U.S. patent application number 09/759892 was filed with the patent office on 2001-10-11 for rapid thermocycling for sample analysis.
Invention is credited to Craighead, James R., Huhmer, Andreas, Landers, James P., Oda, Robert P..
Application Number | 20010029036 09/759892 |
Document ID | / |
Family ID | 21770514 |
Filed Date | 2001-10-11 |
United States Patent
Application |
20010029036 |
Kind Code |
A1 |
Landers, James P. ; et
al. |
October 11, 2001 |
Rapid thermocycling for sample analysis
Abstract
Methods for performing rapid and accurate thermocycling on a
sample are disclosed. Use of non-contact heating and cooling
sources allows precise temperature control with sharp transitions
from one temperature to another to be achieved. A wide range of
temperatures can be accomplished according to these methods. In
addition, thermocycling can be performed without substantial
temperature gradients occurring in the sample. Apparatus for
achieving these methods are also disclosed. A method for pumping a
sample through microchannels on a microchip using a non-contact
heat source is also disclosed.
Inventors: |
Landers, James P.; (Upper
Saint Clair, PA) ; Huhmer, Andreas; (Pittsburgh,
PA) ; Oda, Robert P.; (Stewartville, MN) ;
Craighead, James R.; (Stewartville, MN) |
Correspondence
Address: |
THORP REED & ARMSTRONG, LLP
ONE OXFORD CENTRE
301 GRANT STREET, 14TH FLOOR
PITTSBURGH
PA
15219-1425
US
|
Family ID: |
21770514 |
Appl. No.: |
09/759892 |
Filed: |
January 12, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09759892 |
Jan 12, 2001 |
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09015278 |
Jan 29, 1998 |
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6210882 |
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Current U.S.
Class: |
435/91.1 ;
422/186; 435/287.2 |
Current CPC
Class: |
F16K 13/10 20130101;
B01L 2200/147 20130101; B01L 2300/185 20130101; B01L 2300/1872
20130101; B01L 2400/0442 20130101; B01L 3/5027 20130101; Y10T
436/25 20150115; B01L 7/52 20130101 |
Class at
Publication: |
435/91.1 ;
435/287.2; 422/186 |
International
Class: |
C12P 019/34; B01J
019/08; C12M 001/34 |
Claims
What is claimed is:
1. A method for thermocycling a sample comprising: (a) placing the
sample in a suitable reaction vessel; (b) heating the sample to a
first desired temperature using the optical energy of a non-contact
heat source that directly heats the sample itself; (c) positively
cooling the sample to a second desired temperature by a non-contact
cooling source directed at the reaction vessel; and (d)
sequentially repeating steps (b) and (c) to perform a desired
number of thermocycles
2. The method of claim 1, wherein said heating step can be
accomplished at a rate of between about 10.degree. C./second and
100.degree. C./second and said cooling step can be accomplished at
a rate of between about 5.degree. C./second and 50.degree.
C./second.
3. The method of claim 2, wherein each thermocycle is completed in
between less than 0.5 second and about 20 seconds.
4. The method of claim 1, further including at least one
intermediate heating step to achieve at least one intermediate
temperature lower than said first desired temperature.
5. The method of claim 1, further including at least one
intermediate cooling step to achieve at least one intermediate
temperature higher than said second desired temperature.
6. The method of claim 1, wherein each desired temperature is
maintained for a desired dwell time.
7. The method of claim 6, wherein said desired dwell times range
from milliseconds to about 20 seconds.
8. The method of claim 1, wherein the sample is sequentially: (a)
heated to a first desired temperature and maintained at that
temperature for a desired dwell time; (b) cooled to a second
desired temperature and maintained at the second desired
temperature for a desired dwell time; and (c) heated to a third
desired temperature and maintained at the third desired temperature
for a desired dwell time; wherein the third desired temperature is
higher than the second desired temperature, but lower than the
first desired temperature; and wherein steps (a), (b) and (c) are
sequentially repeated to perform the desired number of
thermocycles.
9. The method of claim 8, wherein said first desired temperature is
between about 90 and 98.degree. C., said second desired temperature
is between about 40 and 75.degree. C., and said third desired
temperature is between about 60 and 80.degree. C.
10. The method of claim 9, wherein the dwell time at said first
desired temperature is between about 1 to 20 seconds, the dwell
time at said second desired temperature is between about 1 to 20
seconds, and the dwell time at said third desired temperature is
between about 1 to 20 seconds.
11. The method of claim 1, wherein the suitable reaction vessel is
selected from the group consisting of a capillary tube, a
microchip, a microchamber and a microtiter plate.
12. The method of claim 1, wherein heating is effected by use of an
IR source.
13. The method of claim 12, wherein said IR source is a halogen
lamp.
14. The method of claim 12, wherein said IR source is a tungsten
lamp.
15. The method of claim 1, wherein cooling is effected by use of a
compressed air source.
16. The method of claim 15, wherein the pressure of the air from
said compressed air source is between about 1 and 150 psi.
17. The method of claim 1, wherein between about 5 and 100
thermocycles are carried out on the sample.
18. The method of claim 1, wherein said method is used to amplify
DNA in said sample.
19. The method of claim 1, wherein a microprocessor is used to
control said heating and cooling steps.
20. The method of claim 19, wherein said first desired temperature
is less than or equal to about 120.degree. C. and said second
desired temperature is greater than or equal to about 4.degree.
C.
21. An apparatus for thermocycling a sample comprising: (a) a
suitable reaction vessel for containing the sample; (b) non-contact
optical energy means for directly heating the sample to a first
desired temperature; (c) non-contact means for positively cooling
the sample to a second desired temperature; (d) means for
monitoring the temperature of said sample; (e) means for
controlling the heating and cooling of said sample.
22. The apparatus of claim 21, wherein said suitable reaction
vessel is selected from the group consisting of a capillary tube, a
microchip, a microchamber and a microtiter plate.
23. The apparatus of claim 21, wherein said heating means is an IR
source.
24. The apparatus of claim 23, wherein said IR source is a halogen
lamp.
25. The apparatus of claim 23, wherein said IR source is a tungsten
lamp.
26. The apparatus of claim 23, wherein said IR source is disposed
in a spaced relationship with respect to said reaction vessel.
27. The apparatus of claim 26, further comprising filter means
interposed between said IR source and said reaction vessel.
28. The apparatus of claim 21, wherein said cooling means is a
compressed air source.
29. The apparatus of claim 28, wherein said compressed air source
has means for chilling air.
30. The apparatus of claim 28, wherein the air from said cooling
means has a pressure of between about 1 and 150 psi.
31. The apparatus of claim 28, wherein the rate of flow of air from
said compressed air source is controlled by a solenoid valve.
32. The apparatus of claim 28, wherein said cooling means is
structured to cause forced air to impinge on said reaction vessel
from a position angularly offset with respect to the direction of
heat applied from said heating means.
33. The apparatus of claim 21, wherein said means for monitoring
the temperature of said sample is disposed adjacent to said
reaction vessel.
34. The apparatus of claim 33, wherein said temperature monitoring
means includes thermocouple means.
35. The apparatus of claim 34, wherein said thermocouple means is
disposed in a second reaction vessel containing a blank.
36. The apparatus of claim 34, wherein said thermocouple means is a
thermo-optical sensing device positioned above a sample in the
reaction vessel.
37. The apparatus of claim 34, wherein said thermocouple means
includes a sealed vessel containing a blank and wherein said sealed
vessel is disposed adjacent to said sample containing reaction
vessel.
38. The apparatus of claim 21, wherein said means for controlling
the heating and cooling of said sample is microprocessor means.
39. The apparatus of claim 38, wherein said microprocessor means is
operatively associated with said heating means, said cooling means
and said temperature monitoring means.
40. The apparatus of claim 39, wherein said microprocessor means
has means for effecting heating at a rate of between about
10.degree. C./second and 100.degree. C./second and cooling at a
rate of between about 5.degree. C./second and 50.degree.
C./second.
41. The apparatus of claim 39, wherein said microprocessor means
has means for completing one thermocycle in between less than 0.5
second and about 20 seconds.
42. The apparatus of claim 39, wherein said microprocessor means
has means for establishing a plurality of desired temperatures and
a plurality of desired dwell times at each desired temperature.
43. The apparatus of claim 39, wherein said microprocessor means
has means for effecting DNA amplification in a sample.
44. The method of claim 1, wherein said method is used to effect
protein folding and unfolding.
45. The method of claim 1, wherein said method is used to effect
activation of an enzyme.
46. The method of claim 1, wherein said method is used to effect
sequencing of a protein or peptide.
47. The apparatus of claim 28, wherein a plurality of compressed
air sources are provided.
48. The apparatus of claim 27, further comprising light restricting
means interposed between said filter means and said reaction
vessel; wherein said light restricting means has an aperture that
can be adjusted to allow the desired amount of light to impinge on
said reaction vessel.
49. The apparatus of claim 21, further comprising stage means on
which said reaction vessel is placed.
50. The apparatus of claim 49, wherein said stage means is
movable.
51. The apparatus of claim 21, further comprising means for
reflecting radiation from said heat source towards said reaction
vessel.
52. The apparatus of claim 51, wherein said reflecting means is a
mirror disposed on one side of said reaction vessel and said
heating means is disposed on the opposite side of said reaction
vessel.
53. The apparatus of claim 52, further comprising a filter means
interposed between said heat source and said reaction vessel.
54. The method of claim 4, further including at least one
intermediate cooling step to achieve at least one intermediate
temperature higher than said second desired temperature.
55. A microchip comprising: an upper portion comprising a plurality
of reservoirs; and a lower portion attached to said upper portion
comprising a plurality of microchannels which are in fluid flow
communication with one or more of said plurality of reservoirs.
56. The microchip of claim 55, wherein said upper portion further
comprises a window portion which is thinner with respect to
adjacent portions of said upper portion.
57. The microchip of claim 56, wherein said upper portion comprises
a sample reservoir at one end of said window and a waste reservoir
at the opposite end of said window.
58. The microchip of claim 57, wherein said upper portion further
comprises an inlet reservoir, a second waste reservoir and an
outlet reservoir.
59. A method for pumping a sample through one or more microchannels
in a microchip comprising: (a) placing the sample in a reservoir in
fluid flow communication with one or more of said microchannels;
(b) sealing the reservoir; and (c) pumping the sample through the
microchannels by heating the reservoir using a non-contact heat
source; wherein heating the sample increases the pressure in said
chip and said pressure increase causes said sample to be pumped
through said microchannels.
60. The method of claim 59, wherein said non-contact heat source is
an IR source.
61. The method of claim 59, further including: (d) stopping the
pumping action of step (c) by cooling the reservoir using a
non-contact cooling source.
62. The method of claim 61, wherein said non-contact cooling source
is compressed air.
63. The method of claim 1, wherein said method is used to effect
denaturation of enzymes.
Description
FIELD OF THE INVENTION
[0001] The present invention relates to methods and apparatus for
performing rapid and accurate heating and cooling of a sample. More
specifically, the present invention relates to methods and
apparatus for performing non-contact, rapid and accurate
thermocycling on micro to nanoliter volume samples, wherein each
cycle can be completed in as little as a few seconds.
BACKGROUND OF THE INVENTION
[0002] Numerous analytical methods require that a sample be heated
to a particular temperature and then cooled to a particular
temperature. Often, sequential heating and cooling steps, known as
thermocycling, are required. Various methods involve cycling
through two or more stages all with different temperatures, and/or
involve maintaining the sample at a particular temperature stage
for a given period of time before moving to the next stage.
Accordingly, thermocycling of samples can become a time consuming
process. In addition, these methods often require the precise
control of temperature at each stage of the cycle; exceeding a
desired temperature can lead to inaccurate results.
[0003] Two factors that are typically important, therefore, in the
performance of effective thermocycling on a sample are the speed
and homogeneity of the apparatus and methods used. Cycle times are
largely defined by how quickly the temperature of the sample can be
changed, and relate to the heat source itself and the rate of heat
transfer to the sample. Uniformity of sample temperature is
important to ensure that reproducible and reliable results are
obtained. Typically, increasing cycle speeds makes it harder to
maintain homogenous sample temperatures.
[0004] The concept of using elevated temperatures to effect
chemical, biological and biochemical reactions is commonly known
and expressed as the law of Arrhenius. Generally, an increase in
temperature of a reaction translates into an increase in the rate
of the reaction. Reaction parameters, such as the activation of the
reaction, the increase in dissolution of the reaction components,
the desolvation of the substrate and the specificity of the
catalysis are temperature dependent. Exact or nearly exact
maintenance of a reaction temperature is often critical in most
biochemical/biological processes to guarantee their successful
completion. Therefore, great efforts are made in the daily routine
of a chemical/biochemical laboratory to control the temperature
conditions during a reaction. It is expected that better
temperature control increases the performance of most reactions,
for example, increasing the specificity of proteolytic
reactions.
[0005] There is particular interest in rapid and homogenous
thermocycling when performing DNA amplification for the polymerase
chain reaction (PCR). PCR is a process by which a single molecule
of DNA (or RNA) from an organism can be amplified by a factor of
10.sup.6 to 10.sup.9. This procedure requires the repetition of
heating and cooling cycles in the presence of an original DNA
target molecule, specific DNA primers, deoxynucleotide
triphosphates, and DNA polymerase enzymes and cofactors. Heating
accounts for a denaturing of the sample while cooling results in
annealing of the sample. At a temperature typically between the
denaturing and annealing temperatures, extension of the annealed
primers using an enzyme occurs to replicate the DNA strand or
portion of the strand. Extension of the primer can also occur at
the same temperature as annealing, depending on the specifics of
the reaction. Each heating/cooling cycle produces a doubling of the
target DNA sequence, leading to an exponential accumulation of the
target sequence. PCR based technology has been applied to a variety
of analyses, including environmental and industrial contaminant
identification, medical and forensic diagnostics, and biological
research.
[0006] There are a number of biochemical reactions that require
accurate and rapid thermocycling. Additionally, there are reactions
whose specificity can be enhanced when conducted in a rapid and
accurate thermocycling environment. The PCR reaction has very high
demands on the accuracy of the thermocycling parameters and is,
therefore, an ideal assay to test the accuracy of the thermocycling
method and apparatus.
[0007] U.S. Pat. No. 4,683,202 generally describes the PCR concept,
in which a stretch of DNA is copied using a polymerase. Generally,
the procedure involves annealing a piece of primer DNA at a first
temperature to any stretch of single-stranded DNA template with a
complementary sequence. The DNA polymerase copies the primed piece
of DNA at a second given temperature. At a third given temperature,
the newly copied DNA and the primer dissociate from the template
DNA, thereby regenerating single-stranded DNA. The temperature of
the sample is returned to the first temperature to allow the primer
to attach itself to any strand of single-stranded DNA with a
complementary sequence, including the DNA strands that were
synthesized in the immediately preceding cycle. In this manner, the
template DNA is amplified or reproduced any number of times,
depending on how many times the template DNA occurs in the sample,
and the number of cycles completed. The procedure can also be
performed using RNA.
[0008] Most existing methods and techniques of thermocycling in
benchtop instrumentation are indirect with respect to the effect of
the heating source on the sample. Most thermocycling approaches
heat and/or cool a circulating medium, such as water or air, that
affects the container which holds the sample and, subsequently,
subjects the sample itself to the desired thermocycling process.
The rate of the cycling process depends on the effectiveness of the
heat transfer between the circulating medium and the sample.
[0009] For example, U.S. Pat. No. 5,504,007 discloses a thermocycle
apparatus having a body containing a thermally conductive liquid.
The liquid is contained within the body of the apparatus, and the
temperature of the liquid alternated between lower and higher
temperatures in repeating cycles. A well or container for holding a
sample of material is held in contact with the liquid and conducts
the cyclic temperature changes of the liquid to the sample.
[0010] U.S. Pat. No. 5,576,218 discloses a method for thermocycling
of nucleic acid assays using a blended fluid stream produced from
constant velocity, constant volume, and constant temperature fluid
streams. Using these streams, a variable temperature, constant
velocity, constant volume fluid stream is introduced into a sample
chamber for heating and cooling the samples contained therein. The
temperature of the blended fluid stream is varied by diverting and
altering the ratio of the constant temperature fluid streams
relative to one another.
[0011] U.S. Pat. No. 5,508,197 discloses a thermocycling system
based on the circulation of temperature controlled water directly
to the underside of a thin-walled polycarbonate microtiter plate.
The water flow is selected from a manifold fed by pumps from heated
reservoirs.
[0012] Other methods are reported for heating a sample through use
of heated air. U.S. Pat. No. 5,187,084 discloses an apparatus and
method for performing thermocycling on a sample using an array of
sample containing vessels supported in a reaction chamber, through
which air at controlled temperatures is forcibly circulated as a
heat-transfer medium in heat exchange relationship with the
vessels. The temperature of the air is controlled as a function of
time to provide a preselectable sequence defining a temperature
profile. The profile is cyclically repetitively reproduced to
effect replication of and amplification of the desired sequence of
the DNA.
[0013] U.S. Pat. No. 5,460,780 discloses a device for rapidly
heating and cooling a reaction vessel through various temperatures
in PCR amplification utilizing a means for heating at least one
side wall of a reaction vessel, means for cooling the heating means
at repeated intervals and means for moving the reaction vessel
and/or heating and cooling relative to each other. In one
embodiment, heated air is used to heat the reaction vessel.
[0014] Similarly, U.S. Pat. No. 5,455,175 demonstrates that rapid,
non-contact PCR can be accomplished in glass capillaries using air
heated by foam lining the chamber in which the capillaries are
placed; the foam is heated first by a halogen lamp.
[0015] Another common approach for thermocycling is through
intimate contact between a reaction vessel holding the reaction
medium and a heating block that is rapidly heated and cooled (for
example, by using a Peltier element that can both heat and cool).
This is the basis of most commercially available PCR
instrumentation.
[0016] For example, U.S. Pat. No. 5,525,300 discloses an apparatus
for generating a temperature gradient across a heat conducting
block.
[0017] U.S. Pat. No. 5,498,392 discloses chip-like devices for
amplifying a preselected polynucleotide in a sample by conducting a
polynucleotide polymerization reaction. The devices comprise a
substrate microfabricated to define a sample inlet port and a
mesoscale flow system, which extends from the inlet port. A
polynucleotide polymerization reaction chamber containing reagents
for polymerization and amplification of a polynucleotide is in
fluid communication with the inlet port. A heat source and,
optionally, a cooling source are used to heat and/or cool the
chip.
[0018] Wilding and co-workers, Nucleic Acids Res., 24:380-385
(1996), demonstrated that PCR could be carried out in a
microfabricated silicon glass chip-like chamber. By contacting
enclosed 12 microliter reaction chambers microfabricated in glass
to a block heater which cycled between two temperatures, they were
able to obtain effective and reproducible PCR amplification, as
confirmed by removing the PCR product and evaluating it using
capillary electrophoresis. Similarly, Northrup and co-workers,
Anal. Chem., 68:4081-4086 (1996), accomplished PCR amplification of
DNA in a microfabricated silicon PCR device that could be directly
interfaced with an electrophoretic chip for PCR product analysis.
The device contained disposable polypropylene liners to retain the
PCR mixture which could be cycled between two temperatures using
polysilicon heaters in direct contact with the PCR chamber and
cooled either passively or by air drawn along the heater surfaces
of the reaction chamber. The device was interfaced with the
electrophoretic chip by forcing it into the 1 mm drilled holes in
the electrophoretic chip.
[0019] All of the above references, however, describe PCR
amplification methods wherein the vessel containing the sample is
contacted directly by a heater or another heat source, which
transfers heat to the vessel in which the sample is contained. The
vessel, in turn, heats the sample. Since these techniques rely on
the intimate contact between the circulating medium and the
reaction vessel, surface-to-volume ratio of the reaction vessel is
of utmost importance to the effectiveness of the heating step; the
higher this ratio the better the PCR reaction.
[0020] PCT publication WO 96/41864 discloses a diode laser heated
microreaction chamber with sample detection means. A heat source,
such as an IR or UV source, is used to heat the reagents to a
thermally induced chemical reaction. Such heating means can be
used, for example, in conjunction with the microfabricated reactor
described in U.S. Pat. No. 5,639,423.
[0021] None of the above references teach methods and apparatus for
performing ultrafast and reliable thermocycling using both a
non-contact heating source and a non-contact cooling source. Nor do
any of the references appear to teach the sharp and rapid
transitions from one temperature to another accomplished by the
present invention.
[0022] The methods and apparatus described above are further
limited with respect to the temperature range and temperature
accuracy in which they operate. If the thermocycling devices are
cooled in an uncontrolled manner through heat dissipation by
convection at ambient temperature, the minimum temperature at which
the device can operate is restricted by the ambient temperature.
This restriction becomes particularly inconvenient and detracts
from the usefulness of the device if the thermocycling of a sample
is done in a microdevice in which thermocycling is coupled with a
downstream analysis step conducted at a lower temperature.
[0023] The possibilities of thermocycling on a device in which
thermocycling is achieved using a heating and/or cooling element
are predetermined by the initial design of the chip, as the
location of the heating and/or cooling element is typically part of
the chip itself. Thus, these microdevices use of thermocycling is
spatially constrained and the devices are not flexible with respect
to the use of heating or cooling on different locations within or
at the microdevice structure.
[0024] In addition, the design of single-use analyses modules for
various diagnostic and monitoring purposes with integrated
heating/cooling element, such as those described in U.S. Pat. No.
5,498,392 is very complex, and becomes cumbersome and difficult to
use especially when numerous samples are to be tested. Therefore,
the inexpensive production of such devices, normally a major
advantage of microfabrication technology, is compromised.
[0025] There is a need, therefore, for improved methods and
apparatus for rapidly heating and cooling analytical samples in a
fast and reliable manner with sharp transition periods. There is a
further need for such methods and apparatus which are both
economical and practical to use.
SUMMARY OF THE INVENTION
[0026] The present invention has met the above-described needs, by
providing methods and apparatus for the rapid and accurate
performance of thermocycling, which are especially suitable for use
with small volume samples. The methods involve the direct heating
of a sample through optical energy and positively cooling the
sample by use of a non-contact cooling source, such as one in which
an air stream is directed at the vessel containing the sample. The
heating and cooling steps are accomplished by use of a non-contact
heat source and a non-contact cooling source, respectively. As used
herein, the term "non-contact" refers to heat sources and/or
cooling sources that are not in direct contact with the reaction
vessel containing the sample to be analyzed.
[0027] It will be appreciated by those skilled in the art that the
devices described herein are novel in that they combine non-contact
heating and non-contact cooling, which can be adapted to a
multitude of cycling conditions. In addition, the thermocycling can
be directed to structural different sections within a microdevice
without spatial constraints.
[0028] Optical energy is generated using an IR source that is not
in direct contact with the sample vessel. The optical energy
provided by the IR source is easily and accurately manipulated so
that the intensity of the optical energy directed towards the
sample can be finely tuned and controlled so that the desired
temperature is achieved and maintained. The transition from one to
another temperature in IR-mediated heating is achieved more rapidly
than with conventional thermocycling methods. Heating by optical
energy mainly affects the sample itself, rather than the container
of the sample and/or its environment. The IR-mediated heating is
primarily achieved through the absorbance of irradiation by
molecules of the sample, for example, the water molecules in the
sample. The heating step can involve heating to one temperature, or
two or more different temperatures depending on the desired
application of the user.
[0029] Positive cooling is accomplished by use of a non-contact
cooling source directed at the vessel containing the sample.
Cooling, like heating, can be accomplished through any number of
steps, with a different temperature being maintained at each
step.
[0030] It may also be desirable to maintain or hold the sample at a
particular temperature for a given length of time prior to heating
or cooling the sample to a different temperature. Such hold time is
referred to herein as "dwell time". The heating and cooling steps,
and the dwell time, if any, can be sequentially repeated to perform
the desired number of thermocycles. According to the methods of the
present invention, each ultrafast thermocycle can be accomplished
in only a few seconds.
[0031] It is therefore an object of the present invention to
provide methods and apparatus for performing rapid thermocycling on
an analytical sample.
[0032] The present invention is also directed to apparatus for
carrying out these methods.
[0033] Another object of the invention is to provide methods and
apparatus that do not allow a predetermined, upper temperature to
be exceeded.
[0034] It is another object of this invention to provide methods
and apparatus for rapidly and accurately varying the temperature of
a sample in accordance with a predetermined temperature
profile.
[0035] Another object of the invention is to provide methods and
apparatus having high precision control of thermocycling
parameters.
[0036] Another object of the invention is to provide methods and
apparatus for performing rapid thermocycling on microliter and
nanoliter volume samples.
[0037] Yet another object of the present invention is to provide a
means for performing PCR under optimal thermal conditions.
[0038] Another object of the present invention is to provide
methods and apparatus that provide non-contact heating and cooling
sources to conduct thermocycling of samples.
[0039] Another object of the invention is to teach a method that
allows thermocycling of samples within an existing channel
structure, for example a sample plug in a separation channel.
[0040] Another object of the invention is to provide methods and
apparatus for performing rapid and reliable repeated thermocycles
over many cycles of amplification.
[0041] It is another object of the invention to provide automated
methods and apparatus for performing rapid and reliable
thermocycling.
[0042] Another object of the present invention is to mediate the
flow of a sample on a microchip using an IR source.
[0043] These and other objects of the invention will be apparent
from the following description of the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0044] FIG. 1A depicts a portion of a microchip used in the methods
and apparatus of the present invention for use with microchannel
thermocycling. FIG. 1B depicts a portion of a microchip used in the
methods and apparatus of the present invention having a widened
microchannel. FIG. 1C is a top plan view of the upper layer of FIG.
1A. FIG. 1D is a cross section taken through line 1D-1D of FIG.
1A.
[0045] FIG. 2 depicts a schematic of a portion of a microchip used
in the methods and apparatus of the present invention for use with
microchannel thermocycling.
[0046] FIG. 3A shows the temperature versus time in ten
thermocycles performed according to the present invention. FIG. 3B
shows the temperature measured in the heating/cooling block of a
conventional benchtop PCR thermocycler (dotted line) and the
corresponding temperature in a PCR sample being heated and cooled
by the block (solid line).
[0047] FIG. 4 illustrates one embodiment of the apparatus of the
present invention.
[0048] FIGS. 5A and 5B illustrate one embodiment of the apparatus
of the present invention using a thermocouple in a sealed
capillary;
[0049] FIG. 5B provides an exploded, front view of the sample
containing vessel and the thermocouple device.
[0050] FIGS. 6A-6D illustrate embodiments of the apparatus of the
present invention using a microchip with an entrenched reservoir,
with a dummy cell (FIGS. 6A and 6B) or with remote temperature
sensing (FIGS. 6C and 6D).
[0051] FIGS. 7A-7D show the results obtained in Example 1:
[0052] FIG. 7A shows the thermocycling profiles obtained with
94.degree. C./54.degree. C./72.degree. C. dwell times of 30 sec/30
sec/60 sec;
[0053] FIG. 7B shows thermocycling profiles obtained with
94.degree. C./54.degree. C./72.degree. C. dwell times of 2 sec/2
sec/4 sec;
[0054] FIG. 7C shows an exploded view of some cycles shown in FIG.
7B; and
[0055] FIG. 7D is an exploded view of one thermocycle shown in FIG.
7A.
[0056] FIGS. 8A-8C show the thermocycles and the gel
electrophoresis resulting from the noncontact-mediated
thermocycling performed according to Example 2.
[0057] FIGS. 9A-9C show the cycle sequencing obtained according to
the methods of Example 3.
[0058] FIG. 10 is a graph of migration time versus relative
fluorescence, determined according to the methods of Example 4.
[0059] FIGS. 11A and 11B show the result obtained with the
embodiment illustrated in FIG. 5. FIG. 11A outlines the temperature
profile generated through cycling between 94.degree. C. for 15 sec
and 68.degree. C. for 60 sec and
[0060] FIG. 11B indicates the product obtained after a successful
PCR mediated amplification of the lambda DNA sequence using the CE
analysis method described in Example 5.
DETAILED DESCRIPTION OF THE INVENTION
[0061] The present invention is generally directed to a method for
performing rapid and accurate thermocycling on a sample comprising
placing the sample in a suitable reaction vessel; heating the
sample to a desired temperature using the optical energy of a
non-contact heat source that directly heats the sample itself;
positively cooling the sample to a desired temperature by a
non-contact cooling source directed at the reaction vessel; and
sequentially repeating the heating and cooling steps to perform a
desired number of thermocycles.
[0062] Applications of the thermocycling method of the present
invention are numerous and generally encompass any analytical
system in which the temperature of a sample is regulated and/or
changed. The present invention is particularly applicable to
analytical systems wherein fast or ultrafast transition from one
temperature to the next is needed, and in which it is important
that exact or nearly exact temperatures be achieved.
[0063] For example, the present methods are suitable for testing
and incubation and treatment of biological samples typically
analyzed in a molecular biology laboratory or a clinical diagnostic
setting. The accuracy of the thermocycling method of the present
invention makes it particularly suitable for use in nucleic acid
replication by the polymerase chain reaction (PCR). Any reaction
that benefits from precise temperature control, rapid heating and
cooling, continuous thermal ramping or other temperature parameters
or variations can be accomplished using this method discussed
herein. Other applications include, but are not limited to, the
activation and acceleration of enzymatic reactions, the
deactivation of enzymes, the treatment/incubation of
protein-protein complexes, DNA-protein complexes, DNA-DNA complexes
and complexes of any of these biomolecules with drugs and/or other
organic or inorganic compounds to induce folding/unfolding and the
association/dissociation of such complexes. The following
applications illustrate the usefulness of the present thermocycling
apparatus and methods, representing only some of the possible
applications.
[0064] A common procedure in the protocols of molecular biology is
the deactivation of proteins through heat. One of the most basic
procedures in molecular biology is the cleavage of proteins and
peptides into discrete fragments by proteases/digestion enzymes,
such as trypsin. A thermocycling procedure is typically used to
activate the enzyme at an elevated temperature followed by: the
incubation of the enzyme during the reaction to sustain the
enzymatic catalysis; the heat inactivation of the enzyme; and the
final treatment/analysis at ambient temperature. Typically, the
reaction components are incubated at 40.degree. C. for 60 min until
the reaction is completed, after which the enzyme activity has to
be stopped to avoid unspecific cleavage under uncontrolled
conditions. Many enzymes, such as trypsin, can be irreversibly
inactivated by incubation for 10 min at higher temperature, such as
95.degree. C. The sample is then cooled back to ambient temperature
and ready for downstream analysis. Such deactivation of enzymes is
taught, for example, in Sequencing of proteins and peptides:
Laboratory Techniques in Biochemistry and Molecular Biology, ed. G.
Allen, pages 73-105.
[0065] The same principle of heat inactivation can be used to
inactivate restriction endonucleases that recognize short DNA
sequences and cleave double stranded DNA at specific sites within
or adjacent to the recognition sequence. Using the appropriate
assay conditions (for example, 40.degree. C. for 60 min) the
digestion reaction can be completed in the recommended time; the
reaction is stopped by incubation of the sample at 65.degree. C.
for 10 min. Some enzymes may be partially or completely resistant
to heat inactivation at 65.degree. C., but they may be inactivated
by incubation for 15 min at 75.degree. C. Such methods are taught,
for example, by Ausubel et al. Short Protocols in Molecular
Biology, 3rd Ed., John Wiley & Sons, Inc. (1995) and Molecular
Cloning: A Laboratory Manual, J. Sambrook, Eds. E. F. Fritsch, T.
Maniatis, 2nd Ed.
[0066] Similar to the heat inactivation of proteins for the control
of enzymatic activity, the sample processing of proteins for
electrophoretic analysis often requires the denaturation of the
protein/peptide analyte before the separation by electrophoretic
means, such as gel electrophoresis and capillary electrophoresis,
takes place. For example, a 5 min heat denaturation (which provides
for the destruction of the tertiary and secondary structure of the
protein/peptide) at 95.degree. C. in an aqueous buffer in the
presence or absence of denaturing reagents, such as SDS detergent,
allows the size dependent separation of proteins and peptides by
electrophoretic means. This is taught, for example, in Gel
Electrophoresis of Proteins: A Practical Approach, Eds. B. D. Hames
and D. Rickwood, page 47, Oxford University Press (1990).
[0067] Thermocycling of samples is also used in a number of
nonenzymatic processes, such as protein/peptide sequencing by
hydrolysis in the presence of acids or bases (for example, 6M HCl
at 110.degree. C. for 24 hours) into amino acids. Studies involving
the investigation of the interaction of biomolecules with drugs
and/or drug candidates are frequently conducted under conditions
requiring precise temperature control to obtain binding
characteristics, such as kinetic association/dissociation
constants.
[0068] These applications for the thermocycling taught by the
present invention will find use, for example, as a diagnostic tool
in hospitals and laboratories such as for identifying specific
genetic characteristics in a sample from a patient, in
biotechnology research such as for the development of new drugs,
identification of desirable genetic characteristics, etc., in
biotechnology industry-wide applications, and in scientific
research and development efforts.
[0069] Thus, the samples subjected to the thermocycling methods of
the present invention will vary depending on the particular
application for which the methods are being used. Samples will
typically be biological samples, although accurate heating and
cooling of non-biological samples is equally within the scope of
this invention. As used herein, the term "samples" further refers
to volumes in the microliter to nanoliter range.
[0070] A suitable reaction vessel according to the methods of the
present invention is one in which extremely low volumes of sample
can be effectively tested, including sample volumes in the
nanoliter range. The sample vessel must be made of a material that
allows the penetration of IR light wavelengths, such as quartz
glass, glass, silicon, transparent plastics, and the like.
Preferably, the reaction vessel or container will have a high
surface-to-volume ratio. A high surface-to-volume ratio leads to a
decrease in the thermal time constant, which can lead to an
increase in the efficiency of the thermocycling. A high
surface-to-volume ratio, while not as important for the heating
step, is related to the effectiveness of the cooling step. Various
examples of suitable reaction vessels can be given, including but
not limited to, microchambers, capillary tubes, microchips and
microtiter plates.
[0071] A preferred example of a suitable reaction vessel is a
microchamber made from thin-walled glass. Another preferred
embodiment is a glass capillary tube. Such capillaries are
typically used in capillary electrophoresis ("CE"). Suitable inner
diameters of the capillaries having an outer diameter of about 370
.mu.m typically vary between about 15 .mu.m and 150 .mu.m. Thermal
gradients that lead to convection are substantially reduced in
capillary tubes. Glass capillary tubes are commercially available
from Polymicron Technologies, Phoenix, Ariz.
[0072] Another preferred example of a suitable reaction vessel is
the channel structure incorporated into a microfabricated device,
such as the microfabricated substrate described by Wilding and
co-workers in Nucleic Acids Res., 24:380-385 (1996). Other reaction
vessels with characteristics suitable for rapid thermocycling are
shown in FIGS. 6A-6D, comprising an entrenched reservoir attached
or incorporated into a microfabricated chip device.
[0073] One preferred embodiment of a microchip for use in the
present invention is illustrated in FIGS. 1A, 1B, 1C and 1D. It
will be appreciated that FIGS. 1A-1D depict only a portion of the
chip, and that the depiction is not drawn to scale. FIG. 1A depicts
a corner of a microchip 2 having a glass upper portion or layer 4
and a glass lower portion or layer 6 wherein the upper and lower
layers fit together, for example, through bonding by high
temperature. Upper layer 4 contains an upwardly open sample
reservoir 8 and an upwardly open waste reservoir 10. A "window" 12
provided in upper layer 4 allows for direct heating of the sample
by an IR source. It will be understood that window 12 can be
provided in a number of ways. For example, the "window" can merely
be a portion of the upper layer 4 of substantially full thickness
of the upper layer 4, or can be an area which has been made thinner
with respect to adjacent portions of the upper layer 4 by means
known in the art, such as etching. A window 12 is more clearly
depicted in FIG. 1D, which is a cross section view taken along line
1-D of FIG. 1A when the upper layer 4 and lower layer 6 are fitted
together. Returning to FIG. 1A, a microchannel 14 is provided in
the lower layer 6, and the area where a PCR reaction occurs is
generally depicted by the elliptical area 16. FIG. 1B shows
essentially the same portion of a microchip as shown in FIG. 1A,
only having a widened microchannel 18 that has a greater volume
than microchannel 16 of FIG. 1A. FIG. 1C is a top plan view of the
upper layer 4 of microchip 2 of FIG. 1A, showing sample reservoir 8
and waste reservoir 10 and window 12. In FIG. 1D, upper layer 4 is
shown having sample reservoir 8 and waste reservoir 10 and window
12. Lower layer 6 is shown having microchannel 14. A second
microchannel 20 connects sample reservoir 8 and microchannel 14. A
third microchannel 22 connects microchannel 14 and waste reservoir
10. FIGS. 1C and 1D are not drawn to scale with respect to FIG. 1A.
It will be understood that the microchip shown in FIGS. 1A-1D can
also be made of plastic or any other material that could be
penetrated by IR light wavelengths. In such an embodiment, the
upper and lower layers could be fit together, for example, by a UV
curing process, and the window could be formed by electroforming
during fabrication of the upper layer.
[0074] FIG. 2 depicts a larger corner 23 than FIGS. 1A-1D of a
microchip for use with the present invention. The sample reservoir
24 and a first waste reservoir 26 are both connected to a first
microchannel 28. The elliptical area 30 generally represents the
area where the PCR reaction occurs. Microchannel 28 can be, for
example, 50 .mu.m width.times.30 .mu.m depth, although other
dimensions are equally within the scope of the present invention.
Microchannel 28 is connected to a second microchannel 34. The
second microchannel 34, a third microchannel 38 coming from inlet
reservoir 40, and a fourth microchannel 42 coming from a second
waste reservoir 44, are in communication with each other and form a
fifth microchannel 46 that leads to an outlet reservoir 47 for
delivery of the sample to the next processing stage or storage, as
desired.
[0075] Any other reaction vessel, such as a microtiter plate, can
be used according to the methods of the present invention, provided
that the vessel is made of a material which allows IR radiation to
directly heat the sample and has a surface-to-volume ratio
sufficient to allow for cooling within the time parameters
discussed below. A method for preparing a suitable microfabricated
device is discussed in the example section. Further guidance in
preparing such microfabricated device is provided, for example, in
U.S. Pat. Nos. 5,250,263; 5,296,114; Harrison et al., Science
261:895-897 (1993); and McCormick et al., Anal. Chem., 69:2626-2630
(1997).
[0076] Heating of the sample is accomplished through the use of
optical energy from a non-contact heat source. Preferably, this
optical energy is derived from an IR light source which emits light
in the wavelengths known to heat water, which is typically in the
wavelength range from about 0.775 .mu.m to 7000 .mu.m. For example,
the infrared activity absorption bands of sea water are 1.6, 2.1,
3.0, 4.7 and 6.9 .mu.m with an absolute maximum for the absorption
coefficient for water at around 3 .mu.m. The IR wavelengths are
directed to the vessel containing the sample, and because the
vessel is made of a clear or translucent material, the IR waves act
directly upon the sample to cause heating of the sample. Although
some heating of the sample might be the result of the reaction
vessel itself absorbing the irradiation of the IR light, heating of
the sample is primarily caused by the direct action of the IR
wavelengths on the sample itself.
[0077] In a preferred embodiment, the optical energy is focused on
the sample by means of IR transmissible lenses so that the sample
is homogeneously irradiated. This technique avoids "hotspots" that
could otherwise result in the creation of undesirable temperature
differences and/or gradients, or the partial boiling of the sample.
The homogeneous treatment of the sample vessel with optical energy
therefore contributes to a sharper temperature profile. The
homogenous sample irradiation can further be enhanced through the
use of a mirror placed on the opposite site of the IR source, such
that the reaction vessel is placed between the IR source and the
mirror. This arrangement reflects the radiation back onto the
sample and substantially reduces thermal gradients in the sample.
Alternatively, the radiation can be delivered by optical
IR-transparent fiberglass, for example, optical fiberglass made
from waterfree quartz glass (Fasertyp IR-QQ, Schott Glaswerke
Wiesbaden, Germany) that is positioned around the reaction vessel
and that provides optimal irradiation of the sample.
[0078] Heating can be effected in either one step, or numerous
steps, depending on the desired application. For example, a
particular methodology might require that the sample be heated to a
first temperature, maintained at that temperature for a given dwell
time, then heated to a higher temperature, and so on. As many
heating steps as necessary can be included.
[0079] Similarly, cooling to a desired temperature can be effected
in one step, or in stepwise reductions with a suitable dwell time
at each temperature step. Positive cooling is preferably effected
by use of a non-contact air source that forces air at or across the
vessel. Preferably, this air source is a compressed air source,
although other sources could also be used. It will be understood by
those skilled in the art that positive cooling results in a more
rapid cooling than simply allowing the vessel to cool to the
desired temperature by heat dissipation. Cooling can be accelerated
by contacting the reaction vessel with a heat sink comprising a
larger surface than the reaction vessel itself; the heat sink is
cooled through the non-contact cooling source. The cooling effect
can also be more rapid if the air from the non-contact cooling
source is at a lower temperature than ambient temperature.
[0080] Accordingly, the methods of the present invention provide
for the use of virtually any temperature profile/dwell time
necessary. For example, cleavage of proteins through use of
proteases or digestion enzymes might require use of different
temperatures, each of which must be precisely maintained for
various amounts of time. Activation of restriction endonucleases
might similarly require achieving and maintaining two or three
different temperatures. Protein or peptide sequencing can require
the steady maintenance of a high temperature for an extended period
of time.
[0081] The PCR reaction typically involves heating a sample to
between about 90 and 96.degree. C., cooling the sample to between
about 40 and 60.degree. C., and heating the sample to between about
70 and 75.degree. C. It will be appreciated by those skilled in the
art that this temperature profile is just a generalization, and
that optimum temperatures or temperature ranges for each stage of
the PCR reaction must be determined based upon the particular
reaction being run. These optimal temperatures will vary depending
on such factors as the particular DNA or RNA being replicated, the
number of cytosine-guanine hydrogen bonds versus the number of
adenosine-thymine hydrogen bonds, the enzyme being used, the length
of the primer and other variables, the effect of which can be
determined by those skilled in the art. Precise maintenance of
these optimum temperatures or temperature ranges is important to
ensure that reliable results are obtained; deviation from the
optimal temperature or temperatures can effect the reaction in
numerous ways. For example, while the temperature at which DNA
denatures is generally between about 90 and 96.degree. C.,
insufficient heating during the denaturation step is a common
reason for a PCR reaction to fail. Similarly, overheating of the
sample during denaturation can result in excessive denaturation of
the polymerase or other enzyme being used.
[0082] Achieving the optimal temperature for the PCR annealing step
is even more critical. An annealing temperature which is too low
will result in non-specific DNA fragments being amplified. At an
annealing temperature which is too high, the primers will anneal
less efficiently resulting in decreased yield of the desired
product and possibly reduced purity.
[0083] Achieving the optimal temperature for the extension reaction
is also important for obtaining the desired PCR result. Temperature
may affect both the rate and accuracy of the extension reaction. If
the rate of the polymerase reaction is too slow, then the newly
synthesized polynucleotide may not contain a site for primer
annealing. Additionally, the denatured polynucleotide sequence for
amplification may contain one or more regions of secondary
structure that may form or disappear according to the temperature
selected. Furthermore, several different enzymes with polymerase
activity may be used for PCR. Each enzyme will have its own optimum
temperature for activity, stability and accuracy.
[0084] Thus, the determination of optimum temperatures for PCR,
enzyme activation, protein denaturation/renaturation, protein
folding and/or unfolding, protein or peptide sequencing and the
other reactions requiring thermocycling becomes important to ensure
the success of such reactions. Also important is the ability to
accurately achieve and maintain these temperatures. Temperature
parameters become even more important when dealing with very small
volumes of sample. For example, when using the microliter or
nanoliter volumes contemplated by the present invention for PCR, a
very specific reaction is needed; even a small percentage of
non-specific reactions can lead to inaccurate results, and/or a
misinterpretation of the results. Temperature variations during the
measurements of physiochemical parameters through thermocycling,
for example kinetic dissociation/association constants of
drug-biomolecular complexes, can lead to the inaccurate assessment
of such parameters. A complete failure of a temperature dependent
process is likely if the process that requires a temperature
dependent activation/inactivation is maintained at suboptimal
temperature conditions, for example, heat inactivation of
enzymes.
[0085] However, it is known to the people skilled in this art that
prelonged exposure of most biochemicals and biomolecules to
elevated temperatures, for example, temperatures greater than
37.degree. C. for most enzymes, results in their rapid,
irreversible inactivation and/or destruction through denaturation,
hydrolysis or dissociation. Therefore, any unnecessary temperature
elevation, such as those experienced with slow temperature
transitions, should be avoided.
[0086] A further contributor to inaccurate PCR results arises from
the inability to perform rapid and sharp transitions between
temperatures. For example, a lag time between the denaturation
temperature and the annealing temperature can result in unspecific
annealing. Long transition times between denaturation and annealing
also promote the premature inactivation of the polymerase enzyme
(Taq-enzyme) resulting in a less specific reaction and in a lower
product yield. According to the methods of the present invention,
such a cycle can be completed in approximately 17 seconds.
[0087] Sharp temperature transitions are equally important for
reactions involving some proteases and peptidases. It is known that
loss of specificity in the protease activity occurs when these
enzymes experience slow temperature transitions. Rapid changes in
temperature are also beneficial in the folding process of proteins.
Shallow temperature gradients are associated with incorrect folding
and the increase in partially folded peptide chains, which will
either not function or will behave in a dysfunctional manner.
[0088] As many cycles as necessary can be performed to achieve the
desired result, such as the desired level of DNA amplification, the
desired level of enzyme activation or the desired protein folding
and/or unfolding. The time for each cycle will vary depending on
numerous factors, such as the amount of volume in the sample, the
temperatures between which the sample is being cycled, the number
of different temperatures in each cycle and the particular
application for which the thermocycling is being performed. A small
volume sample that is cycled between two relatively close
temperatures can be performed in less than one second. The larger
the volume, and/or the larger the temperature differential or
number of different temperature steps, the longer the cycle time.
Effective cycling time between three temperatures can be achieved,
with dwell times at each temperature, of 17 seconds or less. This
would be suitable for the PCR application.
[0089] Other applications, it will be appreciated, require only one
cycle through two or more different temperatures. Rapid transition
between temperatures and the precise maintenance of each
temperature for the desired length of time are important parameters
that are addressed by the present invention.
[0090] The present methods and apparatus utilize both a non-contact
heat source and a non-contact cooling source. The non-contact
approach allows for rapid thermocycling, which can be achieved as
quickly as 1 second or less. The present thermocycling methods are
further characterized as being accurate, in that very precise
temperature control can be achieved. That is, an optimum
temperature can be selected, and this temperature can be achieved
on each and every cycle within .+-.0.5.degree. C. Perhaps most
importantly, the non-contact approach used herein essentially
eliminates lengthy time lags between temperature stages, allowing
for very sharp temperature transitions.
[0091] In addition, the present methods and apparatus are both
economical and convenient. The IR sources of the preferred
embodiment, the IR lamps, are inexpensive, readily obtained and are
easy to use. In addition, because of the non-contact heating and
cooling sources, the reaction vessel is the only part of the
apparatus that needs to be changed with each sample. These vessels
are typically very inexpensive to purchase or prepare. Thus, rapid
and accurate thermocycling of numerous samples can be performed in
an economic manner.
[0092] FIG. 3A shows a plot of temperature versus time (seconds) in
ten thermocycles run according to the present invention, in which
two temperature stages are achieved. The amount of time that
elapses between the highest temperature and the lower temperature
is very small, with the temperature change being effected in about
1 second or less. Similarly, the change from the lowest temperature
back to the highest temperature takes generally less than one
second, and can be done as quickly as 300 to 400 milliseconds. In
contrast, FIG. 3B is representative of a typical temperature
profile for one three-temperature thermocycle obtained from a
commercially available thermocycling instrument. The dotted line
represents the temperature of the heating/cooling block of the
apparatus, and the solid line the temperature of the sample. It can
be seen that the time lags between temperatures--the highest to
lowest temperature about 30 seconds, the lowest to intermediate
temperature about 15 seconds, and the intermediate to highest
temperature about 25 seconds--is sufficiently longer than that
achieved by the methods and apparatus of the present invention.
Desired temperature changes in the sample itself take even longer
to achieve. The temperature transitions in the sample are not
nearly as sharp as those obtained in the block, or those in the
sample according to the present methods. More specifically, the
temperature transition of the sample from the highest to lowest
temperature takes about 100 seconds, and from the intermediate to
highest temperature about 80 seconds. This time lag becomes
important in certain reactions where improper temperatures can lead
to inaccurate results. For example, during the lag time between the
highest and lowest temperature in PCR, unspecific annealing can
occur which can render the results obtained meaningless.
[0093] The present invention is also directed to an apparatus for
performing thermocycling on a sample comprising a suitable reaction
vessel for containing the sample; optical energy, non-contact means
for directly heating the sample to a desired temperature;
non-contact means for positively cooling the sample to a desired
temperature; means for monitoring the temperature of the sample;
and means for controlling the heating and cooling of the
sample.
[0094] Any suitable reaction vessel as described above can be used
in the apparatus of the present invention.
[0095] The non-contact means for directly heating the sample can be
any means known in the art for generating the desired range of
wavelengths in the near IR wavelengths. Typically, the heating
means will be an IR source, such as an IR lamp, an IR diode laser
or an IR laser. An IR lamp is preferred, as it is inexpensive and
easy to use. Preferred IR lamps are halogen lamps and tungsten
filament lamps. Halogen and tungsten filament lamps are powerful,
and can feed several reactions running in parallel. A tungsten lamp
has the advantages of being simple to use and inexpensive, and
almost instantaneously (90% lumen efficiency in 100 msec) reach
very high temperatures. Such lamps are commercially available from
General Electric, Cleveland, Ohio. A particularly preferred lamp is
the CXR, 8V, SOW tungsten lamp available from General Electric.
This lamp is inexpensive and convenient to use, because it
typically has all the optics necessary to focus the IR radiation
onto the sample; no expensive lens system/optics will typically be
required.
[0096] The IR source is positioned remotely (non-contact) from the
sample, such that light emanating from the lamp impinges the
sample. In one embodiment, the lamp is positioned remotely to the
actual sample, and the radiation from the lamp is transferred via
optically IR-transmissible fiberglass or through a combination of
lenses and mirrors. Other embodiments in which the sample is placed
in the path of the IR light source are equally within the scope of
the present invention.
[0097] The heat source can be manipulated, such as through the use
of lenses and filters mounted between the lamp and the reaction
vessel. Such lenses and filters would serve to focus the radiation
as well as to eliminate wavelengths that could interfere with the
reaction taking place and/or the temperature sensing. Filtering and
focussing of the IR light using, for example, IR transmissible
lenses or filters is preferred, as this reduces the occurrence of
temperature gradients in the sample or partial boiling of the
sample.
[0098] As used herein, the terms "direct" or "directly" when used
in reference to heating means that the sample itself is heated by
the heating means, such as through absorption of IR radiation, as
opposed to heating of the vessel containing the sample which in
turn heats the sample. Direct heating of the sample is therefore
achieved even when lenses, filters and the like are used.
[0099] The apparatus of the present invention uses finely tuned
temperature ramping, which allow for rapid heating cycles of the
sample. In addition, heat transfer problems frequently encountered
with solid block heaters are eliminated with the non-contact
approach of the present invention.
[0100] The heater can be powered by any means, such as a low
voltage power supply. Preferred is a 5 volt DC supply system,
although it will be understood that any other suitable means can
also be employed.
[0101] Cooling can be achieved by any non-contact means known in
the art for positively cooling an object. Accordingly, the
non-contact cooling source should also be positioned remotely to
the sample or reaction vessel, while being close enough to effect
the desired level of heat dissipation. Both the heating and cooling
sources should be positioned so as to cover the largest possible
surface area on the sample vessel. The heating and cooling sources
can be alternatively activated to control the temperature of the
sample. It will be understood that more than one cooling source can
be used.
[0102] Positive cooling of the reaction vessel dissipates heat more
rapidly than the use of ambient air. The cooling means can be used
alone or in conjunction with a heat sink. A particularly preferred
cooling source is a compressed air source. Compressed air is
directed at the reaction vessel when cooling of the sample is
desired through use, for example, of a solenoid valve which
regulates the flow of compressed air at or across the sample. The
pressure of the air leaving the compressed air source can have a
pressure of anywhere between 10 and 60 psi, for example. Higher or
lower pressures could also be used. The temperature of the air can
be adjusted to achieve the optimum performance in the thermocycling
process. Although in most cases compressed air at ambient
temperature can create enough of a cooling effect, the use of
cooled, compressed air to more quickly cool the sample, or to cool
the sample below ambient temperature might be desired in some
applications.
[0103] A means for monitoring the temperature of the sample, and a
means for controlling the heating and cooling of the sample, are
also provided. Generally, such monitoring and controlling is
accomplished by use of a microprocessor or computer programmed to
monitor temperature and regulate or change temperature. An example
of such a program is the Labview program, available from National
Instruments, Austin, Texas. Feedback from a temperature sensing
device, such as a thermocouple, is sent to the computer. In one
embodiment, the thermocouple provides an electrical input signal to
the computer or other controller, which signal corresponds to the
temperature of the sample. Preferably, the thermocouple, which can
be coated or uncoated, is placed in a temperature sensing reaction
vessel placed adjacent to the reaction vessel containing the sample
to be tested. The temperature sensing reaction vessel should be of
the same type as the sample containing reaction vessel, only
containing a blank, such as water or a buffer solution instead of
sample. Alternatively, the thermocouple can be placed directly into
the sample vessel, provided that the thermocouple does not
interfere with the particular reaction or affect the thermocycling,
and provided that the thermocouple used does not act as a heat
sink. A suitable thermocouple for use with the present invention is
constantan-copper thermocouple. In some instances it might be an
advantage to sense the sample temperature through a thermosensor
directly measuring the reaction vessel, or the sample itself.
[0104] In another embodiment, temperature is monitored and
controlled through a remote temperature sensing means. For example,
a thermo-optical sensing device can be placed above an open
reaction vessel containing the sample being thermocycled. Such a
device can sense the temperature on a surface, here the surface of
the sample, when positioned remotely from the sample.
[0105] Signals from the computer, in turn, control and regulate the
heating and cooling means, such as through one or more switches
and/or valves. The desired temperature profile, including dwell
times, is programmed into the computer, which is operatively
associated with heating and cooling means so as to control heating
and cooling of the sample based upon feedback from the thermocouple
and the predetermined temperature profile.
[0106] A preferred embodiment of the present apparatus, usable for
example in PCR, is depicted in FIG. 4. The sample to be tested 50
is placed in a suitable reaction vessel 52 made of glass. Adjacent
to the sample containing vessel 52 is a generally identical vessel
54 containing a blank 56, such as a PCR buffer solution. A
thermocouple 58 is submerged in the blank 56 at one end and is
operatively associated with a computer 60 or other microprocessor
at the other end. It will be understood that vessel 52 and vessel
54 are side by side, such that the IR light 65 originating from
lamp 64 impinges generally equally on vessels 52 and 54, as does
the air 77 from compressed air source 72. An electrically
conductive wire 62 connects computer 60 to lamp 64 with the
computer 60 turning the lamp on when heating is desired and off
when the desired temperature is achieved in the blank 56. A filter
66 serves to absorb light 65 emitted from the lamp 64 that might
interfere with the reaction in sample 50. An electrically
conductive wire 68 runs from computer 60 to a computer controlled
solenoid valve 70. Solenoid valve 70 controls the volume of air
coming from compressed air source 72 through tube 74 when cooling
of the sample is desired. Compressed air passes through solenoid
valve 70 into tubing 76 and emerges 77 at reaction vessel 52
containing the sample 50 being thermocycled and the vessel 54
containing blank 56.
[0107] FIGS. 5A and 5B illustrate another embodiment 6f the
apparatus of the present invention. FIG. 5B is an exploded view of
FIG. 5A, showing capillary 100 which contains PCR mix 102 and
solvent 104 and 105, and a temperature-sensing sealed capillary
106. Sealed capillary 106 contains PCR buffer 108 and thermocouple
110, which extends through sealed end 112 as electrically
conductive wire 114 and through sealed end 116 as electrically
conductive wire 118. More specifically, FIG. 5B shows a front view
of capillary 100 and sealed capillary 106, and generally represents
the view that would be seen looking from the direction of lamp 126
toward capillary 100 and sealed capillary 106. Electrically
conductive wires 118 and 114 combine at reference junction 120, as
shown in FIG. 5A. Capillary 110 and sealed capillary 106 are at
equal distance with respect to lamp 126, and horizontally oriented.
With further reference to FIG. 5A, extending from reference
junction 120 is electrically conductive wire 122, connected to
microprocessor 124. Through feedback from the thermocouple 110,
microprocessor 124 controls lamp 126 through electrically
conductive wire 128, and compressed air source 130 through
electrically conductive wire 132. Filter 134 removes selected
wavelengths from the light 133 emerging from lamp 126. A mirror 136
reflects the radiation from lamp 126 back onto capillary 100 and
sealed capillary 106. Use of this embodiment is further described
in Example 5 below.
[0108] FIGS. 6A-6D depict two additional embodiments, in which one
or more entrenched reservoirs are used. FIGS. 6A and 6B show the
apparatus of the present invention in which microchip 140 contains
a first entrenched reservoir 142 and a second entrenched reservoir
144, shown more clearly in the exploded view of FIG. 6B. The first
entrenched reservoir 142 contains a thermocouple 146 and a blank
solution 147, such as PCR buffer. The second entrenched reservoir
144 contains sample 148. As shown in FIG. 6A, microchip 140 is
placed on a movable stage 150, which may be generally ring-like to
leave the underside of microchip 140 exposed, and which can be
motorized or moved manually using knob 152. Cooling jets 154 and
156 are directed around entrenched reservoirs 142 and 144, and
cooling jet 158 is directed underneath reservoirs 142 and 144.
Stage 150 is secured to a vertical leg 160 of a generally "L"
shaped housing, and generally parallel to the lower portion 162.
Lamp 164 has its emitted light 165 filtered by filter 168. The
light 165 to which entrenched reservoirs 142 and 144 are exposed is
further limited by aperture 169 in light restricting means 170. It
will be appreciated that stage 150 is a frame that supports
microchip 140 on its periphery and that microchip 140 is therefore
exposed to light 165 from lamp 164.
[0109] FIGS. 6C and 6D depict an embodiment using only one
entrenched reservoir 174 containing sample 172 within microchip
176. A thermo-optical sensing device 178 is positioned above the
sample 174 in entrenched reservoir 172. FIG. 6C further illustrates
that the aperture 169 in light restricting means 170 can be
adjusted. It will be appreciated that the temperature sensing
means, cooling means and heating means as shown in FIGS. 6A-6D are
operatively associated with a microprocessor, which is not
shown.
[0110] As can be seen from the figures, according to the present
invention both a non-contact heat source and a non-contact cooling
source are used. This allows for repeated introduction of any
number of reaction vessels in and out of the apparatus. Thus, the
present invention provides an economic advantage over other
thermocycling apparatus, in that it is only a relatively
inexpensive microchip, capillary tube, or other reaction vessel
that must be changed for every sample. Some methods provided in the
art require the physical attachment of the heating and/or cooling
means to the reaction vessel itself. Therefore, unless the reaction
vessel could be completely cleaned to ensure that contamination
from one sample to another did not occur, a new chip attached to a
new heating and/or cooling device would have to be provided for
every sample. While for ease of reference only one
sample-containing vessel was shown and/or described in these
embodiments, it is equally within the scope of the invention to
thermocycle two or more samples at the same time. In addition,
because the heating and cooling means are relatively stationary in
the apparatus of the present invention, the reaction vessel can be
moved in any direction relative to the heating and/or cooling
sources.
[0111] The above apparatus provide for rapid heating and cooling of
a sample in a precise and easy to replicate manner. Heating can be
effected for example as quickly as 10.degree. C. per second when
using approximately 15 to 50 .mu.L volumes of sample in a
microchamber and as rapidly as 100.degree. C. per second when using
nanoliter volume samples in a capillary; cooling can be effected
quickly, typically in the range of between about 5 and 50.degree.
C. per second. The increased effectiveness of heating and cooling
improves the cycling process and sharpens the temperature profile.
This means that the desired reaction can be conducted under more
optimal thermal conditions than in conventional instruments.
Thermal gradients in the reaction medium frequently observed in
instrumentation using a contact heat source are detrimental to the
specificity of the reaction. These thermal gradients are
substantially reduced in the IR mediated heating, particularly when
the heat source is strong enough to penetrate the aqueous mixture
and provide sufficient irradiation to the opposite side of the
reaction vessel. Non-contact, rapid cooling, such as that provided
in the present invention, also contributes to the ability to obtain
sharp transition temperatures in minimum time and to achieve fast
and accurate temperature profiles.
[0112] In the PCR art, it has been shown that amplification yields
and product specificity are possible when denaturation or annealing
times are kept to a minimum, provided that denaturation takes place
before annealing. Furthermore, it has also been demonstrated that
there is little change in the product yield with annealing times
longer than 20 seconds, translating into a total cycling time
between 15 and 30 seconds. Such rapid cycling times are hard to
achieve using conventional instrumentation, however, due to
sluggish heat transfer. The present invention is able to perform
such cycling profiles due to its direct way of heating the reaction
medium in conjunction with its very effective cooling system.
[0113] The present invention also teaches methods and apparatus for
use of an IR heat source in conjunction with a microchip that
allows for movement or "pumping" of the sample through the
chip.
[0114] Electrophoretic "chips" consist of glass or plastic
substrates into which a pattern of microchannels, often simple but
sometimes complicated, have been fabricated. Embodiments of such
chips are shown in FIGS. 1 and 2. The microchannels terminate at
reservoirs which are often drilled holes in the structure itself
and which hold volumes as low as a few microliters to as much as
several tens of microliters. The flow or pumping of fluid through
the microchannel architecture, that is, from one reservoir to
another or through any components fabricated within the
microchannels themselves, is typically carried out in one of two
ways: by hydrostatic pressure or by electric field-driven flow
(endosmotic flow or "EOF").
[0115] Microchannel structures on electrophoretic chips are
typically in the micrometer range, with depths ranging from 10-50
.mu.m and widths from 30-100 .mu.m. A microchannel with the
dimensions of 10 .mu.m (deep).times.50 .mu.m (wide).times.3 mm
(long) has a total microchannel volume of 1.5 nanoliters (nL).
Therefore, to flow the equivalent of 20 microchannel volumes of a
given solution through this particular microchannel would require
the pumping of 30 nL of solution. The controlled flow of these
ultralow volumes through the microchannels of microfabricated
electrophoretic devices may be difficult to regulate with
hydrostatic pressure. The low volume pumping of solution on chips
is more conducive to EOF which can be controlled quite accurately
by the magnitude of the voltage applied. A limitation associated
with EO-driven flow, however, is its dependence on two parameters:
1) the ionic strength of the constituents of the solution being
pumped; and 2) the chemical composition of the microchannel wall.
For example, a low, negligible EOF is likely to result when using
solutions containing a large salt concentration, such as 100 mM
NaCl or 2.times.TBE solutions. Low EOF will also result when the
interior channel walls are composed of a neutral or nonionic
substance such as plastic. Under such conditions, EO flow is likely
to be of limited use with respect to its ability to pump solution
through the microchannel architecture. This limits the use of
microfabricated electrophoretic devices as the basic element in the
"laboratory on a chip" concept where a diverse array of biological
and chemical solutions will need to be pumped effectively through
the microchannel architecture.
[0116] The present invention overcomes these limitations in the
art. The ability to do accurate temperature cycling on localized
volumes of solution ranging from as low as a few microliters to up
to several hundred microliters, such as through the methods and
apparatus taught herein, could be exploited for accurate pumping of
small volumes (nL-.mu.L) of solution through microchannel
structures. The basis for the pumping is thermal expansion of
liquids. In a confined space, a change of 100.degree. C. can
result, for example, in the generation of up to 10 psi within the
chamber; if the only exit in the chamber was a microchannel, fluid
would be forced from the chamber through the microchannel. The flow
rate could be controlled very accurately by changes in temperature
as little as 1-2.degree. C.
EXAMPLES
[0117] The following examples are intended to illustrate the
invention and should not be construed as limiting the invention in
any way. The examples illustrate that the present methods and
apparatus can be used to effectively carry out various types of
fast and accurate thermal cycling. Results obtained using the
present methods are comparable to those obtained using conventional
methods, which take considerably longer to complete. In addition to
generic thermal cycling experiments, two different PCR
amplifications were performed using the T-cell receptor
.beta.-chain using standard and quantitative competitive (QC) PCR.
A cycle sequencing reaction was also performed.
[0118] Acrylamide used in the Examples was obtained from Bio-Rad
(Hercules, Calif.). A 5.times.stock solution of tris-borate-EDTA
(TBE; Sigma Chemicals, St. Louis, Mo.) was appropriately diluted
and titrated to pH with sodium hydroxide. Dissolution of
hydroxyethyl cellulose (HEC) was accomplished by heating the TBE
solution to 56.degree. C., and adding the cellulose powder slowly
to the rapidly stirring solution. The turbid solution was mixed on
a stirring hot plate until it cleared (about 15 min at a setting of
2 out of 10), the heat was removed, and the mixture stirred for an
hour. The solution was filtered through an 0.8 mm filter (Nalgene),
and stored at +4.degree. C. Before use, the HEC solution was
brought up to room temperature, and
1-(4-[3-methyl-2,3-dihydro-(benzo-1,3-
-oxazole)-2-methylidene]quinolinium)-3-trimethyl-ammonium propane
diodide (YO-PRO-1) was added (1:1000 dilution of the 1 mM solution
obtained from the manufacturer) to a final concentration of 1
.mu.M.
[0119] For the testing of the IR-mediated thermocycling and
comparison with standard thermocyclers, both PCR and quantitative
competitive (QC)-PCR, the amplification of the T-cell receptor
.beta.-chain was conducted as described by Johnston et al., Nuc.
Acids Res., 23:3074-3075 (1995). Each 15 .mu.L reaction consisted
of final concentrations of 100 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5
mM MgCl.sub.2, and 20 .mu.M each dNTP (dATP, dCTP, dGTP, and dTTP,
Promega, Madison, Wis.). Included in each reaction were 15 ng each
of upstream primer Vb8.2 (CATTATTCATATGGTGCTGGC) and downstream
primer CbSeq (GTCACATTTCTCAGATCCTC), 2.4 .mu.L of diluted TaqStart
Antibody (Clontech, Palo Alto, Calif.)/Taq DNA polymerase (Promega)
mix prepared according to the antibody manufacturer's
recommendations and 1 .mu.L, approximately 5 ng, of PCR product
generated from a TCR-.beta. chain found in an H-Y incompatible
graft undergoing rejection. The templates were also generated as
described by Johnston et al. Reaction mixtures were stored at
4.degree. C., and warmed to room temperature prior to cycling.
[0120] The amplification of a perform fragment and a competitor DNA
fragment was conducted as described above for the T-cell receptor
.beta.-chain. Each 15 .mu.L reaction consisted of final
concentrations of 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM
MgCl.sub.2, and 20 .mu.M each dNTP (dATP, dCTP, dGTP, and dTTP,
Promega, Madison, Wis.). Included in each reaction mixture were 20
pmoles each of primer (AGCTGAGAAGACCTATCAGG) and primer
(GATAAAGTGCGTGCCATAGG), 2.4 .mu.L of diluted TaqStart Antibody
(Clontech, Palo Alto, Calif.)/Taq DNA polymerase (Promega) mix
prepared according to the antibody manufacturer's recommendations,
and approximately 5 ng of PCR product from a reverse-transcribed
and amplified (RT-PCR) reaction for mouse perform and its
competitor. These methods were also carried out according to
Johnston et al.
[0121] The fluorescent cycle sequencing reactions were carried out
using the ABI Prism.TM. dRhodamine Terminator Cycle Sequencing Kit
according to the manufacturer's (Perkin-Elmer, Norwalk, Conn.)
instructions. To do this, 500 ng of template DNA was combined with
3.2 pmoles of the sequencing primer and 8 .mu.L of the Terminator
Ready Reaction Mix in a final volume of 20 .mu.L with sterile,
distilled H.sub.2O. Reaction mixtures were heated at 96.degree. C.
for 10 sec, 50.degree. C. for 5 sec and 60.degree. C. for 240 sec;
for 25 cycles on a model 9600 GeneAmp PCR System
(Perkin-Elmer).
[0122] The microchambers for noncontact-mediated PCR according to
the present invention were made from rectangular borosilicate glass
stock, 500 .mu.m.times.5.0 mm (o.d.)(Wale Apparatus Co.,
Hellertown, Pa.--part #4905-100) cut into 13 mm lengths, with one
end sealed (total volume about 28 .mu.L). The microchambers were
cleaned with sodium ethoxide, rinsed with methanol twice, and
air-dried before being coated with
bis(trimethylsilyl)trifluoroacetamide (bisTMSTFA, Sigma Chemical
Company, St. Louis, Mo.). After coating for 30 min., the chambers
were emptied, flushed twice with methanol, and air-dried.
[0123] The hardware for performing the thermocycling experiments
was constructed in-house. The apparatus included a Dell Pentium PC
outfitted with an analog to digital (A/D) converter board
(ComputerBoards, Inc., Mansfield, Mass.) with a 12 bit resolution
at a voltage range of the input signal between 0-5 volt. The
desired temperature parameters were controlled through a computer
program that was interfaced with the hardware via the analog to
digital (A/D) converter board.
[0124] Briefly, a thermocouple with an outer diameter of 0.005 inch
(Omega, Stamford, Conn.) was inserted into one of a pair of
reaction chambers placed side-by-side in the path of and equal
distance from the optical energy. The copper/constantan
thermocouple was fed to a thermocouple amplifier (Model TAC386-TC,
Omega, Stamford, Conn.) with an output of 1 mV/.degree. C. This
signal was further amplified by an op amp to produce a signal of
about 20 mV/.degree. C. Data acquisition for the thermocouple
reading was at a rate of 10 Hz.
[0125] The air for cooling was controlled by a digital output (TTL)
from the A/D converter board in the computer. This TTL-level output
was fed to a solid-state relay (ODCM-5, Potter-Brumfield) which
controlled a pneumatic valve (24 volt, 53HH8DGB, Peter Paul). The
air pressure, supplied through a gas cylinder, was controlled by a
panel mount regulating valve (B-ORF2, Whitey).
[0126] The infrared light was produced by a tungsten lamp (CXR, 8V,
50 W, General Electric) powered by a 5 volt AC/DC transformer. This
particular type of lamp is commonly used in slide projectors. It is
designed to collect most of the emitted radiation inside the lamp
to focus the entire optical energy on a focal point about 1.5 cm
outside of the lamp in a 2 mm to 4 mm spot. This lamp has a
reflecting film on the inside of the lamp housing which acts as a
mirror for the generated light/heat. The emitted light is collected
inside the bulb the radiation is focused on a spot outside of the
lamp bulb. The lamp intensity was modulated by a digital signal
(TTL-output) from the A/D board to activate the solid-state relay
(OACM-5, Potter-Brumfield).
[0127] The desired temperature profile is programmed into the
computer as a Labview application (National Instruments, Austin,
Tex.) which communicates through the A/C computer board with the
analog devices. The temperature in the sample was maintained
through the exact control of the heating and cooling intervals
based upon feedback from the thermocouple. Closure of the
solid-state relay switches the lamp on to heat the sample while an
open relay turns the lamp off. Cooling was effected by use of
compressed air, controlled through a solenoid valve. On and off
position of the solenoid valve are equivalent to cooling and not
cooling, respectively.
[0128] More specifically, proportional control was used to maintain
the desired temperatures. This method of control varies the
magnitude of heat applied to the sample in proportion to the size
of the error. If the sample temperature was greater than 4.degree.
C. from the programmed temperature, a heat pulse of larger duration
was used. If the difference was only 0.2.degree. C., a heat pulse
of shorter duration was used. The Labview application also
controlled the temperature limits and the duration of the dwell
times of the thermocycling process.
[0129] For comparison, all of the PCR were also carried out using
commercially available methods. Samples were contained in
polyethylene Eppendorf tubes in a Peltier block based PCR. For the
TCR-.beta. amplifications, including the QC-PCR, thirty cycles of
30 sec of denaturation at 94.degree. C., 30 sec of annealing at
55.degree. C., and 60 sec of extension at 72.degree. C. were
carried out. A first cycle included 5 min. of denaturation time at
94.degree. C., and a final cycle included 5 min. of extension time
at 72.degree. C. For the cycle sequencing reaction, the reaction
mixture was heated at 96.degree. C. for 10 sec, 50.degree. C. for 5
sec and 60.degree. C. for 240 sec for 25 cycles in a model 9600
GeneAmp PCR System (Perkin Elmer).
[0130] Following thermocycling, the various samples were analyzed
using gel electrophoresis. DNA amplification products analyzed by
gel electrophoresis were separated on a 3% agarose gel, NuSieve.TM.
3:1 agarose (FMC Bioproducts, Rockland, Me.), which is a blend of
three parts NuSieve and one part SeaKem.TM. LE agarose.
Electrophoresis was carried out using a Hoefer HE 33 (Hoefer
Pharmacia Biotech, San Francisco, Calif.) horizontal apparatus at
5.0 V/cm for approximately 40 min in 1.times.TAE buffer. DNA was
visualized by ethidium bromide staining in TAE buffer after
electrophoresis and observing the DNA fragments over a short
wavelength UV Transilluminator (Fisher Biotech, Pittsburgh,
Pa.).
[0131] The capillary electrophoresis conditions used involved a 50
microns internal diameter.times.20 cm length to detector (27 cm
total length) DB-17-coated .mu.-Sil capillary, (J & W
Scientific, Folsom, Calif., USA). The capillary was fitted in a
PACE.TM. cartridge for use with a Beckman PACE model 2100 equipped
with a laser induced fluorescence (LIF) detector with detection at
510 nm. Excitation of the fluorescent intercalator (YO-PRO-1) was
induced with a 488 nm argon laser. (Beckman Instruments, Fullerton,
Calif., USA). Sample diluted 1:50 with water and then injected
electrokinetically for 2 sec at 3 kV. The sample injection was
flanked by 1 sec (1 kV) electrokinetic injections of water. The
separation was carried out at 7.5 kV (277 V/cm; 9 .mu.A) with the
sample injected at the outlet end of the capillary and
electrophoresed toward the detector (7 cm effective capillary
length) and inlet.
Example 1
[0132] Glass microchambers prepared as described above were filled
with about 5 .mu.L of sample. PCR buffer was used as the sample to
demonstrate the ability of the methods and apparatus of the present
invention to perform fast and accurate thermocycling. A tungsten
lamp was used for heating the sample from a distance of 2 cm with
cooling facilitated by chilled compressed air. A thermocouple was
placed inside the microchamber to monitor the solution temperature
and control the thermocycling. FIG. 7A shows the thermocycling
profiles obtained with 94.degree. C./55.degree. C./72.degree. C.
dwell times of 30 sec/30 sec/60 sec, resulting in roughly 135 sec
cycles. Rapid temperature ramping was possible with a lamp-based
heating of 10.degree. C./sec and compressed air cooling of
20.degree. C./sec. For the five cycles in FIG. 7A, the temperature
variation with the controller set at 94.degree. C. was
93.57.+-.0.26.degree. C.; at 72.degree. C., the temperature was
71.70.+-.0.25.degree. C.; and at 54.degree. C., the temperature was
53.69.+-.0.37.degree. C. FIG. 7D provides an exploded view of the
second temperature cycle of FIG. 7A. The temperature scale is
generally the same as that in FIG. 7A. FIG. 7D shows a dwell time
at the lowest temperature (about 52.degree. C.) of about 4 minutes,
a dwell time at the intermediate temperature (about 70.degree. C.)
of about 7.5 minutes, and a dwell time at the highest temperature
(about 94.degree. C.) of about 4 minutes. Transition times between
temperatures are about 2 seconds or less.
[0133] The cycle time was decreased using a temperature profile of
94.degree. C./54.degree. C./72.degree. C. and dwell times of 2
sec/2 sec/4 sec, respectively. The profile given in FIG. 7B shows
that 17 sec cycles can be attained with results comparable to those
shown in FIG. 7A. The reproducibility associated with the ultrafast
thermocycling was very good as evidenced by the average cycle time
of 16.97.+-.0.43 sec over the course of the 30 cycles shown in FIG.
7B, and the exploded view of some of the cycles shown in FIG. 7C.
The total thermocycling time associated with 17 sec cycles,
including pre-cycle activation/denaturation and post-cycle extend
times, was roughly 12-14 min. This example therefore demonstrates
that the methods and apparatus of the present invention can be used
to effect rapid and accurate thermocycles.
Example 2
Initial Evaluation of the IR-Mediated Thermocycling System for
PCR-Based Amplification of DNA Utilizing the T-Cell Receptor
.beta.-Chain (TCR-.beta.) System
[0134] Two microchambers were placed side-by-side in the IR
pathway, using one as a temperature-sensing vessel and one for
performing the PCR reaction shown generally in FIG. 4. This
configuration allowed for monitoring the solution temperature
through the "dummy" microchamber without inhibiting the PCR
reaction occurring in the sample microchamber. A dual thermocouple
set-up was initially used to determine the optimal positioning so
that both microchambers were irradiated equally. Having determined
this, an accurate thermocycling in both chambers was achieved.
[0135] Using the dual microchamber configuration, successful PCR
amplification was carried out using the TCR-.beta. primer system.
FIGS. 8A and 8B show the results of noncontact-mediated
thermocycling with 30 cycles that are roughly 40 sec each in
duration as a result of dwell times of 8 sec/8 sec/15 sec at about
94.degree. C./54.degree. C./72.degree. C. The expanded scale (FIG.
8B) shows that, in addition to good cycle-to-cycle reproducibility,
the temperature was maintained with fair accuracy at the set
temperatures (94.2.+-.0.6.degree. C.; 71.7.+-.0.6.degree. C.;
54.6.+-.0.4.degree. C. FIG. 8C provides results of a gel
electrophoresis showing that PCR amplification in response to the
thermocycling shown in FIGS. 8A and 8B was successful. The positive
control (lane 2), which involved PCR amplification in a glass
microchamber using a commercial thermocycler, shows the abundant
amplification of a 216 bp DNA product specific to TCR-.beta.. Using
the noncontact-mediated approach with 94.degree. C./54.degree.
C./72.degree. C. dwell times of 30 sec/30 sec/60 sec (with 300 sec
pre-cycle activation/denaturation and post-cycle extend times), PCR
product of a comparable molecular size is observed (lane 4),
although only approximately 30% of the product obtained with the
commercial thermocycler (lane 2). The apparent efficiency of
amplification does not appear to be altered significantly by
reducing the cycle time. Using 94.degree. C./54.degree.
C./72.degree. C. dwell times of 15 sec/15 sec/30 sec with 300 see
pre-cycle activation/denaturation and post-cycle extend times (lane
5), or 8 sec/8 sec/115 see with 150 sec pre-cycle
activation/denaturation and post-cycle extend times (lane 6), a
comparable amount of product is observed. This example demonstrates
that fast and accurate PCR thermocycling can be accomplished using
the present invention.
Example 3
Cycle Sequencing Reaction by IR-Mediated PCR
[0136] The capabilities of the noncontact-mediated thermocycling
were further explored and the ability of the novel approach to
amplify DNA was tested using other PCR methods. In many
laboratories, the DNA sequence is determined using a technique
known as cycle sequencing. The technique is analogous to asymmetric
PCR in which a single primer, target DNA, thermostable DNA
polymerase and nucleotide substrates are repeatedly heated and
cooled to amplify a single strand of the target DNA. In cycle
sequencing, the standard four dNTPs are mixed with a small
proportion of polynucleotide chain-terminating, dye-labeled
dideoxyribonucleotides (ddNTPs) that occasionally substitute for
the standard dNTPs. Repetition of the process allows
polynucleotides not terminated with a ddNTP to act as larger
primers in subsequent cycles. The net effect is enhanced
sensitivity and longer sequence determinations compared to the same
process run isothermally. The major steps in cycle sequencing are,
thus, the thermocycling reactions and the electrophoretic
separation of the dye-labeled polynucleotide chains terminated by a
ddNTP. The sequence is read as a series of fluorescing colored
bands (polynucleotide-ddNMP) moving past a detector in the
electrophoresis instrument, each base represented by a different
color.
[0137] The control standard used with the ABI DNA sequencing kit
(pGEM3ZF+ sequenced with the -21M13 primer) was divided into two
aliquots with PCR amplification carried out with one aliquot using
a commercial contact-mediated thermocycler and the other by
IR-mediated thermocycling according to the methods of the present
invention (both processes in glass microchambers). The
thermocycling parameters used on the commercial instrument
(96.degree. C./50.degree. C./60.degree. C. with dwell times of 10
sec/5 sec/240 sec and 25 cycles) were also used for the IR-mediated
thermocycling. Side-by-side sequencing gel analysis of the
amplified products from both reactions showed that comparable
results were obtained. FIGS. 9A-9C show the results of cycle
sequencing in the microchambers. FIG. 9A shows the thermocycling
sequencing reaction executed in a glass microchamber according to
the example. FIG. 9B shows the sequencing data pGEM32F+ following
cycle sequencing. FIG. 9C provides sequencing data obtained from
the ABI Model 377 sequencer. The dideoxyterminated products
obtained with the IR-mediated thermocycling had a signal strength
of -400, high signal to noise ratio and normal spacing, and
provided sequence out to 430 base pairs. The results from the glass
microchamber were indistinguishable from those routinely obtained
with a standard contact-mediated thermocycler, thus demonstrating
that reliable results can be obtained using the present methods and
apparatus.
Example 4
Rapid Capillary Electrophoresis of DNA Amplified by IR
Heat-Mediated OC-PCR
[0138] IR-mediated PCR was also applied to Quantitative
Competitive-PCR (QC-PCR) (the templates for the amplification
coming from a QC-reverse transcription (RT)-PCR experiment) and the
PCR products were analyzed by a CE-based method. This method is
described in Piatak et al., Science, 259(5102):1749-54 (1993). In
general terms a QC-PCR experiment involves an array of PCR
reactions where a known amount of a "control" competitor RNA
transcript is mixed with an aliquot of an "unknown" target RNA. The
competitor and target DNAs are amplified by PCR under identical
conditions, and the products quantitated. The concentration of
competitor DNA that would result in an equal molar amount of both
competitor and target products is used to deduce the original
concentration of the target DNA transcript. FIG. 10 shows the
results of amplifying such a competitive PCR reaction in the dual
chamber IR-mediated cycler with our standard thermocycling program
using 94.degree. C./54.degree. C./72.degree. C. dwell times of 30
sec/30 sec/60 sec with 300 sec precycle activation/denaturation and
post cycle external times, and then separating the products of that
reaction on a short (7 cm effective length) capillary. This
experiment illustrates that rapid IR-mediated PCR can be easily
combined with PCR fragment sizing and identification based on a
short (less than 3 min) CE analysis time. The separation of QC-PCR
products from the capillary outlet to the inlet provided a rapid
analysis of the two amplification products, 135 see for the
competitor fragment (158 bp) and 145 sec for the target fragment
(198 bp).
[0139] Not only does this example demonstrate the utility of the
thermocycler for another common PCR procedure, competitive PCR
reactions, but the analysis of the DNA products on the short
capillary approximate the migration distance and analysis times
that would be observed for an "on-chip" CE separation. By
integration of "on-chip" PCR with "on-chip" CE analysis, very
favorable total analysis times can be attained which would greatly
facilitate tedious PCR experiments such as competitive-PCR
reactions which involve several PCR reactions over a wide range of
starting competitor and target concentrations. The analysis times
for a complete QC-PCR experiment may take days using conventional
isotope-labeling, amplification and detection methodologies. The
automation offered by integration of the PCR and DNA detection
methods in a chip format would be a great advance for the
quantification of the competitor/target DNA combinations required
to plot useful data.
Example 5
Rapid Amplification of DNA by IR-Mediated PCR in a Capillary
[0140] IR mediated PCR was also conducted using the apparatus shown
in FIG. 5, which allowed for thermocycling of nanoliter volumes in
a small channel-like structure. In this particular example the
sample was thermocycled as a plug of a defined length in a `bulk
solution`. For this experiment a thermocouple was placed into a 8
cm long .mu.sil DB-17 capillary with a 150 .mu.m I.D. (J&W
Scientific, Folsom, Calif.) to serve as a reference reaction vessel
in which the temperature was measured. The thermocouple was
position in the middle of that piece of capillary where about a 2
cm long optical transparent window was burnt into the polyimide
coating surrounding the capillary. The capillary was filled with a
PCR reaction solution without the Taq enzyme and its antibody and
sealed on both ends with epoxy glue to prevent evaporation of
liquid from the capillary during thermocycling. An 8 cm long 100
.mu.m I.D. capillary of the same type DB-17 was used as the actual
reaction vessel in which the PCR thermocycling procedure took
place. Also here, a 2 cm long optical transparent window was burnt
into the polyimide coating in middle of the capillary and both
capillaries were placed into the path of the IR energy. The
capillaries were horizontally aligned 1.5 cm in front of the
tungsten lamp with an xyz translation stage so that the optical
windows of both capillaries were optimally irradiated. A mirror
placed behind the capillaries enhanced the effect of heating. A
stream of compressed air at 18.degree. C. was pointed at the
capillary along their length axis to effect the cooling of the
sample in the capillary.
[0141] The 8 cm long 100 .mu.m I.D. DB-17 capillary was filled with
1% (w/v) hydroxyethylcellulose (HEC) in 1.times.TBE, pH 8.6,
solution except for a 2 cm long plug, corresponding to .about.160
nl volume, in the middle of the capillary at the optical window
which contained the PCR reaction solution. The thermocycling was
tested using a GeneAmp PCR Reagent Kit with native Taq DNA
Polymerase (N801-0043, Perkin Elmer, Norwalk, Conn.) containing the
appropriate lambda control primers and lambda DNA to amplify a
specific DNA sequence of 500 bp length. The PCR reaction solution
was made as a 50 .mu.l stock solution according to the
manufacturer's specifications, except that the 1.25 units of Taq
DNA Polymerase were substituted with 2.5 units of the same enzyme
bound to the TaqStart Antibody (Clontech, Palo Alto, Calif.) for
the hotstart. The thermocycling protocol--a profile depicted in
FIG. 11A--was a two cycle procedure with dwell times at 94.degree.
C. for 5 sec and 68.degree. C. for 20 sec for 25 cycles with a 2.5
min preincubation at 94.degree. C. and a final extension of 11 min
at 68.degree. C. The 50 .mu.l PCR stock solution was divided into
two parts. One part (.about.2 .mu.l) of the solution was partially
used to fill the 2 cm plug in the capillary whereas the second part
was used to conduct the control experiment using dwell times at
94.degree. C. for 15 sec, and 68.degree. C. for 60 sec for 25
cycles with a 5 min preincubation at 94.degree. C. and final
extension of 10 min at 68.degree. C. in a conventional PCR
thermocycler (Progene, Techne, Inc., Princeton, N.J.).
[0142] After the thermocycling of the PCR mixture in the capillary
the sample plug was removed from the capillary and diluted with 9
.mu.l of PCR reaction buffer (10 mM Tris, pH 8.6, 50 mM KCl, 2.5 mM
MgCl.sub.2 and 1 .mu.M of each dNTP) and injected
electrokinetically at 6.1 kV for 20 sec into the capillary
electrophoresis for analysis. The sample injected was flanked with
a 3 sec 3.5 kV electrokinetic injection of water. The control
sample cycled in the conventional PCR thermocycler was injected
unchanged for analysis using the same injection conditions as the
ones described above.
[0143] The analysis of the PCR amplification product by capillary
electrophoresis was conducted using the same instrumentation and
conditions as described in the other examples except the sample
preparation and injection conditions were altered as specified
above and the separation was conducted from the inlet to the outlet
of the capillary.
[0144] Quantitative and qualitative analysis of the product formed
in the sample plug exposed to the PCR thermocycling procedure in
the capillary showed that amplification of the specific lambda DNA
sequence is equivalent to the amplification product obtained from
the control experiment in the conventional apparatus as shown in
FIG. 11B. The PCR reaction has very high demands on the accuracy of
the thermocycling parameters and is therefore an ideal assay to
test the accuracy of the thermocycling method and apparatus. The
successful amplification of the 500 bp product in sample plug in
the capillary is therefore proof of the extremely rapid and
accurate thermocycling achieved with the method and apparatus of
this invention.
[0145] Whereas particular embodiments of this invention have been
described above for purposes of illustration, it will be evident to
those skilled in the art that numerous variations of the details of
the present invention may be made without departing from the
invention as defined in the appended claims.
* * * * *