ORIGINAL
DESCRIPTION
PROTEIN OR PEPTIDE PRINTING METHOD, PROTEIN ARRAY OR PEPTIDE
ARRAY, AND FUNCTIONAL PROTEIN OR FUNCTIONAL PEPTIDE
IDENTIFICATION METHOD
TECHNICAL FIELD
[0001]
The present invention relates to a protein or peptide
printing method, an array produced according to these methods,
and a functional protein or functional peptide identification
method that uses that array. The present application claims
priority on the basis of Japanese Patent Application No.
2010-191060, filed in Japan on August 27, 2010, and Japanese
Patent Application No. 2010-258302, filed in Japan on November
18, 2010, the contents of which are incorporated herein by
reference.
BACKGROUND ART
[0002]
In recent years, methods for patterning molecules on a
substrate have come to be used in various biological fields such
as biochips or biosensors.
[0003]
Attention is particularly focusing on the microcontact
printing (to be referred to as |^CP) method that enables
patterning over large surfaces on the submicron order. This
2
|j.CP method is applied to patterning of proteins and other
biomolecules since it does not require strong acid or strong
base as required by photolithographic patterning.
[0004]
However, since proteins and other biomolecules are
susceptible to denaturation and decomposition, various
modifications have been made to the aforementioned ^CP method
(see, for example, Non-Patent Document 1).
In the method proposed in Non-Patent Document 1, silicon
rubber used for printing is subjected to low-temperature plasma
treatment to increase the hydrophilicity of the silicon rubber
surface. As a result, denaturation and the like of proteins
and other biomolecules are decreased.
Prior Art Documents
Non-Patent Documents
[0005]
Non-Patent Document 1: James, et al., Langmuir, Vol. 14,
pp. 741-744, 1998
DISCLOSURE OF THE INVENTION
Problems to be Solved by the Invention
[0006]
However, since the method proposed in Non-Patent Document
1 uses relief printing technology and proteins and other
biomolecules are printed directly, the protein used as ink dries
3
easily, thereby leaving room for improvement in terms of being
able to print proteins having low storage stability, for
example.
[0007]
With the foregoing in view, an object of the present
invention is to provide a protein or peptide printing method
capable of reducing damage imparted to protein or peptide having
low storage stability and printing the aforementioned protein
or peptide in an arbitrary shape, an array produced according
to these methods, and a functional protein or functional peptide
identification method that uses the array.
Means for Solving the Problems
[0008]
As a result of conducting extensive studies to solve the
aforementioned problems, the inventors of the present invention
found that the problems can be solved by applying intaglio
printing technology.
[0009]
Namely, an embodiment of the present invention provides
the inventions described in (1) to (12) below.
(1) A protein or peptide printing method in one embodiment
of the present invention comprises: (a) a step for preparing
nucleic acids and an acellular protein synthesis system in a
microengraved plate (a microintaglio plate) composed of
4
microscopic grooves having a specific opening shape, (b) a step
for superimposing a substrate on the microengraved plate so as
to contact a protein or peptide to be synthesized in the
microscopic grooves, and (c) a step for synthesizing the protein
or peptide from the nucleic acids using the acellular protein
synthesis system in the microscopic grooves, and immobilizing
the protein or peptide on the substrate along the specific
opening shapes of the microscopic grooves.
(2) In the protein or peptide printing method in one
embodiment of the present invention, the protein or peptide
preferably includes an amino acid sequence as a solid-phase
binding site, and the substrate preferably has a solid-phase
binding site recognition site having affinity for the amino acid
sequence.
(3) In the protein or peptide printing method in one
embodiment of the present invention, the solid-phase binding
site recognition site is preferably nickel ion or cobalt ion.
(4) In the protein or peptide printing method in one
embodiment of the present invention, the amino acid sequence
is preferably polyhistidine.
(5) The protein or peptide printing method in one embodiment
of the present invention comprises: (a) a step for preparing
nucleic acids, a biotinylated puromycin derivative and an
acellular protein synthesis system in a microengraved plate
5
composed of microscopic grooves having a specific opening shape,
(b) a step for superimposing an avidin-labeled substrate on the
microengraved plate so as to contact a protein or peptide to
be synthesized in the microscopic grooves, and (c) a step for
synthesizing a protein or peptide from the nucleic acids using
the acellular protein synthesis system in the microscopic
grooves, and immobilizing the protein or peptide on the
substrate along the specific opening shapes of the microscopic
grooves.
(6) In the protein or peptide printing method in one
embodiment of the present invention, the biotinylated puromycin
derivative is preferably a compound represented by the
following general formula (1):
[Chemical Formula 1]
0=P—CL
H I I H
NH OH
1
c=o
H3N—C—H
OCH3 (1)
(wherein, Z represents a group represented by the following
formula (2), (3) or (4):
6
[Chemical Formula 2]
NH—X*
V, 0 ^N^O
\ II
0 P ~ 0I - I ^ ^ o ^ ° M
• H (2)
NH—X^
(A
X- O ^N^^O
\ II
O P—O.
I - I ^^o^^
° sfi ^
HI r H
* OH (3)
O P—O
* H (4)
(wherein, at least one of X"*" and X^ represents a group represented
by the following formula (5), and the other is a fluorescent
group or hydrogen atom, and * represents a binding site:
[Chemical Formula 3]
0
!
S |] *
O (5)
(wherein, * represents a binding site))).
(7) In the protein or peptide printing method in one
7
embodiment of the present invention, Z is preferably a group
represented by the formula (2).
(8) In the protein or peptide printing method in one
embodiment of the present invention, the acellular protein
synthesis system preferably consists of independently purified
factors required for protein synthesis.
[0010]
(9) In the protein or peptide printing method in one
embodiment of the present invention, in the step (a), the
nucleic acids are preferably DNA that have been labeled at their
solid-phase binding sites, and are immobilized by magnetic
beads that have been labeled at their solid-phase binding site
recognition sites.
(10) In the protein or peptide printing method in one
embodiment of the present invention, in the step (a), the
nucleic acids are preferably DNA that have been labeled with
biotin, and are preferably immobilized by magnetic beads that
have been labeled with streptavidin.
(11) A protein array or peptide array in one embodiment
of the present invention is produced using the aforementioned
protein or peptide printing method.
(12),A functional protein or functional peptide
identification method in one embodiment of the present
invention comprises: carrying out functional screening using
8
the protein array or peptide array, and identifying a protein
or peptide that has been specified by the functional screening
and immobilized in the step (c) by using nucleic acids in the
corresponding microscopic grooves in the step (a).
Effects of the Invention
[0011]
According to the protein or peptide printing method of the
present invention, a protein array or peptide array is obtained
in which the protein or peptide is printed in an arbitrary shape
without imparting damage to protein or peptide having low
storage stability.
According to the present invention, the protein array or
peptide array can be made to have high density, and since this
high-density protein array or high-density peptide array is not
only immobilized with numerous types of proteins or peptides,
but also is immobilized with a large number of protein or peptide
molecules per spot, it has high usage value.
In addition, since the functional protein or functional
peptide identification method of the present invention is able
to rapidly identify a protein or peptide having a desired
function in a high-density protein array or peptide array, it
can be preferably used in molecular evolution engineering
applications.
BRIEF DESCRIPTION OF THE DRAWINGS
9
[0012]
FIG. lA is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. IB is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. IC is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 2A is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 2B is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 20 is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 2D is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 2E is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 3A is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 3B is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 3C is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 4A is a schematic diagram of a protein or peptide
10
printing method in the present embodiment.
FIG. 4B is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 4C is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 4D is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 4E is a schematic diagram of a protein or peptide
printing method in the present embodiment.
FIG. 5 is a microscopic image of an intaglio plate (an
engraved plate) in which magnetic beads have been sealed in an
example.
FIG. 6 is a fluorescence microscopic image of a glass
substrate patterned with GFP-His-tagged protein in an example.
FIG. 7 shows the results of SDS-PAGE in an example.
FIG. 8 is a fluorescence microscopic image of a slide glass
patterned with GFP protein in an example.
BEST MODE FOR CARRYING OUT THE INVENTION
[0013]
«Protein or Peptide Printing Method»
[First Embodiment]
As shown in FIGS. lA to IC, the protein or peptide printing
method of the present embodiment comprises:
(a) a step for preparing nucleic acids 3 and an acellular
11
protein synthesis system 9 in a microengraved plate (a
microintaglio plate) 1 composed of microscopic grooves 2 having
a specific opening shape,
(b) a step for superimposing a substrate 5 on the
microengraved plate 1 so as to contact a protein or peptide 7
to be synthesized in the microscopic grooves 2, and
(c) a step for synthesizing the protein or peptide 7 from
the nucleic acids 3 using the acellular protein synthesis system
9 in the microscopic grooves 2, and immobilizing the protein
or peptide 7 on the substrate 5 along the specific opening shapes
of the microscopic grooves 2.
The following provides an explanation of each step with
reference to FIGS. 2A to 2E.
[0014]
Step (a) is a step for preparing nucleic acids and an
acellular protein synthesis system 19 in the microscopic
grooves 12 in a microengraved plate 11 composed of the
aforementioned microscopic grooves 12 having a specific opening
shape.
[0015]
The aforementioned microengraved plate 11 preferably
consists of a plurality of the microscopic grooves 12. In the
present embodiment, since the microengraved plate 11 used
consists of the microscopic grooves 12 having individual walls,
12
when printing a protein or peptide 17 onto a substrate 15, there
is no concern over leakage and the like between each spot, a
pattern of a fine shape can be printed, and in the step (c) to
be subsequently described, the specific opening shape possessed
by the aforementioned microscopic grooves 12 is printed as is
onto the substrate 15 and is reflected in the shape of the spots.
Accordingly, a high-density protein array 18 can be
produced according to this shape. Moreover, since the shape
of the spots on the substrate 15 is dependent on the opening
shape of the aforementioned microscopic grooves 12, in the
present embodiment, the shape of the spots on the substrate 15
can be determined to have an arbitrary shape.
In addition, in contrast to there being restrictions on
the number of DNA molecules able to be immobilized on a DNA
microarray, in the present embodiment, since a large number of
DNA molecules can be added to the microengraved plate 11, a large
number of protein molecules can be synthesized by using the
acellular protein synthesis system to be subsequently described,
and a protein array can be produced on which is immobilized a
large number of protein molecules per spot. In addition, in
the present embodiment, since the microengraved plate 11 is used
that consists of the microscopic grooves 12, a transcription
stage and translation stage can be carried out all at once,
thereby resulting in greater efficiency.
13
[0016]
The surface of the microengraved plate 11 and the inner
walls of the microscopic grooves 12 can be preferably coated
with a blocking agent for preventing non-specific adsorption
of DNA and other biomolecules, examples of which include
polyethylene glycol (PEG) or 2-methacryloyloxyethyl
phosphorylcholine (MPC). As a result of coating with this
blocking agent, non-specific adsorption of biomolecules to a
substrate surface or microreaction vessel (microreactor) can
be inhibited.
[0017]
The substrate material used for the microengraved plate
11 is preferably a transparent glass or polymer, and for the
purpose of inhibiting leakage, is more preferably an elastomer
material such as polydimethylsiloxane. Furthermore, in the
case of using an elastomer material for the substrate material
used for the microengraved plate 11, there is the advantage of
local deformation of the elastomer making it possible to avoid
detrimental effects on adhesion between the entire intaglio
plate and the substrate 15 that occur when microscopic debris
and other particles are trapped between the intaglio plate and
the substrate 15.
[0018]
In step (a), although there are no particular limitations
14
on the nucleic acids prepared in the microscopic grooves 12
provided they encode a protein or peptide used in printing, DNA
or mRNA is preferable, and DNA is more preferable from the
viewpoint of handling ease.
The DNA is preferably immobilized on the microengraved
plate 11 from the viewpoint of the need to specify positional
information on the microengraved plate 11 of the DNA.
In addition to methods using avidin-biotin binding,
methods such as those utilizing DNA labeled with a functional
group such as an amino group, aldehyde group or SH group and
a solid phase surface-treated with a silane coupling agent
having an amino group, aldehyde group or epoxy group and the
like can also be used, and a method using avidin-biotin binding
is particularly preferable. In this case, avidin is preferably
immobilized on the solid phase while biotin is preferably bound
to the DNA.
[0019]
The aforementioned solid phase preferably consists of
beads from the viewpoint of subsequent recovery of DNA, and
magnetic beads are more preferable from the viewpoint of being
able to be arranged in each of the microscopic grooves 12 of
the microengraved plate 11 in a short period of time.
In addition, in the case of using beads, a larger number
of DNA molecules can be immobilized on the substrate in the case
15
of immobilizing DNA. Since the number of DNA molecules is
reflected in the number of protein molecules produced using the
acellular protein synthesis system, according to the present
embodiment, a larger number of protein molecules can be
immobilized per spot than methods consisting of manufacturing
a protein array from a DNA microarray.
[0020]
In the present embodiment, in the case of using magnetic
beads for the solid phase, a magnetic plate is preferably
arranged beneath the substrate material used for the
microengraved plate 11.
As a result of using the microengraved plate 11 employing
such a structure, magnetic beads 14 can be easily and reliably
arranged in the microscopic grooves 12. More specifically, a
magnet is arranged beneath the substrate material, and a
dispersion of the magnetic beads 14 with DNA 13 immobilized
thereon is dropped onto the substrate material. Due to the
magnetic action of the magnetic beads 14 and a magnetic thin
film, the magnetic beads are attracted into the microscopic
grooves 12, enabling them to be easily arranged therein.
Moreover, by suitably moving the magnet in a planar direction
relative to the substrate, the magnetic beads 14 are dispersed,
and the filling rate of the magnetic beads 14 in the microscopic
grooves 12 improves. The magnetic field strength applied to
16
a substrate for arranging beads with a magnet is preferably 100
gauss to 10,000 gauss in terms of obtaining the desired effect.
In addition, since magnetism of the magnetic plate remains
even after the magnet has been removed, the magnetic beads 14
can continue to be held in a stable arrangement.
[0021]
A metal such as nickel, nickel alloy, iron or iron alloy
can be preferably used for the magnetic material, and in the
present embodiment, a magnetic material having large residual
magnetism is used preferably.
[0022]
The filling rate of the magnetic beads 14 in the microscopic
grooves 12 is dependent on the diameter of the microscopic
grooves 12, and since filling rate increases if the diameter
of the microscopic grooves 12 is slightly larger than the
diameter of the magnetic beads 14, the diameter of the
microscopic grooves 12 is preferably 1 to 2 times the diameter
of the magnetic beads . In addition, in terms of filling a single
magnetic bead 14 into a single microscopic groove 12, the depth
of the microscopic grooves 12 is preferably 1 to 2 times the
diameter of the magnetic beads 14.
[0023]
The microscopic grooves 12 are preferably hydrophilic, and
subjecting the microscopic beads 12 to hydrophilic treatment
17
by irradiating with oxygen plasma and the like facilitates
filling of a liquid in which magnetic beads are dispersed into
the microscopic grooves 12, resulting in an improved filling
rate.
[0024]
In the present embodiment, when preparing amino acids in
the microscopic grooves 12, a mixture of a plurality of types
of DNA as in a DNA library and the like may be mixed with a DNA
amplification reagent, and the mixture may be diluted with a
suitable buffer and the like, followed by dispensing into the
microscopic grooves 12. In addition, a mutant DNA library into
which gene mutations have been introduced may also be used as
a DNA library preferably used in molecular evolution
engineering applications. Here, the DNA is preferably
accurately diluted and dispensed so there is a single DNA
molecule in each of the microscopic grooves 12. There are no
particular limitations on the order in which DNA is mixed with
amplification reagent and diluted, and if the conditions of the
microengraved plate 11 are set and the reaction is carried out
so that DNA is applied to amplification after dispensing,
different types of DNA can be amplified in each of the
microscopic grooves 12.
Here, in the case of amplifying DNA, a PCR reaction is used
preferably, and commercially available reaction solutions
18
required for the reaction can be used. In addition, in the case
of immobilizing DNA in the microscopic grooves 12 on beads, if
an amplification reaction is carried out so that biotin is
incorporated in the DNA and beads are used that have been coated
with avidin, the DNA can be easily immobilized on the beads
through avidin-biotin binding. An example of a method used to
incorporate biotin in DNA consists of a method that uses PCR
primers labeled with biotin.
[0025]
Step (b) is a step for superimposing the substrate 15 on
the aforementioned microengraved plate 11 so that the substrate
15 contacts protein or peptide to be synthesized in the
aforementioned microscopic grooves 12.
The aforementioned step (b) utilizes intaglio printing
technology in which ink is placed in a concave portion of a plate,
and paper and the like is pressed onto the plate from above.
The aforementioned step (b) is a step for dropping a reaction
solution onto grooves in the form of the microscopic grooves
12 on the microengraved plate 11, superimposing the substrate
15 on the aforementioned microengraved plate 11 from above, and
then pressing on the substrate 15 using a hand press and the
like, and in step (c) to be subsequently described, a protein
or peptide 17 is printed onto the substrate 15. Accordingly,
since the specific opening shape of the microscopic grooves 12
19
is reflected as is in the shape of the spots on the substrate
15, according to the present embodiment, protein or peptide of
an arbitrary size and shape can be printed on the substrate.
Thus, if the shape is fine, the shape of the transferred spots
is also fine. As a result of having this fine shape, a
high-density protein array or peptide array can be fabricated.
[0026]
Moreover, according to step (c) to be subsequently
described, protein or peptide can be synthesized from the amino
acids, and the protein or the peptide can be printed on the
substrate without altering the positional information of the
nucleic acids immobilized on an array.
[0027]
Although the aforementioned opening shape of the
aforementioned microscopic grooves 12 is arbitrary, it is
preferably of a shape that allows at least one bead to be filled
therein. For example, the aforementioned opening shape of the
aforementioned microscopic grooves 12 may be circular,
rectangular, hexagonal or linear.
[0028]
Examples of the substrate 15 used in the aforementioned
step (b) include a glass substrate, silicon substrate, polymer
substrate and metal substrate.
In the present embodiment, the surface of the substrate
20
15 superimposed on the microengraved plate 11 is not necessarilyrequired
to be flat, and for example, may be formed to have
surface irregularities in order to increase the surface area
on which the protein or peptide 17 is immobilized. However,
when superimposing the substrate 15 on the microengraved plate
11, the substrate surface of the portion contacted by the
microengraved plate 11 is required to be flat so that reagent
and the like within all of the microscopic grooves 12 on the
microengraved plate 11 is sealed without leaking.
[0029]
Step (c) is a step for synthesizing the protein or peptide
17 from the aforementioned nucleic acids using the
aforementioned acellular protein synthesis system 19 in the
aforementioned microscopic grooves 12, and immobilizing the
protein or peptide 17 on the aforementioned substrate 15 along
the specific opening shape of the aforementioned microscopic
grooves 12.
[0030]
The acellular protein synthesis system refers to a protein
translation system composed of components having the ability
to synthesis protein extracted from suitable cells, and this
system contains elements required for translation, such as
ribosomes, translation initiation factors, translation
elongation factors, dissociation factors or aminoacyl tRNA
21
synthetase. Examples of such a protein translation system
include Escherichia coli extract, rabbit reticulocyte extract
and wheat germ extract. Another example is a reconfigurable
acellular protein synthesis system composed only of factors
obtained by independently purifying the aforementioned
elements required for translation. Reconfigurable acellular
protein synthesis systems are able to enhance translation
efficiency since they are able to more easily prevent
contamination by nucleases and proteases than in the case of
using a conventional cell extract. From the viewpoint of this
translation efficiency, a reconfigurable acellular protein
synthesis system is preferably used for the acellular protein
synthesis system in the present embodiment.
The use of such a system makes it possible to produce the
protein or peptide 17 in the aforementioned microscopic grooves
12.
[0031]
Since synthesized protein is susceptible to deactivation
due to decomposition or denaturation, when printing onto a
substrate, it is necessary to maintain the protein in as stable
a state as possible. In the present embodiment, since the
protein 17 synthesized in the microscopic grooves 12 is printed
as is on the substrate 15, the array 18 can be fabricated while
decreasing protein deactivation as much as possible.
22
[0032]
In the aforementioned step (c), in the case the nucleic
acids used in the acellular protein synthesis system 19 consist
of the DNA 13, a step is included in which mRNA 16 is synthesized
from the aforementioned DNA 13 using an acellular protein
transcription system. The aforementioned mRNA 16 is obtained
from the immobilized DNA 13 that encodes the protein to be
screened, by transcribing with RNA polymerase. An example of
RNA polymerase is T7 RNA polymerase.
In order to carry out the transcription reaction and a
translation reaction to be subsequently described in the
optimum state, the reactions may be carried out by combining
other apparatuses and the like that control the temperature of
the microengraved plate 11, pH conditions in the microscopic
grooves 12 and the like.
In addition, a system that couples transcription and
translation may also be used from the viewpoint of simplicity.
[0033]
In step (c), the aforementioned protein or peptide is
immobilized on the substrate 15 following synthesis of the
aforementioned protein or peptide 17. For example, after
having added required reagents and materials (nucleic acids)
to the microscopic grooves 12 on the microengraved plate 11,
in step (a) , the substrate 15 is used to seal the microengraved
23
plate 11 from above in step (b) . In step (c) , a series of
transcription and translation reactions are carried out after
mixing the reagents to obtain the mRNA 16 from the DNA 13 and
the protein 17 from the mRNA 16, followed by additionally
binding a tag having the translated protein 17 to the
aforementioned substrate 15.
[0034]
In the present embodiment, the aforementioned protein or
peptide contains a solid-phase binding site in the form of an
amino acid sequence in order to immobilize the protein or
peptide to the substrate, and the aforementioned substrate has
a solid-phase binding site recognition site that has affinity
for the aforementioned amino acid sequence.
Examples of this combination of solid-phase binding site
and solid-phase binding site recognition site include the
combination of maltose-binding protein and maltose, G protein
and guanine nucleotide, polyhistidine and a metal ion such as
nickel or cobalt, glutathione-S-transferase and glutathione,
DNA binding protein and DNA, antibody and antigen molecules
(epitopes), carmodulin and carmodulin binding peptide, ATP
binding protein and ATP, estradiol receptor protein and
estradiol, and various other combinations of receptor proteins
and their ligands.
7\mong these, preferable examples of combinations of
24
solid-phase binding sites and solid-phase binding site
recognition sites include maltose binding protein and maltose,
polyhistidine and a metal ion such as nickel or cobalt,
glutathione-S-transferase and glutathione and antibody and
antigen molecules (epitopes), while the combination of
polyhistidine and metal ion such as nickel or cobalt is most
preferable from the viewpoint of ease of use.
Polyhistidine is preferably used in the form of a hexamer
or larger. In order to contain polyhistidine in a protein or
peptide, a base sequence that encodes polyhistidine is
preferably added to the end of cDNA in advance by PCR and the
like.
In addition, the aforementioned solid-phase binding site
recognition site may be formed on the substrate based on a
prescribed pattern such as a circular or rectangular pattern
having a prescribed pitch, a linear pattern of a prescribed
pitch, or a combination thereof. In this case, the
aforementioned protein or peptide is printed in an arbitrary
size and shape corresponding to the pattern of the solid-phase
binding site recognition site patterned on the substrate.
[0035]
Next, the aforementioned superimposed substrate 15 is
separated from the aforementioned microengraved plate 11 (step
d) . The specific opening shape possessed by the aforementioned
25
microscopic grooves 12 is reflected as is in the shape of the
spots on the aforementioned substrate 15. Moreover, the spots
on the aforementioned substrate 15 are printed without altering
positional information of the corresponding DNA 13 immobilized
on the microengraved plate 11.
[0036]
The substrate 15 on which protein or peptide 17 has been
immobilized in this manner is then washed with PBS and the like
to produce the protein array or peptide array 18 (step e ).
[0037]
[Second Embodiment]
As shown in FIGS. 3A to 3C, the protein or peptide printing
method of the present embodiment comprises:
(a) a step for preparing the nucleic acids 3, a biotinylated
puromycin derivative 10 and the acellular protein synthesis
system 9 in the microengraved plate 1 composed of the
microscopic grooves 2 having a specific opening shape,
(b) a step for superimposing the avidin-labeled substrate
5 on the microengraved plate 1 so as to contact the protein or
peptide 7 to be synthesized in the microscopic grooves 2, and
(c) a step for synthesizing the protein or peptide 7 from
the nucleic acids 3 using the acellular protein synthesis system
9 in the microscopic grooves 2, and immobilizing the protein
or peptide 7 on the substrate 5 along the specific opening shapes
26
of the microscopic grooves 2.
The following provides an explanation of each step with
reference to FIGS. 4A to 4E, In FIGS. 4A to 4E, the same
reference symbols are used to indicate those constituent
features in FIGS. 4A to 4E that are the same as those indicated
in the schematic drawings of the protein or peptide printing
method of FIGS. 2A to 2E, and explanations thereof are omitted.
[0038]
In step (a) , DNA immobilized on a solid phase is preferable
for the nucleic acids prepared in the microscopic grooves 12.
A method using avidin-biotin binding is preferably used for
immobilization, and a method consisting of immobilizing avidin
on a solid phase followed by binding biotin to DNA is more
preferable.
[0039]
The substrate 15 used in step (b) can be labeled with avidin,
and a biotinylated protein or peptide 17 can be immobilized in
step (c) . Here, streptavidin is preferable for the avidin used
to label the substrate 15 from the viewpoint of ease of use.
[0040]
In the present embodiment, the biotinylated puromycin
derivative 10 refers to a biotinylated complex of puromycin and
nucleotide. Puromycin is a compound having a chemical
structure that resembles tRNA having an aminoacyl group on the
27
3 ' -end thereof, and has the property of binding to the C terminal
of synthesized protein when protein is synthesized in a
translation system. Consequently, during protein or peptide
synthesis in the present embodiment, the biotinylated puromycin
derivative 10 prepared in the microscopic grooves 12 binds to
the C terminal of the synthesized protein or peptide 17 in step
(a) .
[0041]
In the present embodiment, the aforementioned biotinylated
puromycin derivative is preferably a compound represented by
the aforementioned general formula (1) . In the aforementioned
general formula (1), Z represents a group represented by the
aforementioned formula (2), (3) or (4).
Namely, the aforementioned biotinylated puromycin
derivative is preferably a derivative obtained by biotinylating
deoxycitidyl puromycin, ribocytidyl puromycin or deoxyuridyl
puromycin.
Moreover, in the aforementioned general formula (1) , Z is
preferably a group represented by the aforementioned formula
(2) , and the aforementioned biotinylated puromycin derivative
is particularly preferably a biotinylated deoxycitidyl
puromycin derivative represented by the following formula (6) :
[0042]
[Chemical Formula 4]
28
NH—X=
II "
V, O ^N-^O
0=P—Os,^
^ * ^
NH OH
H3N—C—H "a
(wherein, at least one of X""" and X^ represents a group represented
by the following formula (5), and the other is a fluorescent
group or hydrogen atom:
[0043]
[Chemical Formula 5]
0
!
HN NH
O (5)
(wherein, * represents a binding site)).
[0044]
In the aforementioned formulas (2) to (4) and (6) , at least
one of X"^ and X^ represents a group (biotin) represented by the
aforementioned formula (5) . More specifically, only one of X"""
and X^ may be biotin or both X"'' and X^ may be biotin. As a result
of the puromycin derivative having biotin, biotin is added to
29
the C terminal of the protein or peptide 17 during synthesis
thereof in step (c) . Thus, in the present embodiment, it is
not necessary to add a base sequence that encodes hexahistidine
or other peptide or protein to the end of the cDNA used as a
template.
In addition, in the case of using a mutant DNA library for
the nucleic acids prepared in the microscopic grooves 12 in step
(a) , there are cases in which DNA is present in the mutant DNA
library in which a stop codon has been introduced into the coding
region thereof. In the case of synthesizing protein using such
DNA as a template, a polyhistidine tag cannot be added to the
C terminal if a method is used that adds a base sequence that
preliminarily encodes polyhistidine on the 3'-end of DNA. On
the other hand, in the present embodiment, biotin can be added
to this type of truncated protein. Thus, the protein or peptide
printing method of the present embodiment is preferably used
in molecular evolution engineering techniques.
[0045]
In the aforementioned formula (1), in the case X""" or X^ is
not biotin, the X""" or X^ may be a fluorescent group or hydrogen
atom. Examples of fluorescent groups include commonly used
protein or peptide fluorescent dyes, such as fluorescein,
rhodamine, Cy dye, Alexa® Fluor or HyLyte® Fluor. As a result
of the biotinylated puromycin derivative having a fluorescent
30
group, the amount of protein or peptide immobilized in the
fabricated protein array or peptide array can be confirmed by
measuring fluorescence intensity.
[0046]
The concentration of the biotinylated puromycin derivative
10 based on the total amount of reaction solution added to the
microscopic grooves 12 is preferably 1 ixM to 100 j^M and more
preferably 10 |J,M to 50 |aM. In the case the concentration is
1 |LiM or more, efficiency of protein biotinylation does not
become excessively low, while in the case the concentration is
100 |iM or less, protein expression level does not become
excessively low.
[0047]
Since synthesized protein is susceptible to deactivation
due to decomposition or denaturation, it is necessary to
maintain the protein in as stable a state as possible when
printing onto a substrate. In the present embodiment, since
the protein 17 synthesized in the microscopic grooves 12 is
printed as is onto the substrate 15, an array 18' can be
fabricated in which protein deactivation is inhibited as much
as possible.
[0048]
<
>
The protein array or peptide array of the present embodiment
31
produced using the protein or peptide printing method of the
present embodiment has an arbitrary spot shape and is capable
of accommodating high spot density. In addition, since the
protein array or peptide array is manufactured from the
aforementioned microengraved plate as necessary at the time of
use, denaturation and the like of protein or peptide on the array
can be decreased.
[0049]
<