mL d¾0, then 20 mL ethanol prior to
CF4 plasma treatment. The chips used were then pre-treated by dip-coating, vacuum-sealed and
stored at 4 °C. Prior to use the chips were allowed to warm to room temperature for at least 20
minutes.
Bilayers were formed by passing a series of slugs of 3.6 mg/mL 1,2-diphytanoyl-glycero-
3-phosphocholine lipid (DPhPC, Avanti Polar Lipids, AL, USA) dissolved in 1M KCl, 10 mM
Tris, pH 7.5, at 0.45 /s across the chip. Initially a lipid slug (250 m ) was flowed across the
chip, followed by a 100 m slug of air. Two further slugs of 155 m and 150 m of lipid
solution, each separated by a 100 m slug of air were then passed over the chip. After bilayer
formation the chamber was flushed with 3 mL of buffer at a flow rate of 3 mΐ/s. Electrical
recording of the bilayer formation was carried out at 10 kHz with an integration capacitance of
1.0 pF.
A solution of the biological nanopore was prepared using aHL-(El 11N/K147N) 7 (NN)
(SEQ ID NO: 2) (Stoddart, D. S., et al, (2009), Proceedings of the National Academy of
Sciences of the United States of America 106, p7702-7707) ( 1 mM diluted 1/80, 000) in 1M KC1,
25 mM Tris pH 7.5. A holding potential of +180 mV was applied and the solution flowed over
the chip. Pores were allowed to enter bilayers until 10% occupancy (12 single pores) was
achieved. The sampling rate was then reduced to 7 kHz, the potential reduced to zero, and the
integration capacitance maintained at 1.0 pF.
A control programme, which cycled through periods of positive holding potential
followed by rest periods where no potential was applied, was run for 5 minutes. The control
programme applied a potential of 0 mV for 10 seconds, followed by a potential of +170 mV for a
further 50 seconds and this cycle was repeated up to 20 times.
After five minutes the script was stopped and 5A15xl0A_TBA (SEQ ID NO: 7,
1.25 mM) in 1M KC1, 10 mM Tris pH 7.5 was pipetted into the chamber. The control
programme was then run for a total of 15 minutes. Following this, 5A15xl0A_TBA (1.25 mM)
and thrombin ( 1 mM) (Cat No. T6884, Sigma- Aldrich, Dorset, UK), which had been preincubated
together for a minimum of 5 minutes in 1M KC1, 10 mM Tris pH 7.5, were flowed
into the chamber and the control programme run for a further 15 minutes. At the end of the
experiment the control programme was stopped.
Discussion
Using the above method it was possible to detect characteristic block levels in the
presence and absence of thrombin. Upon the addition of probe 5A15xl0A_TBA (SEQ ID NO:
7) only a block level at level 1 was observed (see Figure 2a). Whereas, when probe
5A15xl0A_TBA had been pre-incubated with thrombin an additional level (level 2; Figure 2b)
was also detected. Upon binding of thrombin to probe 5A15xl0A_TBA a higher than average
current flow was measured, indicating that the abasic region (x) was within the b-barrel. The
difference between the two levels was 30.5 pA (Figure 2b). The same experiment was carried
out with SEQ ID NOs: 8-18 (8 = l lxl9A_TBA, 9 = 13xl7A_TBA, 10 = 15xl5A_TBA, 11 =
17xl3A_TBA, 12 = 19xl lA_TBA, 13 = 21x9A_TBA, 14 = 23x7A_TBA, 15 = 25x5A_TBA, 16
= 27x3A_TBA, 17 = 29xlA_TBA and 18 = 30x0A_TBA) .
Example 2
This example illustrates how a nanopore can be used to detect the concentration of the
protein thrombin in solution.
Materials and Methods
Electrical measurements were acquired using the standard 128 well silicon chips (format
75 m diameter, 20 m depth and 250 um pitch) which were silver plated (WO 2009/077734). In
order to carry-out experiments which allowed determination of the concentration of thrombin,
the same experimental set-up procedure was performed as described in Example 1 (using the
nanopore oHL-(El 11N/K147N)? (SEQ ID NO: 2) and buffer 1M KC1, 10 mM TRIS pH 7.5),
with the same initial control programme (10 seconds at 0 mV, 50 seconds at 170 mV - repeated
up to 20 times) run for 5 minutes.
After five minutes the script was stopped and 5A15xl0A_TBA (1.25 mM) in 1M KC1,
10 mM Tris pH 7.5 was pipetted into the chamber. The control programme was then run for a
total of 15 minutes. Following this, 5A15xl0A_TBA (SEQ ID NO: 7, 1.25 mM) and thrombin
(100 nM) (Cat No. T6884, Sigma-Aldrich, Dorset, UK) which had been pre-incubated together
for at least 5 minutes in 1M KC1, 10 mM Tris pH 7.5 were flowed into the chamber and the
control programme run for a further 15 minutes. The entire solution volume above the chip was
then replaced with a solution of 5A15xl0A_TBA (1.25 mM) and thrombin (250 nM) which had
been pre-incubated for a minimum of 5 minutes in 1M KC1, 10 mM Tris pH 7.5 and the control
programme run for a further 15 minutes. This process was repeated for 500 nM, 750 nM and
1250 nM concentrations of thrombin. At the end of the experiment the control programme was
stopped.
Discussion
Using the above method it was possible to measure the frequency of the events which
corresponded to thrombin bound to probe 5A15xl0A_TBA (SEQ ID NO: 7) (see Figure 2).
This data was then used to produce calibration plots of the concentration of thrombin vs. the ratio
of the thrombin bound events when compared to the total number of blocking events (bound and
unbound combined), see Figure 3 . These calibration plots can then be used to determine the
concentration of an unknown sample of thrombin.
Example 3
This example illustrates how a nanopore can be used to detect the presence of the protein
thrombin utilising a significantly lower concentration of thrombin binding probe.
Materials and Methods
Electrical measurements were acquired using the standard 128 well silicon chips (format
75 m diameter, 20 m depth and 250 um pitch) which were silver plated (WO 2009/077734). In
order to carry-out experiments which allowed detection of thrombin using a much lower
concentration of cholesterol-tagged probe (SEQ ID NO: 19 which has a cholesterol TEG at the
3' end), the same experimental set-up procedure was performed as described in Example 1
(using the nanopore
15 s) were detected, the potential was flipped to -180 mV to manually eject the blocking analyte.
The script was then stopped and probe 17x8A_PDGF (0.5 mM) and PDGF ( 1 mM) (Biorbyt, Cat
No: orb80544, Cambridge, UK) which had been pre-incubated together for a minimum of 5
minutes in 1M KC1, 10 mM Tris pH 7.5 buffer were then added to the cis compartment and the
experiment run for a further 20 minutes. Long blocking events were again removed by flipping
the applied potential. At the end of the experiment the control programme was stopped.
Discussion
Using the above method it was possible to detect characteristic step levels in the presence
and absence of PDGF. By employing probe 17x8A_PDGF (SEQ ID NO: 20) a block level at
level 1 was observed (see Figure 6a). Whereas, when PDGF pre-incubated with 17x8A_PDGF
was added to the experimental solution (level 2) was also detected (see Figure 6b). Figures 7a
and 7b show the step levels produced in the presence and absence of PDGF when another probe,
25x_PDGF (SEQ ID NO: 21), was used.
Example 6
This example illustrates how a nanopore can be used to detect the concentration of PDGF
in solution.
Materials and Methods
Electrical measurements were acquired using the standard 128 well silicon chips (format
75 m diameter, 20 mih depth and 250 um pitch) which were silver plated (WO 2009/077734).
In order to carry-out experiments which allowed determination of the concentration of PDGF,
the experimental set-up procedure was performed as described in Example 1 (using the nanopore
15 s) were detected, the potential was flipped to -180 mV to manually eject the blocking analyte.
The script was then stopped and probe 17x8A_ATP (0.5 mM) and ATP ( 1 mM) (Cat No: A6559,
Sigma-Aldrich, Dorset, UK) which had been pre-incubated together for a minimum of 5 minutes
in 1M KC1, 10 mM TRIS pH 7.5 buffer were then added to the cis compartment and the
experiment run for a further 10 minutes. This process was repeated for 3.3 mM, 10 mM and
100 mM concentrations of ATP. At the end of the experiment the control programme was
stopped.
Discussion
Using the above method it was possible to measure the frequency of the events which
corresponded to ATP bound to probe 17x8A_ATP (SEQ ID NO: 23, see Figure 10a and b). This
data was then used to produce a calibration plot of concentration of ATP vs the ratio of the ATP
bound events when compared to the total number of blocking events (ATP bound and unbound
combined), see Figure 11. This calibration plot can then be used to determine the concentration
of an unknown sample of ATP. A similar event rate increase was observed for ATP as thrombin,
except it was necessary to add a higher concentration of ATP as it has a Kd value in the
micromolar range (Figure 11).
Example 9
This example illustrates how a nanopore can be used to detect the presence of more than
one analyte (e.g. ATP, PDFG and thrombin) in solution.
Materials and Methods
Electrical experiments were set up as described in Example 5 in order to achieve a single
pore (using nanopore