U.S. patent application number 10/756219 was filed with the patent office on 2004-07-22 for device and method for thermal cycling.
This patent application is currently assigned to Applera Corporation. Invention is credited to Sandell, Donald R..
Application Number | 20040142459 10/756219 |
Document ID | / |
Family ID | 27609712 |
Filed Date | 2004-07-22 |
United States Patent
Application |
20040142459 |
Kind Code |
A1 |
Sandell, Donald R. |
July 22, 2004 |
Device and method for thermal cycling
Abstract
A thermal cycling device for performing nucleic acid
amplification on a plurality of biological samples positioned in a
sample well tray. The thermal cycling device includes a sample
block assembly, an optical detection system, and a sample well tray
holder configured to hold the sample well tray. The sample block
assembly is adapted for movement between a first position
permitting the translation of the sample well tray into alignment
with sample block assembly, and a second position, upward relative
to the first position, where the sample block assembly contacts the
sample well tray. A method of performing nucleic acid amplification
on a plurality of biological samples positioned in a sample well
tray in a thermal cycling device is also provided.
Inventors: |
Sandell, Donald R.; (San
Jose, CA) |
Correspondence
Address: |
MILA KASAN, PATENT DEPT.
APPLIED BIOSYSTEMS
850 LINCOLN CENTRE DRIVE
FOSTER CITY
CA
94404
US
|
Assignee: |
Applera Corporation
Foster City
CA
|
Family ID: |
27609712 |
Appl. No.: |
10/756219 |
Filed: |
January 12, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10756219 |
Jan 12, 2004 |
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10058927 |
Jan 30, 2002 |
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6677151 |
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Current U.S.
Class: |
435/287.2 ;
435/287.3; 435/288.7 |
Current CPC
Class: |
C12Q 1/686 20130101;
B01L 9/523 20130101; B01L 2300/0829 20130101; B01L 2300/0654
20130101; B01L 7/52 20130101; B01L 2300/1805 20130101 |
Class at
Publication: |
435/287.2 ;
435/287.3; 435/288.7 |
International
Class: |
C12M 001/34 |
Claims
What is claimed is:
1. A thermal cycling device, comprising: a sample block assembly;
an optical detection system positioned above the sample block
assembly; and a sample well tray holder including a tray-receiving
region configured to hold a sample well tray, the sample well tray
holder configured to translate the sample well tray into alignment
with the sample block assembly, wherein the sample block assembly
is adapted for movement between a first position permitting the
translation of the sample well tray into alignment with the sample
block assembly, and a second position, upward relative to the first
position, where the sample block assembly contacts the sample well
tray.
2. The thermal cycling device of claim 1, wherein the optical
detection system is adapted to remain substantially stationary
during insertion and removal of the sample well tray from the
thermal cycling device.
3. The thermal cycling device of claim 1, wherein the sample block
assembly comprises a sample block for contacting the sample well
tray when the sample block assembly is in the second position.
4. The thermal cycling device of claim 3, further comprising a
positioning mechanism configured to translate the sample block
between the first and second positions.
5. The thermal cycling device of claim 4, wherein the positioning
mechanism comprises a plurality of links.
6. The thermal cycling device of claim 5, wherein the positioning
mechanism is configured so that movement of one of the plurality of
links causes movement of another of the plurality of links, thereby
causing the translation of the sample block assembly between the
first and second positions.
7. The thermal cycling device of claim 5, wherein the positioning
mechanism further comprises a motor, and further wherein the
plurality of links comprises a first link, a second link, and a
third link, and further wherein a first end of the first link is
rotatably connected to the motor, a second end of the first link is
rotatably connected to the first end of both the second link and
the third link, the second link having a second end rotatably
connected to a stationary pivot point, the third link having a
second end rotatably connected to the sample block assembly, and
further wherein the motor causes the first link to translate,
thereby causing the second end of the third link to translate the
sample block assembly between the first and second positions.
8. The thermal cycling device of claim 7, wherein the plurality of
links comprises a first set of links and a second set of links, the
first and second set of links being positioned on opposite sides of
the sample block assembly.
9. The thermal cycling device of claim 5, wherein the plurality of
links comprises a first link and a second link, the first link
having a first end rotatably connected to a stationary pivot point,
the first link having a second end comprising a handle for
manipulation of the first link, the second link having a first end
rotatably connected to a pivot point on the first link, the second
link having a second end rotatably connected to the sample block
assembly, wherein the rotation of the first link about the
stationary pivot point causes the second link to translate, thereby
translating the sample block assembly between the first and second
positions.
10. The thermal cycling device of claim 9, wherein the handle of
the first link further comprises a door corresponding to an opening
in the thermal cycling device, wherein the door covers the opening
in the thermal cycling device when the sample block assembly is in
the second position.
11. The thermal cycling device of claim 9, wherein the plurality of
links comprises a first set of links and a second set of links, the
first and second set of links being positioned on opposite sides of
the sample block assembly.
12. The thermal cycling device of claim 5, wherein the plurality of
links comprises a first link and a second link, the first link
being rotatably connected to a stationary pivot point, the first
link having a first end rotatably connected to the second link, the
first link having a second end comprising a handle for manual
manipulation of the first link, the second link having a first end
rotatably connected to the first end of the first link, the second
link having a second end rotatably connected to the sample block
assembly, wherein the rotation of the first link about the
stationary pivot point causes the second link to translate, thereby
translating the sample block assembly between the first and second
positions.
13. The thermal cycling device of claim 12, wherein the plurality
of links comprises a first set of links and a second set of links,
the first and second set of links being positioned on opposite
sides of the sample block assembly.
14. The thermal cycling device of claim 1, wherein the thermal
cycling device is configured to perform thermal cycling when the
sample well tray is aligned with the sample block assembly and the
sample block assembly is positioned in the second position.
15. The thermal cycling device of claim 1, wherein the
tray-receiving region of the sample well tray holder comprises a
recess in which the sample well tray may be positioned.
16. The thermal cycling device of claim 1, wherein the thermal
cycling device is a real-time PCR machine.
17. A method of performing nucleic acid amplification on a
plurality of biological samples positioned in a sample well tray in
a thermal cycling device, comprising the steps of: placing the
sample well tray onto a tray-receiving region of a sample well tray
holder; translating the sample well tray holder and sample well
tray into the thermal cycling device until the sample well tray is
aligned with a sample block assembly positioned beneath the sample
well tray; translating the sample block assembly from a first
position wherein the sample block assembly permits the sample well
tray to translate into alignment with the sample block assembly, to
a second position wherein the sample block assembly is positioned
vertically upward relative to the first position to contact the
sample well tray; thermally cycling the device while simultaneously
optically detecting the samples; translating the sample block
assembly from the second position to the first position; and
removing the sample well tray from the thermal cycling device,
wherein the optical detection system remains substantially
stationary throughout the above steps.
18. The method of performing nucleic acid amplification of claim
17, wherein the steps of translating the sample block assembly
include the step of imparting a force on a first link in order to
create movement of the first link.
19. The method of performing nucleic acid amplification of claim
18, wherein the movement of the first link imparts a force on a
second link to create movement of the second link and the sample
block assembly.
20. A thermal cycling device, comprising: an optical detection
system; a sample block adapted for movement along a first path,
toward and away from the optical detection system; and a sample
well tray holder including a tray-receiving region, the sample well
tray holder being adapted for movement along a second path, toward
and away from a position whereat the tray-receiving region is
disposed between the optical detection system and the sample block,
wherein the optical detection system is adapted to remain
substantially stationary during movement of the sample block and
the sample well tray holder along the first and second paths.
21. The thermal cycling device of claim 20, wherein the sample
block is configured to allow the sample well tray holder to move
along the second path when the sample block is in a first position
away from the optical detection system.
22. The thermal cycling device of claim 21, wherein the sample
block is configured to contact a sample well tray received in the
tray-receiving region of the sample well tray holder when the
tray-receiving region is disposed between the optical detection
system and the sample block, and the sample block is in a second
position toward the optical detection system.
23. The thermal cycling device of claim 22, further comprising a
positioning mechanism configured to translate the sample block
between the first and second positions.
24. The thermal cycling device of claim 23, wherein the positioning
mechanism comprises a plurality of links.
25. The thermal cycling device of claim 24, wherein the positioning
mechanism is configured so that movement of one of the plurality of
links causes movement of another of the plurality of links, thereby
causing the translation of the sample block between the first and
second positions.
26. The thermal cycling device of claim 24, wherein the positioning
mechanism further comprises a motor, and further wherein the
plurality of links comprises a first link, a second link, and a
third link, and further wherein a first end of the first link is
rotatably connected to the motor, a second end of the first link is
rotatably connected to the first end of both the second link and
the third link, the second link having a second end rotatably
connected to a stationary pivot point, the third link having a
second end rotatably connected to the sample block, and further
wherein the motor causes the first link to translate, thereby
causing the second end of the third link to translate the sample
block between the first and second positions.
27. The thermal cycling device of claim 26, wherein the plurality
of links comprises a first set of links and a second set of links,
the first and second set of links being positioned on opposite
sides of the sample block.
28. The thermal cycling device of claim 24, wherein the plurality
of links comprises a first link and a second link, the first link
having a first end rotatably connected to a stationary pivot point,
the first link having a second end comprising a handle for
manipulation of the first link, the second link having a first end
rotatably connected to a pivot point on the first link, the second
link having a second end rotatably connected to the sample block,
wherein the rotation of the first link about the stationary pivot
point causes the second link to translate, thereby translating the
sample block between the first and second positions.
29. The thermal cycling device of claim 28, wherein the handle of
the first link further comprises a door corresponding to an opening
in the thermal cycling device, wherein the door covers the opening
in the thermal cycling device when the sample block is in the
second position.
30. The thermal cycling device of claim 28, wherein the plurality
of links comprises a first set of links and a second set of links,
the first and second set of links being positioned on opposite
sides of the sample block.
31. The thermal cycling device of claim 24, wherein the plurality
of links comprises a first link and a second link, the first link
being rotatably connected to a stationary pivot point, the first
link having a first end rotatably connected to the second link, the
first link having a second end comprising a handle for manual
manipulation of the first link, the second link having a first end
rotatably connected to the first end of the first link, the second
link having a second end rotatably connected to the sample block,
wherein the rotation of the first link about the stationary pivot
point causes the second link to translate, thereby translating the
sample block between the first and second positions.
32. The thermal cycling device of claim 31, wherein the plurality
of links comprises a first set of links and a second set of links,
the first and second set of links being positioned on opposite
sides of the sample block.
33. The thermal cycling device of claim 20, wherein the thermal
cycling device is configured to perform thermal cycling when the
tray-receiving region of the sample well tray holder is disposed
between the optical detection system and the sample block, and the
sample block is in a position toward the optical detection
system.
34. The thermal cycling device of claim 20, wherein the
tray-receiving region of the sample well tray holder comprises a
recess in which a sample well tray may be positioned.
35. The thermal cycling device of claim 20, wherein the thermal
cycling device is a real-time PCR machine.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 10/058,927, filed Jan. 30, 2002, which is
incorporated herein by reference.
FIELD OF THE INVENTION
[0002] The present invention relates generally to a thermal cycling
device and method of performing nucleic acid amplification on a
plurality of biological samples positioned in a sample well tray.
More particularly, the present invention relates in one aspect to a
thermal cycling device and method of real-time detection of a
nucleic acid amplification process such as polymerase chain
reaction (PCR).
BACKGROUND
[0003] Biological testing has become an important tool in detecting
and monitoring diseases. In the biological testing field, thermal
cycling is used to amplify nucleic acids by, for example,
performing PCR and other reactions. PCR in particular has become a
valuable research tool with applications such as cloning, analysis
of genetic expression, DNA sequencing, and drug discovery.
[0004] Recent developments in the field have spurred growth in the
number of tests that are performed. One method for increasing the
throughput of such biological testing is to provide real-time
detection capability during thermal cycling. Real-time detection
increases the efficiency of the biological testing because the
characteristics of the samples can be detected while the sample
well tray remains positioned in the thermal cycling device,
therefore not requiring removal of the sample well tray to a
separate area prior to testing of the samples. In typical real-time
thermal cycling devices, the sample well tray is removed after
detection is completed.
SUMMARY OF THE INVENTION
[0005] Various aspects of the invention generally relate to a
thermal cycling device in which the sample block assembly may be
vertically moved so that the sample well tray may be inserted and
removed from the thermal cycling device. The thermal cycling device
can be a real-time device. During such movement of the sample block
assembly and sample well tray, the optical detection system can
remain substantially stationary.
[0006] According to one aspect, the invention comprises a thermal
cycling device. The thermal cycling device includes a sample block
assembly, an optical detection system, and a sample well tray
holder. The sample well tray holder includes a tray-receiving
region configured to hold a sample well tray. The optical detection
system is positioned above the sample block assembly. The sample
well tray holder is configured to translate the sample well tray
into alignment with the sample block assembly. The sample block
assembly is adapted for movement between a first position
permitting the translation of the sample well tray into alignment
with the sample block assembly, and a second position, upward
relative to the first position, where the sample block assembly
contacts the sample well tray.
[0007] In another aspect, the optical detection system is adapted
to remain substantially stationary during insertion and removal of
the sample well tray from the thermal cycling device. In a further
aspect, the thermal cycling device further includes a positioning
mechanism configured to translate the sample block between the
first and second positions.
[0008] In yet another aspect, the invention comprises a method of
performing nucleic acid amplification on a plurality of biological
samples positioned in a sample well tray in a thermal cycling
device. The method includes the step of placing the sample well
tray into a sample well tray holder. The method further includes
the step of translating the sample well tray holder and sample well
tray into the thermal cycling device until the sample well tray is
aligned with a sample block assembly positioned beneath the sample
well tray. The method further includes the step of translating the
sample block assembly from a first position to a second position.
In the first position, the sample block assembly permits the sample
well tray to translate into alignment with the sample block
assembly. In the second position, the sample block assembly is
positioned vertically upward relative to the first position to
contact the sample well tray.
[0009] The method can further comprise the step of thermally
cycling the device while simultaneously optically detecting the
samples. The method can further comprise translating the sample
block assembly from the second position to the first position.
Finally, the method can comprise the step of removing the sample
well tray holder and sample well tray from the thermal cycling
device. In various embodiments, the optical detection system
remains substantially stationary throughout the above steps.
[0010] In another aspect, the invention comprises a thermal cycling
device. The thermal cycling device includes an optical detection
system, a sample block, and a sample well tray holder. The sample
block is adapted for movement along a first path, toward and away
from the optical detection system. The sample well tray holder
includes a tray-receiving region. The sample well tray holder is
adapted for movement along a second path, toward and away from a
position whereat the tray-receiving region is disposed between the
optical detection system and the sample block. The optical
detection system can be adapted to remain substantially stationary
during movement of the sample block and the sample well tray holder
along the first and second paths.
[0011] It is to be understood that both the foregoing general
description and the following detailed description are exemplary
and explanatory only and are not restrictive of the invention, as
claimed.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] The accompanying drawings, which are incorporated in and
constitute a part of this specification, illustrate several
embodiments of the invention. In the drawings,
[0013] FIG. 1 is a front view of an exemplary embodiment of a
thermal cycling device according to the present invention;
[0014] FIG. 2A is side view of an embodiment of the device of FIG.
1, with a sample well tray positioned outside of the device;
[0015] FIG. 2B is a side view of the device of FIG. 1, with the
sample well tray inserted into the device;
[0016] FIG. 2C is a side view of the device of FIG. 1, with the
sample well tray inserted into the device and a sample block
assembly in an upward position for engaging the sample well
tray;
[0017] FIG. 3A is a side view of another embodiment of the thermal
cycling device of the invention, with a sample well tray positioned
outside of the device;
[0018] FIG. 3B is a side view of the device of FIG. 3A, with the
sample well tray inserted into the device;
[0019] FIG. 3C is a side view of the device of FIG. 3A, with the
sample well tray inserted into the device and a sample block
assembly in an upward position for engaging the sample well
tray;
[0020] FIG. 4A is side view of yet another embodiment of the
thermal cycling device of the invention, with the sample well tray
positioned outside of the device;
[0021] FIG. 4B is a side view of the device of FIG. 4A, with the
sample well tray inserted into the device;
[0022] FIG. 4C is a side view of the device of FIG. 4A, with the
sample well tray inserted into the device and a sample block
assembly in an upward position for engaging the sample well
tray;
[0023] FIG. 5 is a side cross sectional view of a sample well tray
holder, used with the present invention, with a sample well tray
positioned thereon; and
[0024] FIG. 6 is a perspective view of one embodiment of a sample
block assembly used in the device of the invention.
DESCRIPTION OF CERTAIN EMBODIMENTS
[0025] Reference will now be made to certain exemplary embodiments
of the invention, examples of which are illustrated in the
accompanying drawings. Wherever possible, the same reference
numbers are used in the drawings and the description to refer to
the same or like parts.
[0026] In accordance with certain embodiments, a thermal cycling
device is provided. In one aspect, the thermal cycling device may
perform nucleic acid amplification on a plurality of biological
samples positioned in a sample well tray. In certain embodiments,
the thermal cycling device includes a sample block assembly, an
optical detection system positioned above the sample block
assembly, and a sample well tray holder with a tray-receiving
region configured to hold the sample well tray. In certain aspects,
the sample block assembly is adapted for movement between a first
position permitting the translation of the sample well tray into
alignment with the sample block assembly, and a second position,
upward relative to the first position, where the sample block
assembly contacts the sample well tray. The thermal cycling device
may also include a positioning mechanism for translating the sample
block between the first and second positions.
[0027] Although the terms "horizontal," "vertical," "upward," and
"downward" are used in describing various aspects of the present
invention, it should be understood that such terms are for purposes
more easily describing the invention, and do not limit the scope of
the invention.
[0028] In various embodiments, such as illustrated in FIGS. 1,
2A-2C, and 5-6, the thermal cycling device 10 for performing
nucleic acid amplification on a plurality of biological samples
includes one or more of: a sample block assembly 50; an optical
detection system 12 for detecting the characteristics of the
samples positioned in a sample well tray 14; a sample well tray
holder 30; and a positioning mechanism 70 connected to the sample
block assembly, the positioning mechanism being configured to
impart vertical movement on the sample block assembly.
[0029] The thermal cycling device is typically configured to
perform nucleic acid amplification. One common method of performing
nucleic acid amplification of biological samples is polymerase
chain reaction (PCR). Various PCR methods are known in the art, as
described in, for example, U.S. Pat. Nos. 5,928,907 and 6,015,674
to Woudenberg et al., the complete disclosures of which are hereby
incorporated by reference for any purpose. Other methods of nucleic
acid amplification include, for example, ligase chain reaction,
oligonucleotide litigations assay, and hybridization assay. These
and other methods are described in greater detail in U.S. Pat. Nos.
5,928,907 and 6,015,674.
[0030] In one embodiment, the thermal cycling device performs
real-time detection of the nucleic acid amplification of the
samples during thermal cycling. Real-time detection systems are
known in the art, as also described in greater detail in, for
example, U.S. Pat. Nos. 5,928,907 and 6,015,674 to Woudenberg et
al., incorporated herein above. During real-time detection, various
characteristics of the samples are detected during the thermal
cycling in a manner known in the art. Real-time detection permits
more accurate and efficient detection and monitoring of the samples
during the nucleic acid amplification.
[0031] In accordance with various embodiments, the thermal cycling
device includes an optical detection system. As embodied herein and
shown in FIGS. 1 and 2A-2C, an optical detection system 12 is
positioned above the sample block assembly 50. The optical
detection system 12 is configured to detect and monitor the
characteristics of the samples in the sample well tray 14 in
real-time during the thermal cycling. Suitable structures and
methods for the optical detection system 12 are well known in the
art. The optical detection system may use any known structure or
method. In one example, the optical detection system would include
a quartz bulb with a CCD camera, in a manner known in the art. In
another example, the optical detection system may include a
fluorescence based system with a lens and a fiber optics for each
cable as described in U.S. Pat. Nos. 5,928,907 and 6,015,674 to
Woudenberg et al, incorporated herein above. Alternatively, the
optical detection system may include any known system using a
single light source for each sample well, in a manner known in the
art. Likewise, the optical detection system may include any other
type suitable for use with the thermal cycling device of the
present invention.
[0032] In various embodiments, optical detection system 12 is
substantially stationarily mounted in the thermal cycling device.
The optical detection system can be configured so that the optical
detection system remains substantially stationary during insertion
of a sample well tray holder and sample well tray into the thermal
cycling device, during thermal cycling of the sample well tray,
during removal of the sample well tray holder and sample well tray
from the thermal cycling device, and at all stages in between the
above steps. By remaining substantially stationary, the optical
system reduces the potential for misalignment of the optical
components. For purposes of this invention, the term "substantially
stationary" does not mean that the optical detection system is
completely stationary, rather, the term includes any vibrations or
movements caused by normal operation of the thermal cycling
device.
[0033] The thermal cycling device may be configured for use with
any type of sample well tray, including, for example, 96-well
sample well trays, 384-well sample trays, and microcard sample
trays. The size and shape of these sample well trays are well known
in the art. Examples of 96-well sample well trays suitable for use
in the present invention are described in WO 00/25922 to Moring et
al., the complete disclosure of which is hereby incorporated by
reference for any purpose. Examples of sample well trays of the
microcard type suitable for use in the present invention are
described in WO 01/28684 to Frye et al., the complete disclosure of
which is hereby incorporated by reference for any purpose,
WO97/36681 to Woudenberg et al., the complete disclosure of which
is hereby incorporated by reference for any purpose, U.S.
application Ser. No. 09/897,500, filed Jul. 3, 2001, assigned to
the assignee of the present invention, the complete disclosure of
which is hereby incorporated by reference for any purpose, and U.S.
Application Ser. No. 09/977,225, filed Oct. 16, 2001, assigned to
the assignee of the present application, the complete disclosure of
which is hereby incorporated by reference for any purpose. Sample
well trays having any number of sample wells and sample well sizes
may also be used with the thermal cycling device of the present
invention. In the example shown in the figures, the volume of the
sample wells may vary anywhere from about 0.01 .mu.l to thousands
of microliters (.mu.l), with a volume between 10 to 500 .mu.l being
typical.
[0034] As embodied herein and shown in FIGS. 1, 2A-2C, and 5, the
sample well tray 14 can include a rectangular top portion 16 having
a top surface 18 and bottom surface 24. The top surface 18 defines
openings for a plurality of sample wells 20 of any known size and
shape. In the example shown in FIGS. 1-6, the sample well tray
includes ninety-six sample wells positioned in a well-known
8.times.12 array. In the embodiment shown, the top portion 16 of
the sample well tray is rectangular. In the embodiment shown in the
figures, the sample wells are conical shape recesses extending
downwardly from the top surface 18 in a known manner. Each sample
well includes a sample well bottom surface 22 for engaging with
corresponding recesses in the sample block assembly 50. It is well
understood that any type of sample well configuration may be used
with the present invention, including for example, a 384-well
sample well tray and a microcard type sample tray.
[0035] In accordance with various embodiments, the thermal cycling
device can include a sample well tray holder having a
tray-receiving region configured to hold the sample well tray. The
sample well tray holder can be configured to translate the sample
well tray into alignment with a sample block assembly. As described
herein and shown in FIGS. 1, 2A-2C, and 5, the sample well tray
holder is generally designated by reference number 30. The sample
well tray holder is configured so that the sample well tray may be
supported thereon, particularly during insertion of the sample well
tray into the thermal cycling device, and during removal of the
sample well tray from the thermal cycling device. In various
embodiments, the sample well tray holder 30 is generally
rectangular in shape.
[0036] With particular reference to FIG. 5, the sample well tray
holder 30 includes a top surface 32 and a side surface 34 that
extends around the periphery of the sample well tray holder. The
side surface in the front of the device is designated by reference
number 36. The sample well tray holder further includes a
tray-receiving region configured to hold a sample well tray. In the
embodiment shown in FIG. 5, the tray-receiving region is defined by
a downwardly projecting holder structure 38 in the top surface 32.
The downwardly projecting holder structure 38 is positioned on a
first recessed portion 40 of the top surface 32. The downwardly
projecting holder structure 38 includes a horizontally projecting
annular projection 42 for engaging the top surface of the first
recessed portion 40 of the top surface 32. The downwardly
projecting holder structure 38 further comprises a projection 44
that slopes inwardly. The inside of the projection 44 defines a
rectangular opening or recess slightly smaller than the sample well
tray 16. The rectangular opening or recess is dimensioned to
receive a sample well tray. In particular, the projection 44 is
dimensioned so that the bottom surface 24 of the sample well tray
may rest on the top surface of the projection 44, as shown in FIG.
5. The projecting holder structure may be shaped to be angled
inwardly in order to ease the removal of the sample well tray from
the sample well tray holder.
[0037] The sample well tray holder 30 and sample well tray 14 are
dimensioned so that they are capable of passing between the optical
detection system 12 and the sample block assembly 50 without
interference during insertion into and removal from the thermal
cycling device. The sample well tray is configured so that it can
horizontally translate into and out of the thermal cycling device
on the sample well tray holder. In order to facilitate insertion or
removal of the sample well tray holder, bearing surfaces (not
shown) may be provided on the sample well tray holder and/or
thermal cycling device. The sample well tray holder may be
horizontally translated either manually or automatically.
[0038] In accordance with various embodiments, the thermal cycling
device can include a sample block assembly configured to receive
the sample well tray thereon. As described herein and shown in
FIGS. 1, 2A-2C, 5, and 6, a sample block assembly is generally
designated by reference number 50. It is to be understood that the
sample block assembly shown in FIG. 6 is by way of example only,
and the invention is not limited to the sample block assembly shown
in FIG. 6. The sample block assembly shown in FIG. 6 includes a
sample block 58 and a heat sink 56. Sample blocks are well known in
the art. Sample blocks may be made of any suitable material, such
as aluminum. The sample block assembly typically includes at least
one heating element. In one embodiment, the at least one heating
element includes a peltier heater. Methods of heating and cooling a
sample block during and after thermal cycling are known in the art.
The sample block 58 shown in FIG. 6 includes a top surface 54 with
a plurality of recess 52 on the top surface. The recesses are
arranged to correspond to the sample wells of the sample well tray.
For example, in the embodiment shown in FIG. 6, the sample block
assembly includes ninety-six recesses for engaging with a 96-well
sample well tray. Alternatively, the sample block assembly can have
any number of recesses. For example, the number of recesses can
equal the number of sample wells. In an embodiment with a 384-well
sample tray, the sample block assembly would typically have at
least 384 recesses. In an embodiment using a microcard type sample
tray, the sample block need not have recesses.
[0039] Heat sink 56 may be any known type of heat sink.
Additionally, a convection unit such as a fan may be positioned
adjacent the sample block assembly. In the embodiment shown in
FIGS. 1, 2A-2C, and 5-6, the convection unit comprises a fan 66
positioned below the sample block assembly 50. In one embodiment,
the fan 66 creates a flow of cooling air against the heat sink 56
in order to cool the sample block. Alternatively, the fan may be
used with a heater in order to create a flow of hot air against the
heat sink in order to heat the sample block. In certain
embodiments, the fan is mounted so that it moves vertically with
the sample block assembly. In other embodiments, the fan may be
stationarily mounted in the thermal cycling device
[0040] In accordance with various embodiments, the thermal cycling
device can include a positioning mechanism connected to the sample
block assembly, the positioning mechanism being configured to
vertically translate the sample block assembly between a first or
"downward" position and a second or "upward" position. The
positioning mechanism can be configured to translate the sample
block assembly between the first position, where the sample block
assembly permits the translation of the sample well tray into
alignment with the sample block assembly, and the second position,
upward relative to the first position, where the sample block
assembly contacts the sample well tray.
[0041] An embodiment of the positioning mechanism is illustrated in
FIGS. 1 and 2A-2C. In the embodiment shown in FIGS. 1 and 2A-2C,
the positioning mechanism is generally designated by reference
number 70. The positioning mechanism is connected to the sample
block assembly 50. The positioning mechanism allows insertion and
removal of the sample well tray by moving the sample block assembly
in the vertical direction. FIGS. 2A and 2B show the downward or
"first" position of the sample block assembly. In the downward
position, a gap is created between the top of the sample block
assembly 50 and a bottom portion 94 of the optical detection system
of sufficient size so that the sample well tray holder and sample
well tray may be inserted therebetween. In the first position, the
sample block is "away" from the optical detection system.
[0042] In a second or "upward" position shown in FIG. 2C, the
sample block assembly 50 is vertically upward relative to the
downward or "first" position. In the upward position, the top
surface 54 of the sample block 58 presses against the bottom of the
sample well tray 14 so that the recesses 52 mate with the sample
well bottom surfaces 22. In various embodiments using a microcard,
a top surface of the sample block can press against a bottom
surface of the microcard. In the second position, the sample block
is "toward" the optical detection system. The sample block assembly
is adapted for movement toward and away from the optical detection
system along a predetermined vertical path.
[0043] In the embodiment shown in FIGS. 1 and 2A-2C, the
positioning mechanism 70 includes a plurality of links. The
arrangement of links shown in FIGS. 1 and 2A-2C is by way of
example only. The plurality of links includes a first link 78 as
shown in FIGS. 2A-2C. The first link 78 is shown as being in the
shape of a connecting rod, however, the first link may have any
number of different shapes. First link 78 includes a first end 80
rotatably connected to a motor 72 at a pivot point 74. Motor 72 can
be any known type of motor that is capable of imparting a
translational or rotational force on the first link 78. As shown in
FIGS. 2A-2C, the motor causes pivot point 74 of the first end 80 to
revolve around a central axis 76 of the motor. The revolution of
the first end 80 about the central axis of the motor causes the
first link to translate.
[0044] As shown in FIGS. 2A-2C, a second end 82 of the first link
is rotatably connected to a first end of a second link 84 at pivot
point 88. The second link has a second end rotatably connected to
stationary pivot point 86. The second link 84 pivots about
stationary pivot point 86 when the motor causes movement of the
first link 78.
[0045] The second end 82 of the first link is rotatably connected
to a first end of a third link 90 at pivot point 88. The second end
of the third link 90 is rotatably connected to the sample block
assembly at pivot point 92. By revolution of the first end of the
first link about the central axis 76 of the motor, the first link
causes the first end of the second link 84 to rotate partially
about the stationary pivot point 86, thus causing the third link to
press upward against the sample block assembly at pivot point 92.
The positioning mechanism is connected to the sample block assembly
by, for example, a pin at pivot point 92. As a result of this
linkage arrangement, the positioning mechanism causes the sample
block assembly to move vertically from the downward or "first"
position shown in FIGS. 2A and 2B to the upward or "second"
position shown in FIG. 2C. It should be understood that the
positioning mechanism of FIGS. 2A-2C is by way of example only.
[0046] As shown in FIG. 1, the positioning mechanism 70 may include
two sets of links, one on each lateral side of the sample block
assembly. The second set of links is a mirror image of the first
set of links. In FIG. 1, the second set of links includes first
link (not shown), second link 84', and third link 90'. With a
configuration having two sets of links, an individual motor may be
utilized for each of the sets of links, or alternatively, a single
motor may be utilized for both sets of links. In another variation,
a single set of links may be used instead of two sets of links. In
a further variation, more than two sets of links may be used.
[0047] The positioning mechanism may also include at least one
guide member for guiding the sample block assembly in the vertical
direction. The guide member can be configured to prevent the sample
block assembly from moving in the horizontal direction. Any known
type of guide member may be utilized. In the embodiment shown in
FIGS. 1 and 2A-2C, the guide member includes a plurality of
vertical shafts 96 fixedly attached to the lateral sides of the
sample block assembly 50. As shown in FIG. 1, the vertical shafts
are positioned on each lateral side of the sample well tray holder
30 and sample well tray 14. Each vertical shaft 96 is received
within bearing member 98. Bearing member is stationarily mounted
adjacent the optical detection system. Each vertical shaft 96
slides within a corresponding cylindrical opening in the bearing
member 98. The bearing members 98 and vertical shafts 96 may
include any type of known bearing arrangement.
[0048] Alternatively, in another variation, the vertical shaft
could be stationarily fixed to the thermal cycling device so that
the sample block assembly translates vertically relative to the
vertical shaft. With such an arrangement, the bearing structures
would be mounted within cylindrical openings in the sample block
assembly for receiving the vertical shafts.
[0049] The guide member may be any other type of known guide member
capable of limiting movement of the sample block assembly in the
horizontal direction as the sample block assembly is moved in the
vertical direction. For example, the guide member could include any
type of vertical guiding structure adjacent the sample block
assembly. It should be understood that the guide member shown in
FIGS. 2A-2C is by way of example only.
[0050] An operation of the thermal cycling device for the
embodiment of FIGS. 1 and 2A-2C is further described below. First,
with the sample well tray holder 30 in an outward position as shown
in FIG. 2A, a sample well tray 14 is placed in the sample well tray
holder. The sample well tray can be dropped into the recess defined
by downwardly projecting holder structure 38 shown in FIG. 5. The
sample well tray 14 may be placed in the sample well tray holder 30
either manually or robotically.
[0051] In FIG. 2A, the sample block assembly 50 is in a downward or
"first" position so that a gap is created between the optical
detection system 12 and the uppermost surface of the sample block
58. The gap that is created is larger than the vertical dimension
of the sample well tray holder 30 and sample well tray 14.
[0052] After the sample well tray 14 is placed in the sample well
tray holder 30, the sample well tray holder is horizontally
translated into the thermal cycling device 10 until the sample well
tray reaches a position where the sample wells of the sample well
tray align with the recesses 52 of the sample block 58. The
horizontal translation may be caused by an operator or a robot
pressing on the sample well tray. In the embodiment shown in FIGS.
1 and 2A-2C, the sample well tray holder 30 can be horizontally
translated until each of the ninety-six sample wells align with a
corresponding recess 52 in the sample block 58. FIG. 2B shows the
sample well tray holder 30 and sample well tray 14 in the position
where the sample wells 20 are aligned with corresponding recesses
in the sample block 58. As shown in FIG. 2B, the sample block
assembly 50 can remain in the downward position until the sample
well tray is fully inserted into the thermal cycling device and
aligned.
[0053] After the sample well tray 14 has been fully inserted into
the thermal cycling device 10 and proper alignment has been
achieved between the sample wells 20 and the recesses 52 of the
sample block (as shown in FIG. 2B), the motor 72 can be actuated to
begin a revolution of the first end 80 of the first link 78. As the
first end 80 of the first link 78 begins to revolve around the
central axis 76 of the motor, the pivot point 88 is moved leftward
as shown in FIG. 2C, and the pivot point 92 of the second end of
the third link imparts an upward force on the sample block assembly
50. As a result, the sample block assembly 50 is moved upward so
that the top surface 54 of the sample block firmly contacts the
bottom surface of the sample well tray 14. In the upward position
(also referred to as the "second position") shown in FIG. 2C, the
sample block assembly 50 is firmly positioned against the sample
well tray 14 so that the sample wells 22 are seated against the
sample block. The thermal cycling device 10 is now ready for
thermal cycling processes.
[0054] At any desired time, e.g., after the thermal cycling
processes are completed, the sample well tray 14 can be removed by
actuating the motor so that the sample block assembly 50 moves to a
downward position (as shown in FIG. 2B), and then horizontally
translating the sample well tray holder 30 and sample well tray 14
to the position shown in FIG. 2A. The sample well tray 14 may then
be removed from the sample well tray holder 30.
[0055] The amount of vertical displacement of the sample block
assembly 50 between the downward ("first") and upward ("second")
positions depends on the specific application, the type and size of
sample well tray that is utilized, and other practical concerns.
For example, in an application for use with a 96-well sample well
tray, the amount of vertical displacement would typically be
between about 0.5 to 1.5 inches, but it could be much greater or
much less. In an application with a 384-well sample tray having
smaller sample wells, or a microcard, the amount of vertical
displacement of the sample block assembly may be less. For
practical purposes however, it may also be desirable to vertically
displace the sample block assembly a much greater distance in order
to provide better access to the inside of the device for inspection
or maintenance.
[0056] In accordance with various embodiments, the optical
detection system 12 can be mounted in a substantially stationary
manner in the thermal cycling device during insertion and removal
of the sample well tray to and from the thermal cycling device,
during thermal cycling, and during all steps therebetween.
[0057] In accordance with further various embodiments of the
positioning mechanism, the plurality of links comprises a first
link and a second link. The first link has a first end rotatably
connected to a stationary pivot point. The first link also has a
second end comprising a handle for manual manipulation of the first
link. The second link has a first end rotatably connected to a
pivot point on the first link. The second link also has a second
end rotatably connected to the sample block assembly.
[0058] Further various embodiments of the sample block assembly
positioning mechanism contemplate structure such as shown in FIGS.
3A-3C. The positioning mechanism is generally designated by the
reference number 100 in FIGS. 3A-3C. The positioning mechanism
includes a plurality of links such as first link 102 and second
link 104. As shown in FIG. 3A, the first link 102 has a first end
rotatably connected to a stationary pivot point 106 and a second
end defining a handle 108 for manual manipulation of the first
link. In FIGS. 3A-3C, the first link 102 is in the shape of a
connecting rod with a bend as shown in FIG. 3A. The handle 108 of
the first link 102 defines a door 112 corresponding to an opening
114 in the thermal cycling device. The door 112 is configured to
cover the opening 114 in the thermal cycling device when the handle
is actuated in a manner described below. Although the door is shown
having an arcuate shape on the inner surface, any other suitable
shape is also acceptable.
[0059] As shown in FIG. 3A, the second link 104 has a first end
rotatably connected to a pivot point 118 positioned on first link
102. The second link 104 has a second end rotatably connected to
the sample block assembly 50 at pivot point 120. By the linkage
arrangement described above, the actuation of the handle 108 will
cause the sample block assembly 50 to translate in the vertical
direction.
[0060] An operation of the thermal cycling device for the
embodiment of FIGS. 3A-3C will be briefly described below. To the
extent that the following operation is similar to the operation
described above for the embodiment shown in FIGS. 1 and 2A-2C, a
detailed description of the operation will not be repeated.
Moreover, the same reference numbers will be used to refer to the
same or like parts as shown in the embodiment of FIGS. 1 and 2A-2C.
FIG. 3A shows the sample well tray holder 30 and sample well tray
14 in an outward position. In FIG. 3A, the sample block assembly 50
is in the downward or "first" position. The sample well tray holder
30 is then inserted into the thermal cycling device 10 by
translating in the horizontal direction until the sample well tray
14 reaches its proper aligned position (shown in FIG. 3B) between
the optical detection system and the sample block assembly.
[0061] After the sample well tray 14 reaches its aligned position,
an operator may manually press against the handle 108 to rotate the
first link 102 about the stationary pivot point 106. In another
embodiment, the handle may be rotated robotically. In either case,
the clockwise rotation (in reference to FIGS. 3A-3C) of the first
link 102 results in the pivot point 118 moving upward, thereby
causing the pivot point 120 on the second link 104 to move upward.
The upward movement of the second link results in translation of
the sample block assembly 50 in an upward vertical direction to an
upward or "second" position (shown in FIG. 3C). The positioning
mechanism is configured so that the door 112 is fully closed as
shown in FIG. 3C when the top surface of the sample block firmly
contacts the sample well tray. When the sample block assembly is in
the upward position, as shown in FIG. 3C, the thermal cycling
device is ready for thermal cycling processes.
[0062] At any desired time, e.g., upon completion of the thermal
cycling processes, the handle 108 may be rotated counterclockwise,
thereby translating the sample block assembly 50 back to the
downward position shown in FIG. 3B. The sample well tray holder can
then be slid from the thermal cycling device and returned to the
position shown in FIG. 3A, and the sample well tray 14 may be
removed from the sample well tray holder.
[0063] In accordance with still further embodiments of the
positioning mechanism, the plurality of links can comprise a first
link and a second link. The first link is rotatably connected to a
stationary pivot point. The first link has a first end rotatably
connected to the second link and a second end comprising a handle
for manual manipulation of the first link. The second link has a
first end rotatably connected to the first end of the first link
and a second end rotatably connected to the sample block
assembly.
[0064] Such embodiments of the positioning mechanism include that
shown in FIGS. 4A-4C. As shown in FIGS. 4A-4C, the positioning
mechanism is generally designated by reference number 130. The
positioning mechanism 130 includes a plurality of links such as
first link 132 and second link 134. As shown in FIGS. 4A-4C, the
first link 132 is rotatably connected to a stationary pivot point
136. The first link 132 has a first end rotatably connected to the
second link 134 at a pivot point 138. The first link includes a
second end comprising a handle 140 for manual or automatic
manipulation of the first link 132. The second link 134 includes a
first end rotatably connected to the first end of the first link at
pivot point 138. The second link 134 further includes a second end
rotatably connected to the sample block assembly 50 at pivot point
142.
[0065] As shown in FIGS. 4A-4C, the first link 132 includes a first
segment 144 and a second segment 146. In FIGS. 4A-4C, the first
segment 144 and second segment 146 of the first link are
substantially perpendicular to each other. This angle is by way of
example only, as the linkages may have various configurations. By
the linkage arrangement described above, the actuation of the
handle 140 will cause the sample block assembly to translate in the
vertical direction.
[0066] An operation of the thermal cycling device for the
positioning mechanism of FIGS. 4A-4C will be briefly described
below. To the extent that the following operation is similar to the
operation for the other embodiments described above, a detailed
description of the operation will not be repeated. FIG. 4A shows
the sample well tray holder 30 and sample well tray 14 in an
outward position. In FIG. 4A, the sample block assembly 50 is in
the downward or "first" position. The sample well tray holder 30 is
then inserted into the thermal cycling device 10 by translating in
the horizontal direction until the sample well tray reaches its
proper aligned position (shown in FIG. 4B).
[0067] After the sample well tray reaches its aligned position, an
operator may manually or automatically press downward against the
handle 140 to rotate the first link 132 about the stationary pivot
point 136 in a counterclockwise direction (in reference to FIGS.
4A-4C). This counterclockwise rotation of the first link 132
results in the pivot point 138 moving upwardly thereby causing the
second link 134 to move upwardly. The upward movement of the second
link results in translation of the sample block assembly 50 in an
upward vertical direction to an upward or "second" position. FIG.
4C shows the sample block assembly in the upward or "second"
position. When the sample block assembly is in the upward position,
as shown in FIG. 4C, the thermal cycling device is ready for
thermal cycling processes.
[0068] At any desired time, e.g., upon completion of the thermal
cycling processes, the handle 104 may be rotated clockwise, thereby
translating the sample block assembly 50 back to the downward
position as shown in FIG. 4B. The sample well tray holder 30 can
then be slid from the thermal cycling device and returned to the
position shown in FIG. 4A, and the sample well tray 14 may be
removed from the sample well tray holder.
[0069] The sample block assembly positioning mechanisms shown in
the figures are provided for purposes of example only. Other
positioning mechanisms could be, for example, a hydraulic, a
spring, a lever, a cam, a solenoid, or any other suitable
motion-producing device.
[0070] As is clear from the above description, the present
invention includes a method of performing nucleic acid
amplification on a plurality of biological samples positioned in a
sample well tray in a thermal cycling device. The method includes
the step of placing the sample well tray into a sample well tray
holder. The sample well tray 14 shown in the figures is configured
for placement into a corresponding recess in the sample well tray
holder 30.
[0071] The method further includes the step of translating the
sample well tray holder and sample well tray into the thermal
cycling device until the sample well tray is aligned with a sample
block assembly positioned beneath the sample well tray. In one
aspect, the translation of the sample well tray holder is in the
horizontal direction. The aligned position is shown for example in
FIG. 2B. The method further includes the step of translating the
sample block assembly from a first position to a second position.
In one aspect, the translation of the sample block assembly is in
the vertical direction. In the first position, the sample block
assembly permits the sample well tray to translate into alignment
with the sample block assembly. The first position of the sample
block assembly 50 is shown for example in FIG. 2B. In the second
position, the sample block assembly is positioned vertically upward
relative to the first position in order to contact the sample block
assembly to the sample well tray. The second position of the sample
block assembly 50 is shown for example in FIG. 2C.
[0072] The method further comprises thermally cycling the device
while simultaneously optically detecting the samples. An optical
detection system 12 is positioned within the thermal cycling device
10 for detecting the characteristics of the sample. The method
further comprises translating the sample block assembly from the
second position to the first position. Finally, the method
comprises the step of removing the sample well tray from the
thermal cycling device. The optical detection system remains
substantially stationary throughout the above steps.
[0073] It is clear that the present invention is not limited to the
examples shown. For example, a thermal cycling device could be
configured to handle several sample well trays, e.g., positioned
side by side. Such an arrangement could include a corresponding
optical system and sample block.
[0074] It will be apparent to those skilled in the art that various
modifications and variations can be made to the structure. Thus, it
should be understood that the invention is not limited to the
examples discussed in the specification. Rather, the present
invention is intended to cover modifications and variations.
* * * * *