The present invention relates to a thermal cycler apparatus, for use in thermal cycling
reactions. Aspects of the invention relate to methods for performing thermal cycling
reactions.
BACKGROUND TO THE INVENTION
Thermal cycling applications are an integral part of contemporary molecular biology.
For example, the polymerase chain reaction (PCR), which is used to amplify nucleic
acids, uses a series of DNA melting, annealing, and polymerisation steps at different
temperatures to greatly 'amplify' the amount of DNA in a sample. Other thermal cycling
applications are also known.
A typical thermal cycling apparatus consists of a metal sample block containing an
appropriate number of recesses to receive one or more reaction vessels. The sample
block may be shaped to conform to a 96-well plate format or individual reaction-tubes
that are generally 0.5m I or 0.2m I micro-centrifuge (Eppendorf) tubes. The metal block
acts as a thermal mass that transfers its thermal energy to and from the reaction
samples. In general thermal cycling energy is provided using a Thermoelectric Cooling
(TEC) device, also commonly known as a Peltier Effect element (PE). A thermal cycling
apparatus will generally also use a heat sink to assist in heat transfer to and from the
Peltier and a large fan or the like, to remove the excess heat generated by the Peltier
and transferred to the heat sink during cooling.
Peltier elements are solid-state devices that convert an electric current into a
temperature gradient. They consist of two sides - a hot side and a cold side. The
module acts as a heat pump in that it moves heat from the cold side to the hot side.
Switching the direction of current flow will swap the hot and cold side states and
regulating this current flow is used to cycle temperature of the sample block in order to
provide the heating and cooling required for PCR. The hot side of the Peltier requires a
method of removing that heat for the unit to function properly and to cool effectively.
The more efficient the means of removing this heat from the hot side, the colder the
cold side will operate and the more quickly the cold side will reach its optimum
temperature for thermal transfer. This is limited by the mass of the heat sink used and
the airflow of the fan used to remove the excess heat from the heat sink. In general a
thermal cycler design becomes a compromise between the power rating for a specific
heat sink, and the size of the heat sink and fans that can be accommodated in the
design. In standard Peltier block thermal cyclers, the heat sink and fan units represent
the majority of the unit and mass of the device.
Although convenient, such thermal cyclers suffer from a number of disadvantages. Key
among these is that a Peltier element suffers from reduced efficiency when being used
for both heating and cooling - for example, the Peltier device has significant thermal
mass in the form of a heat sink which must itself be heated or cooled to enable efficient
thermal transfer to the sample block. Achieving a reasonable efficiency for both heating
and cooling is complex, and most thermal cycler designs must find a compromise
between the heating and cooling functions of the Peltier element and the desired rate
of thermal transfer to the sample block. As a consequence of this compromise,
conventional thermal cyclers typically achieve a maximum heating or cooling rate of no
more than 3 degrees Celsius per second and have a high power overhead to achieve
these modest rates of performance.
The present invention provides an alternative thermal cycler arrangement.
SUMMARY OF THE INVENTION
According to the present invention, there is provided a thermal cycler comprising:
a sample block for receiving a sample;
a Peltier-type thermoelectric element adjacent the sample block, configured for
cooling the sample block;
a non-Peltier-type heating device adjacent the sample block, configured for
heating the sample block;
a heat sink, separated from the sample block and Peltier-type element; and
a heat pipe connecting the heat sink to the Peltier-type element, which permits
thermal energy to transfer from the Peltier-type element to the heat sink.
A thermal cycler according to the present invention separates the heating and cooling
functions, allowing each to be optimised for the desired function. Further, the use of
separate heater and cooler elements means that the thermal mass of the heat sink
need not influence the performance of the Peltier and the efficiency of heating and
cooling the sample block. In addition, a conventional heating element, for example an
electrical resistance heating element, is in general more efficient than a Peltier-type
element used for both heating and cooling; the Peltier-type element is more efficient
when used for cooling only or when heating only.
In the preferred arrangement, the sample block is sandwiched between the Peltier-type
element and the non-Peltier-type heating device; for example, the element and the
device are located on opposed faces of the sample block. Conventional thermal cycler
devices use a stacked arrangement, in which the sample block is positioned above the
Peltier element, which is positioned above the heat sink, which is positioned above the
cooling fans. Sample tubes are loaded into the sample block from above. This
conventional arrangement means that there is no position in which a non-Peltier-type
heater may be conveniently located, other than between the sample block and the
Peltier element, which would further reduce efficiency due to the need to cool through
the heater.
The cycler may further comprise an optics assembly - for example, including a light
source and light detector, optionally with one or more lenses. This allows the cycler to
be used in detecting fluorescence or other signal from a reaction as the reaction
proceeds in real time. The light source and light sensor may encompass any
electromagnetic radiation, not merely visible light. The cycler may also comprise filters
to restrict light of particular wavelengths. The cycler may further comprise a second
light source; this allows for a relatively low-cost two-label detection system, where the
two sources illuminate at different wavelengths. Where the cycler is intended to use a
plurality of samples or reaction vessels in each cycling reaction, the cycler may
conveniently comprise at least one light source / sensor combination for each sample.
In preferred embodiments of the invention, the light source is an LED or similar, while
the light sensor is a photodiode or the like. The sensor is conveniently a log-response
detector, which allows for a wider dynamic range, and a wider copy number of nucleic
acids which can be detected. This arrangement allows for simple, robust components
to be used without the requirement for lenses or complex optics arrangements. Such a
source / sensor combination has been found to be sufficient to obtain qualitative
information on the progress of a reaction (for example, that amplification is occurring).
For many applications, such data is sufficient, and it is not necessary to quantitate the
progress of the reaction.
The use of an LED / photodiode arrangement also reduces the need for critical
positioning or distancing of the source and sensor with respect to the sample, again
thereby making the cycler more robust. Conveniently the source and sensor operate at
different wavelengths of light; for example, a preferred source is an LED emitting light
at 490 nm, while a preferred sensor is most sensitive to light at 530 nm. This is
consistent with typical fluorophores used in biochemical reactions. Modulated
illumination of the LED or LEDs can be used, in order to help remove noise and
background from the signal.
Where the sample block is sandwiched between the Peltier-type element and the
heating device, the sample block will preferably be sized and shaped to receive
multiple sample tubes arranged in a linear manner, or a strip of sample tubes. This
ensures uniform heating and cooling. The Peltier and heating elements are preferably
located above and below the sample block in normal use, and the sample block is
orientated to receive the sample holder from the side (rather than from above as with
conventional cyclers). This arrangement has an additional advantage over conventional
arrangements, in that a side opening means that it is less likely that foreign objects will
fall into the opening and either contaminate the sample, or obscure any optical
assembly which may be present within the cycler.
The construction of the sample block sandwiched between heating element and Peltier
allows optimum shape and size to receive a sample holder and to provide thermal
transfer whilst enabling a design with minimal mass. In combination with high surface
to area ratio tubes, thermal transfer rates to the reaction from the sample block is
highly efficient.
The sample holder need not be received generally horizontally; an angle of less than
90 degrees may be sufficient, for example, less than 80, 70, 60, 50, 45, 40 degrees.
The sample block may be removable from the thermal cycler; this allows use of
replaceable or interchangeable blocks, for example to accommodate different sizes or
arrangements of sample tubes.
The non-Peltier-type heating device may be any suitable heater, and is preferably an
electrical resistance heater. Other heating devices may be used. The heating device
may include one or more openings to allow light to pass through the device; this allows
a light source and detector combination to be used which is located outside the sample
block / heater.
Preferably the Peltier-type element is configured so as to be deactivated when the
heater is activated; and preferably also vice versa. When the heater is activated and
the Peltier element deactivated, the element acts as a thermal insulator that restricts
heat loss from the sample block to the heat pipe and heat sink assembly. This
significantly reduces the time required to heat the sample block, and so improves utility.
Uniquely, the arrangement of the Peltier in this configuration acts as a 'thermal gate',
providing a block to thermal loss during heating when switched off, whilst also providing
an efficient cooling pathway when it is switched on.
Heat is removed from the hot side of the Peltier during the cooling phase of the thermal
cycle via a heat pipe. The heat pipe preferably has a generally flat cross section, and
may include micro-channel pipes containing acetone, or other cooling fluid. For
example, Flat Cool Pipes from Amec Thermasol are suitable. Conventional heat pipes
are typically based on round section copper pipes filled with water as a cooling fluid;
these conventional pipes are less efficient than the preferred pipes, which also provide
a much more compact footprint. With conventional heat pipes, the fan and heat sink
may need to be stacked above the block which leads to considerable height of the unit.
Flat Cool Pipes or similar allow the lateral, sequential positioning of components where
the conventional method is limited to vertical stacking of components. This provides a
compact positioning of parts. Critically it allows the heat sink to be arranged below the
heat pipe that provides a highly efficient space footprint compared to conventional
assemblies.
The heat pipe is preferably generally S-shaped, with the upper section contacting the
heat sink, and the lower section contacting the Peltier element. The upper section is
inclined (preferably around 20°, but in certain embodiments up to 90°) and the lower
section is generally horizontal (preferably around 0°, but in certain embodiments up to
90°) . The lower section is preferably smaller in area (for example, less than 10%, 20%,
30%, 40, 50% in area) of the upper section. For maximum efficiency at least the last
20% of the heat pipe is preferably inclined to be higher than the lower part where the
heat is being generated, though in general greater than 50% of the heat pipe is inclined
to provide the upper section. This allows efficient thermal transfer from the heat source,
and also allows re-circulation of the cooling fluid within the pipe. Of course, it will be
appreciated that the use of an S-shaped heat pipe is not essential to the invention, and
that other shapes, including generally horizontal pipes, may be used.
The upper section of the heat pipe is connected to a heat sink, which may optionally
also comprise an axial fan. This is used to remove excessive heat generated and
transferred to the upper section of the heat pipe. The heat sink may be of any
convenient form or material, but optionally it will be a forged aluminium pad with pin
fins. Pins are preferably arranged in a 'dense' format of greater than 16 pins per cm2.
Heat is removed from the heat sink using a high airflow fan, typically with airflow
greater than 10, 20, 30 or 40 CFM (cubic feet per minute). Airflow via direct
impingement is used to remove excess heat from the heat sink and is directed out of
the device. Where alternative 'fin' heat sinks are used, axial, blower, tangential, or any
convenient fan may provide the required airflow.
The cycler may further comprise a computer processor, which may be used for any or
all of monitoring and controlling the light source and detector, temperature regulation,
the cycling program, and the like. The processor is conveniently user-programmable, to
allow selection of appropriate cycling programs for particular reactions. For example,
the cycler may comprise a user interface, such as a keypad or touch-screen, allowing a
desired cycling program to be selected, input or edited.
The computer processor may be mounted on a substrate, such as a circuit board or a
PCB. In preferred embodiments of the invention, the remaining components of the
cycler - for example, the Peltier-type element, the heater, the sample block, and the
heat sink and pipe - are secured to the substrate. For example, the components may
be bolted to the substrate. This allows for ease of construction and assembly, and
permits a smaller footprint for the cycler. Of course, not all of the components need be
secured directly to the substrate; some of the components may be secured to others
(for example, the heater may be secured to the substrate, with the sample block
secured to the heater and the Peltier element secured to the sample block). A casing
may enclose the substrate and the remaining components.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1 shows an external view of a thermal cycler in accordance with an embodiment
of the invention;
Figure 2 shows an external view of the underside of the thermal cycler of Figure 1;
Figure 3 shows a side view of the internal chassis components of the thermal cycler of
Figure 1;
Figure 4 shows an internal view of the thermal cycler of Figure 1; and
Figure 5 shows the construction of the optical assembly and sample block of the
thermal cycler of Figure 1.
DETAILED DESCRIPTION OF THE INVENTION
Referring first of all to Figure 1, this shows an exterior view of a thermal cycler in
accordance with the present invention. The cycler 10 includes an outer casing 12
formed with a carrying handle 14. The upper surface of the casing 12 is provided with a
touchscreen interface 16 allowing the user to operate the cycler. The front of the casing
provides an opening 18 into which can be inserted a sample holder 20, which includes
(in this embodiment) three sample tubes 22 of thin-walled plastic.
The underside of the cycler 10 is shown in Figure 2. The outer casing includes an
opening 24 within which is mounted a cooling fan 26 which is adjacent a heat sink 28.
The casing is formed with supports 30 which raise the fan 26 off the benchtop, allowing
air to circulate.
The internal architecture of the cycler 10 is shown in Figure 3. The outer casing 12 is
not shown in this figure. A PCB substrate 32 is provided, on which are mounted the
various electronic components needed to control and operate the cycler (for example,
operating the user interface via the touchscreen; activating the heating and cooling
elements; and operating the optical assembly). Secured to the substrate 32 via bolts 34
are the heat sink 28 and fan 26 assembly. Also secured to the substrate 32, but
separated from the heat sink 28, is the sample block 34.
A Peltier element 36 is mounted beneath the sample block 34, in thermal contact
therewith. Above the sample block 34 is an electrical resistance heater 38.
The Peltier element 36 is secured to a heat pipe 40, of the flat-section type formed with
micro channels, using acetone as a coolant. The heat pipe 40 is generally S-shaped,
and includes an upper section 42 in contact with the heat sink 28 and fan 26, and a
lower section 44 in contact with the Peltier element 36. The upper section 42 is inclined
at around 20°, while the lower section 44 is generally horizontal (at around 0°) . The
lower section 44 is around half the area of the upper section 42.
A view of the internal chassis is shown in Figure 4. The substrate 32 carries the
electronic components and processor needed to operate the cycler, while the
remaining components are secured to the substrate 32 with bolts 46 or other fasteners.
In this figure, a portion of the heat pipe 40 and the sample block 34 can be seen. The
whole assembly can be simply mounted within the casing 12 for ease of manufacture.
The sample block assembly 34 is shown in more detail in Figure 5. The block includes
various components of the optical assembly (not shown in the other figures). A PCB 46
including three LEDs 48 is located within an optics assembly former 50, which includes
three apertures 52 for receiving sample tubes, and an opening 54 for allowing light
from the LEDs to pass. A 490 nm glass excitation filter 56 is placed in the opening
above the LEDs 48, and the electrical heater 38 above the filter. The heater 38
includes three apertures 58 aligning with the LEDs. The sample block 34 is then placed
in the former 50, and a 535 nm glass emission filter 60 placed at the rear of the sample
block 34. The sample block may include apertures aligning with the LEDs and the
emission filter, or may be transparent to light of the appropriate wavelength, or may
include waveguides in suitable locations. The whole assembly may then be put
together with the other components of the cycler.
In use, the cycler operates as follows. A user may program a desired cycling program
using the touchscreen interface 16. This causes the control electronics to operate the
components in the appropriate manner. A sample may then be loaded into the sample
tubes 22 of the sample holder 20, and the holder then inserted into the sample block 34
via opening 18.
When the user presses a "START" icon (or similar) on the touchscreen, the heater 38
and Peltier element 36 are operated in an appropriate manner. The heater 38 is first
activated to raise the temperature of the sample to a desired first temperature.
Simultaneously the Peltier element 36 is deactivated, such that it acts as a thermal
insulator between the sample block and the heat pipe 40, retaining heat within the
sample block. When the sample block has reached the desired temperature for the
desired time, the heater 38 may be deactivated, and the Peltier element 36 activated.
The Peltier element 36 is operated so as to cool the sample block 34; heat is
transferred from the sample block to the heat pipe 40. The heat pipe 40 then transfers
heat from the lower section 44 to the upper section 42; heat is then dissipated via the
heat sink 28 and fan 26. The cycle then repeats as desired.
In addition to this, the optics assembly may also be used to monitor the progress of the
cycling reaction, either while cycling, or afterwards. The LEDs are actuated to
illuminate the sample; emitted light is then detected by a light sensor. The intensity or
simply the presence or absence of emitted light may be monitored either over time or at
a particular time point. This allows for real time PCR to be carried out.
The cycler as described herein has several advantages over conventional prior art
cyclers. Firstly, overall efficiency is improved by separating the heating and cooling
functions, and using a non-Peltier heater. The use of a heat pipe to remove waste heat
from the Peltier element, in combination with the separation of heating and cooling
functions and the use of the Peltier element as a "gate" when the heater is activated,
permits physical separation of the sample block / heater / cooler assembly and the heat
sink / fan assembly, giving the cycler an improved physical footprint.
Further, the overall thermal profile of the 'thermal waste heat' is low. In a standard
thermal cycler which uses a single Peltier element to both heat and cool, the heat sink
can rise to in excess of 65C to 85C. With the present system the heat sink may only
rise to 40C-45C, significantly lower. This in part is due to the recycling of energy within
the linear flat heat pipe which has not been used in PCR instruments previously. The
heat pipe ensures an efficient removal of heat from the hot side of the Peltier during
cooling, which re-cycles the thermal energy and rapidly cools the hot side of the Peltier.
The heat energy released by the heat sink is much lower, and therefore the power
requirement of the Peltier much less.
The whole assembly can then operate at multiple power inputs which is significant. For
example, a portable, field based unit requires a very low power profile such that it may
be powered by batteries. Cyclers in accordance with the present invention can run off
less than 50W total power and still provide cycle times for 30x cycles of under 30
minutes. Increasing the power decreases the cycle times and does not over burden the
heat exchange mechanism. The present design enables this 'multi-power' ability. 100W
input reduces the cycle times down to 20 minutes and 150W reduces the times down to
15 minutes. In particular, in preferred embodiments of the invention in use, the cycler
undergoes 30 or more standard cycles of 5 seconds each at 50°, 72° and 95°C in under
30 minutes, when operated at a power of 50W or less; 30 or more standard cycles of 5
seconds each at 50°, 72° and 95°C cycles in under 20 minutes, when operated at a
power of 100W or less; or 30 or more standard cycles of 5 seconds each at 50°,
72° and 95°C cycles in under 20 minutes, when operated at a power of 150W or less.
By comparison, standard block thermal cyclers require >500W, rapid block cyclers
such as Finnzymes Piko thermal cycler require 180W, and air cyclers such as the
lightCycler 2.0 from Roche require 800W.
In fact, in tests when operating a cycler of the invention at 50W; the heat pipe varied
between 47°C to 57°C, with the heat sink at 40°C constant. At 100W; the heat pipe was
at 50°C to 60°C, and the heat sink at 48°C constant. At 150W; the heat pipe was at
53°C to 63°C, and the heat sink 49°C constant.
So with variable power delivery the cooling efficiency remains high and in all
circumstances the heat sink does not exceed 50°C meaning that vented air will sit
significantly below 40°C. The benefit of this is that as the ambient temperature
increases, the performance of the unit will remain unperturbed.
Another benefit of the system is that it is less sensitive to changing outside ambient
temperatures, again because of the efficiency of the arrangement and because there
are multiple routes to remove heat from the system. This is again important for portable
units. So even in ambient temperatures in excess of 50C the unit still returns similar
thermal cycling times as conventional units. This is because the fan and heat sink have
significant overhead so that if the ambient temperature goes up, more of the heat is
removed from the system by the fan and heat sink, rather than the evaporative
properties of the heat sink. In fact, we believe that certain embodiments of the invention
may operate in ambient temperatures of up to 55C or more, whereas standard Peltier
cyclers can only operate to 30-40C.
The configuration allows use of a low mass sample block made from aluminium or
thermoelastomer polymers that have high thermal transfer properties; these allow
flexibility in the block which means consumables do not get stuck and allows a good
resistance fit which is not generally possible with solid blocks and long, thin walled
tubes.
Other advantages of the present invention will be apparent.

CLAIMS:
1. A thermal cycler comprising:
a sample block for receiving a sample;
a Peltier-type thermoelectric element adjacent the sample block, configured for
cooling the sample block;
a non-Peltier-type heating device adjacent the sample block, configured for
heating the sample block;
a heat sink, separated from the sample block and Peltier-type element; and
a heat pipe connecting the heat sink to the Peltier-type element, which permits
thermal energy to transfer from the Peltier-type element to the heat sink.
2. The cycler of claim 1 wherein the sample block is sandwiched between the Peltiertype
element and the non-Peltier-type heating device.
3. The cycler of claim 1 further comprising an optics assembly.
4. The cycler of claim 3 wherein the optics assembly comprises a light source and light
detector, optionally with one or more lenses.
5. The cycler of claim 1 wherein the sample block is sized and shaped to receive
multiple sample tubes arranged in a linear manner, or a strip of sample tubes.
6. The cycler of claim 1 wherein the sample block is sized and shaped to receive a
sample holder from the side when in use.
7. The cycler of claim 1 wherein the sample block is removable from the thermal cycler.
8. The cycler of claim 1 wherein the non-Peltier-type heating device is an electrical
resistance heater.
9. The cycler of claim 1 wherein the non-Peltier-type heating device includes one or
more openings to allow light to pass through the device.
10. The cycler of claim 1 wherein the Peltier-type element is configured so as to be
deactivated when the non-Peltier-type heater is activated.
11. The cycler of claim 1 further comprising a computer processor.
12. The cycler of claim 11 wherein the cycler comprises a user interface allowing user
interaction with the computer processor.
13. The cycler of claim 11 wherein the computer processor is mounted on a substrate.
14. The cycler of claim 13 wherein the Peltier-type element, the heater, the sample
block, and the heat sink and pipe are also secured to the substrate.
15. The cycler of claim 1 wherein the heat pipe has a flat cross section, and includes
micro-channel pipes containing a cooling fluid.
16. The cycler of claim 1 wherein the heat pipe is generally S-shaped, with the upper
section contacting the heat sink, and the lower section contacting the Peltier element.
17. The cycler of claim 16 wherein the upper section is inclined and the lower section is
generally flat.
18. The cycler of claim 16 wherein the lower section is smaller in area than the upper
section.
19. The cycler of claim 1 wherein, in use, the cycler undergoes 30 or more standard
cycles of 5 seconds each at 50°, 72° and 95°C in under 30 minutes, when operated at a
power of 50W or less.
20. The cycler of claim 1 wherein, in use, the cycler undergoes 30 or more standard
cycles of 5 seconds each at 50°, 72° and 95°C cycles in under 20 minutes, when
operated at a power of 100W or less.
2 1. The cycler of claim 1 wherein, in use, the cycler undergoes 30 or more standard
cycles of 5 seconds each at 50°, 72° and 95°C cycles in under 20 minutes, when
operated at a power of 150W or less.
22. The cycler of claim 1 further comprising one or more batteries to provide electrical
power.
23. The cycler of claim 1 configured to operate at a selectable power input.
24. The cycler of claim 1 wherein, when the cycler undergoes 30 or more standard
cycles of 5 seconds each at 50°, 72° and 95°C in use at room temperature, the heat
sink does not rise above 50°C.
25. The cycler of claim 1 wherein, when the cycler undergoes 30 or more standard
cycles of 5 seconds each at 50°, 72° and 95°C in use at room temperature, the heat
pipe does not rise above 63°C.