U.S. patent application number 13/909000 was filed with the patent office on 2013-12-19 for multilevel microfluidic systems and methods.
This patent application is currently assigned to Fluidigm Corporation. The applicant listed for this patent is Fluidigm Corporation. Invention is credited to Geoffrey Facer, Brian Fowler, Emerson Cheung Quan, Marc Unger.
Application Number | 20130337457 13/909000 |
Document ID | / |
Family ID | 41162251 |
Filed Date | 2013-12-19 |
United States Patent
Application |
20130337457 |
Kind Code |
A1 |
Facer; Geoffrey ; et
al. |
December 19, 2013 |
Multilevel Microfluidic Systems and Methods
Abstract
Multilevel microfluidic devices include a control line that can
simultaneously actuate valves for both sample and reagent lines.
Microfluidic devices are configured to contain a first reagent in a
first chamber and a second reagent in a second chamber, where
either or both of the first and second reagents are contained at a
desired or selected pressure. Operation of a microfluidic device
includes transmitting second reagent from the second chamber to the
first chamber, for mixing or contact with the first reagent.
Microfluidic device features such as channels, valves, chambers,
can be at least partially contained, embedded, or formed by or
within one or more layers or levels of an elastomeric block.
Inventors: |
Facer; Geoffrey; (Lane Cove,
AU) ; Fowler; Brian; (San Mateo, CA) ; Quan;
Emerson Cheung; (San Francisco, CA) ; Unger;
Marc; (San Mateo, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Fluidigm Corporation |
South San Francisco |
CA |
US |
|
|
Assignee: |
Fluidigm Corporation
South San Francisco
CA
|
Family ID: |
41162251 |
Appl. No.: |
13/909000 |
Filed: |
June 3, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
12422612 |
Apr 13, 2009 |
8475743 |
|
|
13909000 |
|
|
|
|
61044417 |
Apr 11, 2008 |
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Current U.S.
Class: |
435/6.12 |
Current CPC
Class: |
C12Q 1/686 20130101;
B01L 3/502738 20130101; Y10T 137/2559 20150401; B01L 2300/0627
20130101; B01L 2300/0874 20130101; B01L 3/502707 20130101; B01L
2200/16 20130101; F16K 99/0026 20130101; Y10T 137/0329 20150401;
Y10T 137/2169 20150401; B01F 5/02 20130101; B01L 2300/123 20130101;
B01F 13/0059 20130101; B33Y 80/00 20141201; B01L 2200/10 20130101;
F16K 99/0059 20130101; Y10T 137/87249 20150401; Y10T 137/2164
20150401; G01N 2021/0346 20130101; Y10T 137/2688 20150401; B01L
2400/0481 20130101; B01L 2300/0887 20130101; B01L 2300/0816
20130101; B01L 2400/0638 20130101; F16K 2099/008 20130101; F16K
99/0015 20130101; F16K 2099/0084 20130101; Y10T 137/2655 20150401;
B01L 2200/12 20130101 |
Class at
Publication: |
435/6.12 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A method of mixing materials in a microfluidic device,
comprising: flowing a first material through a first flow channel
formed in a first layer of a substrate; flowing the first material
through a first isolation valve, wherein the first isolation valve
is disposed along the first flow channel, comprises a first portion
of a control channel formed in a second layer of the substrate
adjacent to the first layer, and is configured to control flow
through the first flow channel into a first chamber; flowing the
first material from the first flow channel into the first chamber;
flowing a second material through a second flow channel formed in a
third layer of the substrate adjacent to the second layer; flowing
the second material through a second isolation valve, wherein the
second isolation valve is disposed along the second flow channel,
comprises a second portion of the control channel formed in a
second layer of the substrate, and is configured to control flow
through the second flow channel into the second chamber; flowing
the second material from the second flow channel into the second
chamber; actuating the control channel so as to inhibit flow
through the first and second isolation valves; flowing the first
material from the first chamber through an interface valve into the
second chamber, so as to mix the first material with the second
material, wherein the interface valve comprises a portion of an
interface channel formed in a fourth layer of the substrate
adjacent to the third layer, and is configured to control between
the first chamber and the second chamber.
2. The method of claim 2, wherein the first isolation valve
comprises a first deflectable membrane, the second isolation valve
comprises a second deflectable membrane, and actuating the control
channel comprises actuating the first and second deflectable
membranes.
3. The method of claim 2, further comprising actuating an interface
channel to provide fluid communication between the first chamber
and the second chamber.
4. The method of claim 3, wherein the interface valve comprises a
portion of an interface channel formed in a fourth layer of the
substrate adjacent to the third layer, and is configured to control
flow through a reaction channel formed in the third layer.
5. The method of claim 3, wherein the interface valve comprises a
deflectable membrane, and actuating the interface channel comprises
actuating the deflectable membrane.
6. The method of claim 3, comprising holding the first material in
the first chamber at first pressure and holding the second material
in the second chamber at a second pressure, prior to flowing the
first material into the second chamber.
7. The method of claim 6, wherein the first pressure is greater
than the second pressure.
8. The method of claim 6, wherein the first pressure is about 10
psi and the second pressure is about 0 psi.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. patent application
Ser. No. 12/422,612, filed Apr. 13, 2009, which claims the benefit
U.S. Provisional Application No. 61/044,417, filed Apr. 11, 2008.
This application is also related to U.S. patent application Ser.
No. 11/043,895 filed Jan. 25, 2005 (Attorney Docket No.
020174-012800US). The entire content of each of the
above-referenced filings is incorporated herein by reference.
BACKGROUND OF THE INVENTION
[0002] Embodiments of the present invention relate to the fields of
microfluidics, lab-on-a-chip, Polymerase Chain Reactions ("PCR"),
biochemical analysis, protein crystallization and screening for
protein crystallization conditions, microfabrication, laboratory
robotics, immunoassays, and automated biological screening and
analysis, among others.
[0003] Microfluidic devices can be defined as devices having one or
more fluidic pathways, often called channels, microchannels,
trenches, lines, or recesses, having a cross-sectional dimension
below 1000 .mu.m, and which offer benefits such as increased
throughput and reduction of reaction volumes. Relatedly, there is a
continuing trend toward increasing the number of reactions that can
be performed with a microfluidic device. For example, it is often
desirable to provide devices having a high density of reaction
chambers. Despite significant recent advances in microfluidic
technology, existing fabrication techniques often present obstacles
which preclude the development of even more efficient devices.
[0004] Hence, there remains a continuing need for improved
manufacturing methods for producing microfluidic devices having a
higher density of reaction or detection zones per unit area of the
microfluidic device. At least some of these objectives will be met
by embodiments of the present invention.
BRIEF SUMMARY OF THE INVENTION
[0005] Embodiments of the present invention provide microfluidic
devices having a high density of reaction chambers or zones per
unit area, as well as methods for their use and manufacture. Such
devices can be made smaller than existing devices, and often
provide improved performance characteristics. The general benefits
of using microfluidic systems include a substantial reduction in
time, cost, and space requirements for the devices utilized to
conduct the analysis or synthesis. For example, many diagnostic
assays require the use of expensive reagents, and it may be
difficult or expensive to obtain large testing samples. Devices
which can utilize smaller amounts of reagent and sample are able to
provide more data points at a lower cost. Exemplary embodiments are
well suited for use in crystal formation and amplification
reactions. In some cases, microfluidic devices may have a control
line that can simultaneously actuate valves for both sample and
reagent lines. Relatedly, microfluidic devices may be configured to
contain a first reagent in a first chamber and a second reagent in
a second chamber, where either or both of the first and second
reagents are contained at a desired or selected pressure. In some
cases, operation of the microfluidic device includes transmitting
second reagent from the second chamber to the first chamber, for
mixing or contact with the first reagent. Microfluidic device
features such as channels, valves, chambers, can be at least
partially contained, embedded, or formed by or within one or more
layers or levels of an elastomeric block.
[0006] In one aspect, embodiments of the present invention
encompass microfluidic devices having a first flow channel, a
second flow channel, and a control channel. The first flow channel
can be formed in a first layer of an elastomeric substrate, the
control channel can be formed in a second layer of an elastomeric
substrate, and the second flow channel can be formed in a third
layer of an elastomeric substrate. Often, the second layer is
adjacent to the first layer, and the third layer is adjacent to the
second layer. A change in pressure within the first control channel
can modulate fluid flow within the first and second flow channels.
Microfluidic devices can also include a first isolation valve
disposed along the first flow channel, where the first control
channel controls operation of the first isolation valve. The first
isolation valve may include a deflectable membrane. Microfluidic
devices can also include a second isolation valve disposed along
the second flow channel, where the first control channel controls
operation of the second isolation valve. The second isolation valve
may include a deflectable membrane. Microfluidic devices may also
include a first chamber disposed at least partially within the
first layer, and a second chamber disposed at least partially
within the first layer. The first chamber can be in fluid
communication with the first flow channel. The second chamber can
be in fluid communication with the second flow channel. In some
embodiments, a change in pressure within the first control channel
simultaneously modulates fluid flow within the first and second
flow channels.
[0007] In another aspect, embodiments of the present invention
encompass a microfluidic device having an elastomeric substrate
with multiple layers. For example, the elastomeric substrate can
have a first layer, a second layer, and a third layer, where the
second layer is disposed between the first and third layers. The
device can also include a first chamber formed at least partially
within the first layer of the elastomeric substrate, and a second
chamber formed at least partially within the first layer of the
elastomeric substrate. Further, the device may include a first
control channel formed in the second layer of the elastomeric
substrate. Often, the device is configured so that a change in
pressure within the first control channel modulates a first fluid
flow passing through the first layer and into the first chamber,
and also modulates a second fluid flow passing through the third
layer and into the second chamber. In some instances, the device
includes an interface channel that provides fluid communication
between the first chamber and the second chamber. For example, the
interface channel may be formed in the third layer. In some cases,
the interface channel is in fluid communication with the second
flow channel. The device may also include an interface valve
disposed along the interface channel. The interface valve may
modulate flow through the interface channel between the first and
second chambers. In some embodiments, the interface valve comprises
a deflectable membrane.
[0008] In one aspect, embodiments of the present invention provide
a microfluidic device. The device can include a first flow channel
formed in a first layer of an elastomeric substrate, a first
chamber in fluid communication with the first flow channel, and a
first isolation valve disposed along the first flow channel. The
first isolation valve can include a first portion of a control
channel formed in a second layer of the elastomeric substrate
adjacent to the first layer. The first isolation valve can be
configured to control flow through the first flow channel into the
first chamber. The device may also include a second flow channel
formed in a third layer of the elastomeric substrate adjacent to
the second layer, a second chamber in fluid communication with the
second flow channel, and a second isolation valve disposed along
the second flow channel. The second isolation valve can include a
second portion of the control channel formed in a second layer of
the elastomeric substrate. The second isolation valve can be
configured to control flow through the second flow channel into the
second chamber. The device can also include a reaction channel
formed in the third layer of the elastomeric substrate, in fluid
communication with the first chamber and the second chamber, and an
interface valve disposed along the reaction channel between the
first and second chamber. The interface valve can include a portion
of an interface channel formed in a fourth layer of the elastomeric
substrate adjacent to the third layer, and can be configured to
control flow through the reaction channel. In some embodiments, the
first isolation valve includes a deflectable membrane. In some
embodiments, the second isolation valve includes a deflectable
membrane. In some embodiments, the interface valve includes a
deflectable membrane. The first chamber can define a first chamber
volume, the second chamber can define a second chamber volume. In
some cases, the first chamber volume is less than the second
chamber volume. In some cases, the first chamber volume is greater
than the second chamber volume. In some cases, the first chamber
volume is equal to the second chamber volume.
[0009] In another aspect, embodiments of the present invention
encompass methods of mixing or reacting materials in a microfluidic
device. An exemplary mixing technique includes flowing a first
material through a first flow channel formed in a first layer of an
elastomeric substrate, and flowing the first material through a
first isolation valve. The first isolation valve can be disposed
along the first flow channel, can include a first portion of a
control channel formed in a second layer of the elastomeric
substrate adjacent to the first layer, and can be configured to
control flow through the first flow channel into a first chamber.
The technique can also include flowing the first material from the
first flow channel into the first chamber. Further, the mixing
process can include flowing a second material through a second flow
channel formed in a third layer of the elastomeric substrate
adjacent to the second layer, and flowing the second material
through a second isolation valve. The second isolation valve can be
disposed along the second flow channel, can include a second
portion of the control channel formed in a second layer of the
elastomeric substrate, and can be configured to control flow
through the second flow channel into the second chamber. The mixing
procedure can also include flowing the second material from the
second flow channel into the second chamber, actuating the control
channel so as to inhibit flow through the first and second
isolation valves, and flowing the first material from the first
chamber through an interface valve into the second chamber, so as
to mix the first material with the second material. The interface
valve can include a portion of an interface channel formed in a
fourth layer of the elastomeric substrate adjacent to the third
layer, and can be configured to control flow between the first
chamber and the second chamber. In some embodiments, a first
isolation valve includes a first deflectable membrane, a second
isolation valve includes a second deflectable membrane, and the
process of actuating the control channel includes actuating the
first and second deflectable membranes. In some embodiments, mixing
techniques can include actuating an interface channel to provide
fluid communication between the first chamber and the second
chamber. An interface valve can include a portion of an interface
channel formed in a fourth layer of the elastomeric substrate
adjacent to the third layer, and can be configured to control flow
through a reaction channel formed in the third layer. In some
cases, an interface valve can include a deflectable membrane, and
the process of actuating the interface channel can include
actuating the deflectable membrane. Exemplary mixing techniques may
also include holding the first material in the first chamber at
first pressure and holding the second material in the second
chamber at a second pressure, prior to flowing the first material
into the second chamber. In some cases, the first pressure is
greater than the second pressure. In some cases, the first pressure
can be about 10 psi and the second pressure can be about 0 psi.
[0010] In yet another aspect, embodiments of the present invention
include a microfluidic device having a plurality of first flow
channels formed in a first layer of an elastomeric substrate, and a
plurality of first chambers. Each one of the plurality of first
chambers can be in fluid communication with a corresponding first
flow channel of the plurality of first flow channels. A
microfluidic device can also include a plurality of control
channels formed in a second layer of the elastomeric substrate
adjacent to the first layer, and a plurality of first isolation
valves. Each one of the plurality of first isolation valves can be
disposed along a corresponding first flow channel of the plurality
of first flow channels, can include a first portion of a
corresponding control channel of the plurality of control channels,
and can be configured to control flow through the corresponding
first flow channel into a corresponding first chamber of the
plurality of first chambers. Further, a microfluidic device can
have a plurality of second flow channels formed in a third layer of
the elastomeric substrate adjacent to the second layer, and a
plurality of second chambers. Each one of the plurality of second
chambers can be in fluid communication with a corresponding second
flow channel of the plurality of second flow channels. A
microfluidic device can also have a plurality of second isolation
valves. Each one of the plurality of second isolation valves can be
disposed along a corresponding second flow channel of the plurality
of second flow channels, can include a second portion of the
corresponding control channel of the plurality of control channels,
and can be configured to control flow through the corresponding
second flow channel into a corresponding second chamber of the
plurality of second chambers. Still further, a microfluidic device
can have a plurality of reaction channels formed in the third layer
of the elastomeric substrate. Each one of the plurality of reaction
channels can be in fluid communication with a corresponding first
chamber of the plurality of first chambers and a corresponding
second chamber of the plurality of second chambers. A microfluidic
device may also include a plurality of interface valves. Each one
of the plurality of interface valves can be disposed along a
corresponding reaction channel of the plurality of reaction
channels between the corresponding first chamber and the
corresponding second chamber, can include a portion of a
corresponding interface channel of a plurality of interface
channels formed in a fourth layer of the elastomeric substrate
adjacent to the third layer, and can be configured to control flow
through the corresponding reaction channel.
[0011] In a still further aspect, embodiments of the present
invention encompass a microfluidic device having a first flow
channel formed in a first layer of an elastomeric substrate, a
first control channel formed in a second layer of an elastomeric
substrate, and a second flow channel formed in a third layer of an
elastomeric substrate. The second layer can be adjacent to and
between the first layer and the third layer. The microfluidic
device can be configured so that a change in pressure within the
first control channel simultaneously modulates fluid flow within
the first and second flow channels.
[0012] For a fuller understanding of the nature and advantages of
the present invention, reference should be had to the ensuing
detailed description taken in conjunction with the accompanying
drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] FIG. 1 depicts a perspective view of a unit cell of a
microfluidic device according to embodiments of the present
invention.
[0014] FIG. 1A shows an exploded perspective view of individual
layers of a unit cell of a microfluidic device according to
embodiments of the present invention.
[0015] FIGS. 1B to 1E show microfluidic molds according to
embodiments of the present invention.
[0016] FIG. 2 illustrates a perspective view of unit cell of a
microfluidic device according to embodiments of the present
invention.
[0017] FIG. 3 illustrates a perspective view of a microfluidic
device matrix having multiple unit cells according to embodiments
of the present invention.
[0018] FIG. 4 illustrates a perspective view of a microfluidic
device matrix having multiple unit cells according to embodiments
of the present invention.
[0019] FIGS. 5A to 5C show cross-section views of a microfluidic
device unit cell according to embodiments of the present
invention.
[0020] FIGS. 6A and 6B show a microfluidic device according to
embodiments of the present invention.
[0021] FIG. 7 illustrates a microfluidic device according to
embodiments of the present invention.
[0022] FIG. 8 illustrates a microfluidic device according to
embodiments of the present invention.
[0023] FIG. 9 illustrates a photomicrograph, with scale bar, of an
exemplary microfluidic device according to embodiments of the
present invention.
[0024] FIG. 10 illustrates a reader image of an exemplary
microfluidic device according to embodiments of the present
invention.
[0025] FIG. 11 illustrates a reader image of an exemplary
microfluidic device according to embodiments of the present
invention.
[0026] FIG. 12 illustrates a reader image of an exemplary
microfluidic device according to embodiments of the present
invention.
[0027] FIG. 13 illustrates an exemplary microfluidic device,
showing channel connections between input wells and an elastomeric
block, according to embodiments of the present invention.
[0028] FIG. 14 illustrates aspects of a microfluidic system and
method according to embodiments of the present invention.
DETAILED DESCRIPTION OF THE INVENTION
[0029] It is understood that the invention is not limited to the
particular methodology, protocols, and reagents, etc., described
herein, as these may vary as the skilled artisan will recognize. It
is also to be understood that the terminology used herein is used
for the purpose of describing particular embodiments only, and is
not intended to limit the scope of the invention. It is also to be
noted that as used herein and in the appended claims, the singular
forms "a," "an," and "the" include the plural reference unless the
context clearly dictates otherwise. Thus, for example, a reference
to "a cell" is a reference to one or more cells and equivalents
thereof known to those skilled in the art.
[0030] Unless defined otherwise, all technical and scientific terms
used herein have the same meanings as commonly understood by one of
ordinary skill in the art to which the invention pertains. The
embodiments of the invention and the various features and
advantageous details thereof are explained more fully with
reference to the non-limiting embodiments and examples that are
described and/or illustrated in the accompanying drawings and
detailed in the following description. It should be noted that the
features illustrated in the drawings are not necessarily drawn to
scale, and features of one embodiment may be employed with other
embodiments as the skilled artisan would recognize, even if not
explicitly stated herein. Descriptions of well-known components and
processing techniques may be omitted so as to not unnecessarily
obscure the embodiments of the invention. The examples used herein
are intended merely to facilitate an understanding of ways in which
the invention may be practiced and to further enable those of skill
in the art to practice the embodiments of the invention.
Accordingly, the examples and embodiments herein should not be
construed as limiting the scope of the invention, which is defined
solely by the appended claims and applicable law. Moreover, it is
noted that like reference numerals reference similar parts
throughout the several views of the drawings.
[0031] Accordingly, provided immediately below is a "Definition"
section, where certain terms related to the invention are defined
specifically for clarity, but all of the definitions are consistent
with how a skilled artisan would understand these terms. Particular
methods, devices, and materials are described, although any methods
and materials similar or equivalent to those described herein can
be used in the practice or testing of the invention. All references
referred to herein are incorporated by reference herein in their
entirety.
DEFINITIONS
[0032] PNA is peptide nucleic acid
[0033] LNA is locked nucleic acid
[0034] DA is dynamic array
[0035] PCR is polymerase chain reaction
[0036] BSA is bovine serum albumin
[0037] FRET is fluorescence resonance energy transfer
[0038] GT is genotyping
[0039] PEG is polyethylene glycol
[0040] PLP is padlock probe
[0041] The term "adjacent" as used herein, generally refers to the
positioning of the primer with respect to the probe on its
complementary strand of the target nucleic acid analyte. The primer
and probe may be separated in a range of about 1 to about 20
nucleotides, more specifically, in a range of about 1 to about 10
nucleotides, or may directly abut one another.
[0042] The term "analyte" as used herein, generally refers to a
nucleic acid molecule or mixture of nucleic acid molecules, defined
infra, that is to be detected or quantified using the methods of
the invention. The terms "target nucleic acid analyte" and "nucleic
acid analyte" are used interchangeably with the term "analyte" for
the purposes of this invention.
[0043] The terms "complementary" or "complementarity" as used
herein, may include the natural binding of polynucleotides under
permissive salt and temperature conditions by base-pairing. For
example, the sequence "A-G-T" binds to the complementary sequence
"T-C-A." Complementarity between two single-stranded molecules may
be "partial," in which only some of the nucleic acids bind, or it
may be complete when total complementarity exists between the
single stranded molecules. The degree of complementarity between
nucleic acid strands has significant effects on the efficiency and
strength of hybridization between nucleic acid strands. This is of
particular importance in amplification reactions, which depend upon
binding between nucleic acids strands and in the design and use of
molecules.
[0044] The term "covalently attached" as used herein, generally
refers to an attachment of one molecular moiety to another
molecular moiety through covalent chemical bonds.
[0045] The term "dye" as used herein, generally refers to any
organic or inorganic molecule that absorbs electromagnetic
radiation at a wavelength greater than or equal 340 nm.
[0046] The term "fluorescent dye" as used herein, generally refers
to any dye that emits electromagnetic radiation of longer
wavelength by a fluorescent mechanism upon irradiation by a source
of electromagnetic radiation, such as a lamp, a photodiode, or a
laser.
[0047] The term "GT sample buffer," as used herein generally refers
to a buffer that is capable of blocking binding sites on the
surface of the reaction channels and chambers in a DA chip. The
buffer protects the reaction components from depletion during the
chip loading process or reaction. It may also reduce the usage of
additional Taq-Gold Polymerase by less than about 80% for reagent
costs. A 20.times.GT buffer may include a combination of betaine
(FW 117.15), BSA, Superblock.RTM. T20 (in PBS) (Thermo Scientific,
Rockford, Ill.), Superblock.RTM. (in PBS) (Thermo Scientific,
Rockford, Ill.), Superblock.RTM. (in TBS) (Thermo Scientific,
Rockford, Ill.), Superblock.RTM. T20 (in TBS) (Thermo Scientific,
Rockford, Ill.), glycerol, PEG 20,000, PEG MME550, PEG MME5000, and
Tween 20.
[0048] The term "homogenous assay" as used herein, generally refers
to a method to detect or quantify a nucleic acid analyte that
requires no post-assay processing to record the result of the
assay. The homogenous assays may be carried out in closed tubes or
microfluidic arrays where no further addition of reagents or
supplementary chemicals are necessary to record the result once the
assay is started. Homogenous assays allow recordation of the result
of the assay in real time, meaning that the result of the assay can
be continuously recorded as the assay progresses in time.
[0049] The term "hydrolysis probes" as used herein are generally
described in U.S. Pat. No. 5,210,015 incorporated herein by
reference in its entirety. Hydrolysis probes take advantage of the
5'-nuclease activity present in the thermostable Taq polymerase
enzyme used in the PCR reaction (TaqMan.RTM. probe technology,
Applied Biosystems, Foster City Calif.). The hydrolysis probe is
labeled with a fluorescent detector dye such as fluorescin, and an
acceptor dye or quencher. In general, the fluorescent dye is
covalently attached to the 5' end of the probe and the quencher is
attached to the 3' end of the probe, and when the probe is intact,
the fluorescence of the detector dye is quenched by fluorescence
resonance energy transfer (FRET). The probe may anneal downstream
of one of the primers that defines one end of the amplification
target site on the nucleic acid target analyte in the PCR reaction.
Using the polymerase activity of the Taq enzyme, amplification of
the target nucleic acid analyte is directed by one primer that is
upstream of the probe and a second primer that is downstream of the
probe but anneals to the opposite strand of the target nucleic
acid. As the upstream primer is extended, the Taq polymerase
reaches the region where the labeled probe is annealed, recognizes
the probe-template hybrid as a substrate, and hydrolyzes
phosphodiester bonds of the probe. The hydrolysis reaction
irrevocably releases the quenching effect of the quencher dye on
the reporter dye, thus resulting in increasing detector
fluorescence with each successive PCR cycle. In particular, the
hydrolysis probes of the invention may capable of detecting 8-mer
or 9-mer motifs that are common in the human and other
transcriptomes and may have a high T.sub.m of about 70.degree. C.
enabled by LNA analogs.
[0050] The term "label" as used herein refers to any atom or
molecule which can be used to provide a detectable and/or
quantifiable signal. In particular, the label can be attached to a
nucleic acid or protein. Labels may provide signals detectable by
fluorescence, radioactivity, colorimetric, X-ray diffraction or
absorption, magnetism, enzymatic activity, and the like.
[0051] The term "nucleic acid" as used herein generally refers to
cDNA, DNA, RNA, single-stranded or double-stranded and any chemical
modification thereof, such as PNA and LNA. LNAs are described in
U.S. Pat. Nos. 6,794,499, 6,670,461, 6,262,490, and 6,770,748
herein incorporated by reference in their entirety. Nucleic acids
may be of any size. Nucleic acid modifications may include addition
of chemical groups that incorporate additional charge,
polarizability, hydrogen bonding, electrostatic interaction, and
functionality to the individual nucleic acid bases or to the
nucleic acid as a whole. Such modifications may include modified
bases such as 2'-position sugar modifications, 5-position
pyrimidine modifications, 8-position purine modifications,
modifications at cytosine exocylcic amines, substitutions of
5-bromo-uracil, backbone modifications, methylations, unusual base
pairing combinations such as the isobases isocytidine and
isoguanidine and the like. The nucleic acid can be derived from a
completely chemical synthesis process, such as a solid phase
mediated chemical synthesis, or from a biological origin, such as
through isolation from almost any species that can provide nucleic
acid, or from processes that involve the manipulation of nucleic
acids by molecular biology tools, such as DNA replication, PCR
amplification, reverse transcription, or from a combination of
those processes.
[0052] The term "nucleic acid probe" as used herein is a nucleic
acid that carriers at least one covalently attached dye, such as a
fluorescent dye. In particular, the probe does not contain a
sequence complementary to sequences used to prime the PCR
reaction.
[0053] The term "padlock probe" or "PLP" as used herein, generally
refers to linear oligonucleotides having a length of about 100 base
pairs. The sequences at the 3' and 5' ends of the PLP are
complementary to adjacent sequences in the target nucleic acid
analyte. In the central, noncomplementary region of the PLP there
is a "tag sequence" that may be used to identify the specific PLP.
The tag sequence may be flanked by universal primer sites or unique
and/or specific primer sites, which allow PCR amplification of the
tag sequence. Upon hybridization to the target, the 5' and 3' ends
of the PLP are brought into close proximity and may be subsequently
ligated. The resulting product is a circular probe molecule
catenated to the target nucleic acid analyte. The tag regions of
circularized PLPs may be amplified and quantified and/or detected
using TAQMAN.RTM. Real Time PCR, for example. The presence and
amount of amplicon may be correlated with the presence and quantity
of target sequence in the sample. For descriptions of PLPs see,
e.g., Landegren et al., 2003, Padlock and proximity probes for in
situ and array-based analyses: tools for the post-genomic era,
Comparative and Functional Genomics 4:525-30; Nilsson et al., 2006,
Analyzing genes using closing and replicating circles Trends
Biotechnol. 24:83-8; Nilsson et al., 1994, Padlock probes:
circularizing oligonucleotides for localized DNA detection, Science
265:2085-8. The above references are incorporated by reference
herein in their entirety.
[0054] The term "PCR," as used herein, generally refers to a method
for amplifying, detecting, or quantifying a specific region of an
analyte. One skilled in the art appreciates that there are several
variations on the basic PCR technique such as allele-specific PCR,
assembly PCR or polymerase cycling assembly (PCA), colony PCR,
helicase-dependent amplification, hot start PCR,
intersequence-specific (ISSR) PCR, inverse PCR, ligation-mediated
PCR, methylation-specific PCR, multiplex ligation dependent probe
amplification, multiplex PCR, nested PCR, overlap-extension PCR,
quantitative PCR, quantitative real-time PCR, RT-PCR, thermal
asymmetric interlaces (TAIL) PCR, touchdown PCR, and PAN-AC.
Additionally, one skilled in the art would understand how to
practice these variations on the basic PCR technique.
[0055] The phase "preliminary amplification reaction" as used
herein, generally refers to processes for preparing the sample
prior to running the homogenous assay. The term "pre-amplified
sample" may be used interchangeably with the phrase "preliminary
amplification reaction" for the purposes of the invention
herein.
[0056] The term "purification," as used herein, generally refers to
any process by which proteins, polypeptides, or nucleic acids are
separated from other elements or compounds on the basis of charge,
molecular size, or binding affinity.
[0057] The term "quencher" as used herein, generally refers to dye
that reduces the emission of fluorescence of another dye.
[0058] The term "querying" as used herein, generally refers to
determining whether a target-specific probe is associated with
(e.g., bound to or cantenated with) the nucleic acid analyte, and
optionally quantifying the amount of target-specific probe in the
sample.
[0059] A "sample" as used herein, generally refers to a sample of
tissue or fluid from a human or animal including, but not limited
to plasma, serum, spinal fluid, lymph fluid, the external sections
of the skin, respiratory, intestinal and genitourinary tracts,
tears, saliva, blood cells, tumors, organs, tissue and sample of in
vitro cell culture constituents. In particular, the sample may be
single cells, paraffin embedded tissue samples, and needle
biopsies. Moreover, a sample may include environmental samples such
as lake water, and food samples.
[0060] The phrase "substantially purified," or "substantially
isolated," as used herein generally includes nucleic or amino acid
sequences that are removed from their natural environment, isolated
or separated, and are at least about 60% free, specifically at
least about 75% free, and most specifically at least about 90% free
from other components with which they may be associated with, and
includes recombinant or cloned nucleic acid isolates and chemically
synthesized analogs or analogs biologically synthesized by
systems.
[0061] Given the tremendous diversity of polymer chemistries,
precursors, synthetic methods, reaction conditions, and potential
additives, there are a huge number of possible elastomer systems
that could be used to make elastomeric blocks, layers, membranes,
microvalves, pumps, and the like. Variations in the materials used
may in some cases be driven by the need for particular material
properties, i.e. solvent resistance, stiffness, gas permeability,
or temperature stability. There are many, many types of elastomeric
polymers. A brief description of the most common classes of
elastomers is presented here, with the intent of showing that even
with relatively "standard" polymers, many possibilities for bonding
exist. Common elastomeric polymers include polyisoprene,
polybutadiene, polychloroprene, polyisobutylene,
poly(styrene-butadiene-styrene), the polyurethanes, and silicones
or polysiloxanes.
[0062] Polyisoprene, polybutadiene, and polychloroprene are all
polymerized from diene monomers, and therefore have one double bond
per monomer when polymerized. This double bond allows the polymers
to be converted to elastomers by vulcanization (generally, sulfur
is used to form crosslinks between the double bonds by heating).
This would easily allow homogeneous multilayer soft lithography by
incomplete vulcanization of the layers to be bonded; photoresist
encapsulation would be possible by a similar mechanism.
[0063] Pure polyisobutylene has no double bonds, but is crosslinked
to use as an elastomer by including a small amount (.about.1%) of
isoprene in the polymerization. The isoprene monomers give pendant
double bonds on the polyisobutylene backbone, which may then be
vulcanized as above.
[0064] Poly(styrene-butadiene-styrene) is produced by living
anionic polymerization (that is, there is no natural
chain-terminating step in the reaction), so "live" polymer ends can
exist in the cured polymer. This makes it a natural candidate for a
photoresist encapsulation system (where there will be plenty of
unreacted monomer in the liquid layer poured on top of the cured
layer). Incomplete curing would allow homogeneous multilayer soft
lithography (A to A bonding). The chemistry also facilitates making
one layer with extra butadiene ("A") and coupling agent and the
other layer ("B") with a butadiene deficit (for heterogeneous
multilayer soft lithography). SBS is a "thermoset elastomer",
meaning that above a certain temperature it melts and becomes
plastic (as opposed to elastic); reducing the temperature yields
the elastomer again. Thus, layers can be bonded together by
heating.
[0065] Polyurethanes are produced from di-isocyanates (A-A) and
di-alcohols or di-amines (B-B); since there are a large variety of
di-isocyanates and di-alcohols/amines, the number of different
types of polyurethanes is huge. The A vs. B nature of the polymers,
however, make them useful for heterogeneous multilayer soft
lithography just as RTV 615 is: by using excess A-A in one layer
and excess B-B in the other layer.
[0066] Silicone polymers have great structural variety, and provide
a great number of commercially available formulations. The
vinyl-to-(Si--H) crosslinking of RTV 615 (which allows both
heterogeneous multilayer soft lithography and photoresist
encapsulation) has already been discussed, but this is only one of
several crosslinking methods used in silicone polymer
chemistry.
[0067] In addition to the use of the simple "pure" polymers
discussed above, crosslinking agents may be added. Some agents
(like the monomers bearing pendant double bonds for vulcanization)
are suitable for allowing homogeneous (A to A) multilayer soft
lithography or photoresist encapsulation; in such an approach the
same agent is incorporated into both elastomer layers.
Complementary agents (i.e. one monomer bearing a pendant double
bond, and another bearing a pendant Si--H group) are suitable for
heterogeneous (A to B) multilayer soft lithography. In this
approach complementary agents are added to adjacent layers.
[0068] The following is a non-exclusive list of elastomeric
materials which may be utilized in connection with the present
invention: polyisoprene, polybutadiene, polychloroprene,
polyisobutylene, poly(styrene-butadiene-styrene), the
polyurethanes, and silicone polymers; or
poly(bis(fluoroalkoxy)phosphazene) (PNF, Eypel-F),
poly(carborane-siloxanes) (Dexsil), poly(acrylonitrile-butadiene)
(nitrile rubber), poly(1-butene),
poly(chlorotrifluoroethylene-vinylidene fluoride) copolymers
(Kel-F), poly(ethyl vinyl ether), poly(vinylidene fluoride),
poly(vinylidene fluoride-hexafluoropropylene) copolymer (Viton),
elastomeric compositions of polyvinylchloride (PVC), polysulfone,
polycarbonate, polymethylmethacrylate (PMMA), and
polytertrafluoroethylene (Teflon).
[0069] Allcock et al, Contemporary Polymer Chemistry, 2nd Ed.
describes elastomers in general as polymers existing at a
temperature between their glass transition temperature and
liquefaction temperature. Elastomeric materials exhibit elastic
properties because the polymer chains readily undergo torsional
motion to permit uncoiling of the backbone chains in response to a
force, with the backbone chains recoiling to assume the prior shape
in the absence of the force. In general, elastomers deform when
force is applied, but then return to their original shape when the
force is removed. The elasticity exhibited by elastomeric materials
may be characterized by a Young's modulus. Materials having a
Young's modulus of between about 1 Pa to about 1 TPa, or between
about 10 Pa to about 100 GPa, or between about 20 Pa to about 1
GPa, or between about 50 Pa to about 10 MPa, or between about 100
Pa to about 1 MPa are useful in accordance with embodiments of the
present invention, although materials having a Young's modulus
outside of these ranges could also be utilized depending upon the
needs of a particular application. In some cases, materials can
have a Young's modulus of about 100 MPA (megapascals) or less. In
other embodiments, the Young's modulus of the material is about 75
MPA or less, about 50 MPa or less, about 25 MPa or less, about 10
MPa or less, about 8 MPa or less, about 5 MPa or less, or about 2
MPa or less.
[0070] Embodiments of the present invention provide a microfluidic
device that includes features such as channels, valves, and
chambers, that are at least partially contained, embedded, or
formed by or within one or more layers or levels of an elastomeric
block. An exemplary microfluidic device has a reagent flow channel,
or reagent line, formed in a first layer of an elastomer. The
reagent flow channel includes a containment valve and a chamber
conduit. The microfluidic device may also have a control channel,
or containment line, formed in a second layer of the elastomer
adjacent to the first layer. Further, the microfluidic device may
contain a sample flow channel, or sample line, formed in a third
layer of the elastomer adjacent to the second layer. The sample
flow channel may include a containment valve and a chamber conduit.
The control channel can be in operative association with both the
reagent flow channel containment valve and the sample flow channel
containment valve. The microfluidic device can include a reagent
chamber in fluid communication with the reagent line, and a sample
chamber in fluid communication with the sample line. The reagent
chamber and the sample chamber may be in fluid communication with
each other by way of a reaction flow channel or reaction line,
formed in the third layer of the elastomer. The reaction line may
include an interface valve. The microfluidic device may also
include an interface channel formed in a fourth layer of the
elastomer adjacent to the third layer. The interface channel can be
in operative association with the reaction flow channel interface
valve.
[0071] Embodiments of the present invention also encompass methods
of making and using the microfluidic devices disclosed herein. For
example, operation of a microfluidic device can involve opening one
or more isolation valves, closing one or more interface valves, and
flowing material past the isolation valves and into one or more
chambers, optionally under pressure. Techniques may also include
changing the pressure in a containment line to close the isolation
valves, so as to seal off the individual chambers, and changing the
pressure in an interface line, so as to open an interface valve. A
first material in a first chamber can flow past an open interface
valve and into a second chamber, where the first material mixes or
reacts with a second material contained therein.
[0072] Turning now to the drawings, FIG. 1 depicts a perspective
view of a unit cell 100 of a microfluidic device, according to
embodiments of the present invention. Unit cell 100 includes a
first channel 130, a first isolation valve 132, a first chamber
140, a second channel 110, a second isolation valve 112, a second
chamber 120, a control channel 150, an interface channel 160, an
interface valve 162, and a reaction channel 170. Typically, these
features are at least partially contained, embedded, or formed by
or within an elastomeric block 180. As shown here, first channel
130 is at least partially disposed within a first layer 181 of
elastomeric block 180. Control channel 150 is at least partially
disposed within a second layer 182 of elastomeric block 180, where
the second layer is adjacent to the first layer. Second channel 110
is at least partially disposed within a third layer 183 of
elastomeric block 180, where the third layer is adjacent to the
second layer. Interface channel 160 is at least partially disposed
within a fourth layer 184 of elastomeric block 180, where the
fourth layer is adjacent to the third layer.
[0073] With reference to the "A" arrows, a first material, such as
an assay reagent, can flow through first channel 130, past first
isolation valve 132, and into first chamber 140. Similarly, with
reference to the "B" arrows, a second material, such as an assay
sample, can flow through second channel 110, past second isolation
valve 112, through via 111, and into second chamber 120. To allow
flow into the reaction chambers 140, 120, first and second
isolation valves 132, 112, respectively, are both in an open valve
state. To prevent or inhibit flow between first reaction chamber
140 and second reaction chamber 120 through reaction channel 170,
interface valve 162 is in a closed valve state. Under such
conditions, first channel 130 is in open fluid communication with
first reaction chamber 140, and second channel 110 is in fluid
communication with second reaction chamber 120, whereas fluid
communication between the first and second chambers is interrupted
or inhibited. Reaction chamber sizes may vary. In some embodiments,
the volume of second reaction chamber 120 is different or greater
than the volume of first reaction chamber 140. For example, the
volume of second reaction chamber 120 can be ten times greater than
the volume of first reaction chamber 140. Materials can be loaded
into their respective chambers under pressure. Relatedly, materials
can be loaded into chambers at certain concentrations. In some
cases, a reagent solution is loaded into a chamber at a 10.times.
concentration, and is then diluted when reacted with a sample
solution contained in another chamber.
[0074] After the first and second materials have been loaded into
first and second reaction chambers 140, 120 respectively, the
control channel 150 can be activated so as to transform each of
first and second isolation valves 132, 112 from an open valve state
to a closed valve state. In this way the materials can be confined,
optionally under pressure, within the reaction chambers. Hence, it
is understood that a single control channel, for example control
channel 150, can control flow of a first material into a first
reaction chamber, and can also control flow of a second material
into a second reaction chamber. Operation of a single control
channel can thus act to isolate a first volume of material or
solution within the first chamber via actuation of the first
isolation valve 132, and can also isolate a second volume of
material or solution within the second chamber via actuation of the
second isolation valve 112. Relatedly, operation of a single
control channel can cause a first deflection in a first direction
at first isolation valve 132, and a second deflection in a second
direction at second isolation valve 112, where first direction is
opposite to second direction. For example, the deflection in the
first isolation valve can be in the upward direction, and the
deflection in the second isolation valve can be in the downward
direction. Accordingly, control of more than one isolation valve
can be effected simultaneously by operation of the single control
channel. Materials can be confined within the reaction chambers
under any suitable amount of pressure. In some embodiments, the
pressure in the first reaction chamber 140 is different or greater
than the pressure in the second reaction chamber 120. For example,
a first material such as a reagent can be disposed in first
reaction chamber 140 at a first pressure that is within a range
from about 0 psi to about 15 psi. Relatedly, a second material such
as a sample can be disposed in second reaction chamber 120 at a
second pressure that is within a range from about 0 psi to about 10
psi. In some instances, material can be contained in the first
reaction chamber 140 at about 10 psi, and material can be contained
in the second reaction chamber 120 at about 0 psi. Often, loading
of the microfluidic device involves introducing material into first
channel 130 or second channel 110, or both, under pressure. A
pressurizing mechanism can be used to drive materials into the
chambers.
[0075] In some cases, embodiments are directed to systems and
methods for conducting one or more reactions at one or more
selected temperatures or ranges of temperatures over time. A
microfluidic system may include a plurality of separate reaction
chambers formed in a multi-layer elastomeric block. The system may
also include a thermal transfer device proximal to or near at least
one of the reaction chambers. The thermal transfer device can be
formed to contact a thermal control source. Reagents for carrying
out a desired reaction can be introduced into a microfluidic array
device or matrix. The array device or matrix can be contacted with
the thermal control device such that the thermal control device is
in thermal communication with the thermal control source so that a
temperature of the reaction in at least one of the reaction chamber
is changed or controlled as a result of a change in temperature of
the thermal control source. Exemplary thermal cycling techniques
are discussed in U.S. Patent Publication No. 2007/0196912, the
content of which is incorporated herein by reference. In some
embodiments, a microfluidic device or chip can be coupled with or
in operative association with an Integrated Heat Spreader (IHS).
Such heating mechanisms are discussed in U.S. Pat. No. 7,307,802,
the content of which is incorporated herein by reference.
[0076] FIG. 1A shows an exploded perspective view of individual
layers of a unit cell 100 of a microfluidic device, according to
embodiments of the present invention. Each layer typically includes
an elastomeric membrane with one or more recesses, channels,
chambers, or the like. As depicted here, first layer 181 of unit
cell 100 includes a first channel 130 in fluid communication with a
first chamber 140. First layer 181 also includes a second chamber
120. Second layer 182 includes a control channel 150, a first via
111, and a second via 131. Third layer 183 includes a second
channel 110 and a reaction channel 170. As further discussed
elsewhere herein, unit cell 100 can be configured so that second
channel 110 and reaction channel 170 are in fluid communication
with second chamber 120, optionally by way of via 111. For example,
creating a fluid passage that extends from second channel 110 to
reaction channel 170 can involve removing a portion of second layer
182 that is disposed below second chamber 120. Creation of this
fluid passage can also involve removing a corresponding portion of
third layer 183 that is disposed below second chamber 120.
Similarly, unit cell 100 can be configured so that reaction channel
170 is in fluid communication with first chamber 140, optionally by
way of via 131. For example, creating a fluid passage that extends
from first channel 130 to reaction channel 170 can involve removing
a portion of second layer 182 that is disposed below first chamber
140. Creation of this fluid passage can also involve removing a
corresponding portion of third layer 183 that is disposed below
first chamber 140. Fourth layer 184 includes an interface channel
160.
[0077] Hence, as shown here, first channel 130 is at least
partially contained within a first layer 181. Control channel 150,
via 111, and via 131 are each at least partially contained within a
second layer 182, where the second layer is adjacent to the first
layer. Second channel 110 and reaction channel 170 are at least
partially contained within a third layer 183, where the third layer
is adjacent to the second layer. As shown here, vias 131, 111 are
disposed in second layer 182. It is understood that corresponding
vias can be formed in third layer 183, so as to provide fluid
communication from chamber 140 through via 131 and into channel
170, and fluid communication from chamber 120 through via 111 and
into the intersection of channels 110 and 170. Interface channel
160 is at least partially contained within a fourth layer 184,
where the fourth layer is adjacent to the third layer. First
chamber 140 is at least partially contained within first layer 181.
First chamber 140 in some instances can also be least partially
contained within or in communication with passages located in
second layer 182 and third layer 183, thus providing fluid
communication between first chamber 140 and first channel 130, and
between first chamber 140 and reaction channel 170. Second chamber
120 is at least partially contained within first layer 181. In some
instances second chamber 120 can be at least partially contained
within or in communication with passages located in second layer
182 and third layer 183, thus providing fluid communication between
second chamber 120 and reaction channel 170.
[0078] According to the embodiment shown in FIG. 1, reaction
channel 170 and interface valve 162 are not located within the same
plane or level as first chamber 140 and second chamber 120. For
example, reaction channel 170 is disposed in third layer 183,
interface valve 162 operates at or near the boundary or junction
between fourth layer 184 and third layer 183, and first and second
chambers 140, 120 are disposed in first layer 181. As the routing
passage or reaction channel 170 passes in a lower or different
layer than that of the chambers, this allows the chambers to be
located in close proximity with one another. In some embodiments, a
sidewall of first chamber 140 and a facing sidewall of second
chamber 120 are separated by a distance of about 120 microns. In
related embodiments, a distance between facing sidewalls of first
and second chambers is within a range from about 40 microns to
about 225 microns. For example, a first chamber sidewall and a
facing second chamber sidewall can be separated by a distance of
about 50 microns, about 60 microns, about 70 microns, or about 80
microns. Often, interface valve 162 is about 50 microns in width.
Hence, the distance between facing sidewalls of first and second
chambers can be less than, about the same as, or more than the
diameter or width of the interface valve which controls or
modulates flow between the chambers. Accordingly, microfluidic
devices employing such architecture can present extremely large
numbers of chambers within a given area. Such high densities may be
difficult to achieve in situations where a valve that controls flow
between two chambers is disposed in the same layer as the
chambers.
[0079] First chamber 140 can have a width within a range from about
25 microns to about 75 microns, a length within a range from about
80 microns to about 240 microns, and a height within a range from
about 30 microns to about 90 microns. Relatedly, first chamber 140
can have a volume within a range from about 0.1 nanoliters to about
10 nanoliters. For example, first chamber 140 can have a width of
50 microns, a length of 162.5 microns, a height of 60 microns, and
a volume of 0.49 nanoliters. Second chamber 120 can have a width
within a range from about 70 microns to about 210 microns, a length
within a range from about 80 microns to about 240 microns, and a
height within a range from about 150 microns to about 450 microns.
Relatedly, second chamber 120 can have a volume within a range from
about 1 nanoliter to about 20 nanoliters. For example, second
chamber 120 can have a width of 137.5 microns, a length of 162.5
microns, a height of 300 microns, and a volume of 6.7 nanoliters. A
microfluidic device according to embodiments of the present
invention can provide a center-to-center distance between first
chamber 120 and second chamber of about 300 microns. In some cases,
this center-to-center distance is within a range from about 250
microns to about 350 microns. Optionally, the center-to-center
distance between the first chamber and the second chamber is about
312.5 microns.
[0080] In some embodiments, a microfluidic device can include one
or more layers that have been prepared according to spin or pour
fabrication protocols. For example, a spin protocol can involve
placing a polymeric material on a patterned disc or mold, and
spinning the disc to create a layer of polymer across the disc.
Exemplary polymers include polymethylmethacrylate, polystyrene,
polypropylene, polyester, fluoropolymers, polytetrafluoroethylene,
polycarbonate, polysilicon, and polydimethylsiloxane (PDMS). A pour
protocol can involve pouring a PDMS material, for example, on a
patterned template or mold, which can result in a layer of PDMS
which can be peeled or pulled off the mold intact. Often, a layer
prepared by a pour fabrication technique is thicker than a layer
prepared by a spin fabrication technique. Elastomeric blocks can
include one or more pour or spin layers, in any desired
combination. In some embodiments, first layer 181 can be fabricated
according to a pour protocol. For example, PDMS can be poured onto
a mold that has raised portions corresponding to the various
desired fluid flow channels and chambers. FIG. 1B shows an
exemplary mold 190b which can be used to fabricate first layer 181
of FIG. 1A. After curing, the first layer can be peeled away from
the mold. First layer 181 can include openings, recesses, or other
voids that at least partially form or define first channel 130,
first chamber 140, and second chamber 120. To create second layer
182, PDMS can be placed onto a mold that has raised portions
corresponding to the various desired containment or control
channels. FIG. 1C shows an exemplary mold 190c which can be used to
fabricate second layer 182 of FIG. 1A. Mold 190c can also include,
for example, raised or contoured portions 191c that form
corresponding marks in second layer 182. These marks can be used
during a laser ablation procedure, such that the laser ablation is
directed toward the marks during the ablation. Mold 190c can be
spun, so as to provide a thin layer of PDMS across the mold. Second
layer 182 can include openings, recesses, or other voids that at
least partially form or define control channel 150. In some cases,
second layer 182 can be exposed to one or more laser ablations. An
ablative laser beam directed to second layer 182 can form vias 111,
131. After second layer 182 is sufficiently cured, first layer 181
can be aligned and contacted with the second layer. The first layer
can adhere with the second layer, and both layers can be peeled off
mold 190c simultaneously. To create third layer 183, PDMS can be
placed onto a mold that has raised portions corresponding to the
various desired containment or control channels. FIG. 1D shows an
exemplary mold 190d which can be used to fabricate third layer 183
of FIG. 1A. The mold can be spun, so as to provide a thin layer of
PDMS across the mold. Third layer 183 can include openings,
recesses, or other voids that at least partially form or define
second channel 110 and reaction channel 170. After third layer 183
is sufficiently cured, the combined first layer 181 and second
layer 182 can be aligned and contacted with the third layer. The
third layer can adhere with the second layer, and all three layers
can be peeled off mold 190d simultaneously. To create fourth layer
184, PDMS can be placed onto a mold that has raised portions
corresponding to the various desired containment or control
channels. FIG. 1E shows an exemplary mold 190e which can be used to
fabricate fourth layer 184 of FIG. 1A. The mold can be spun, so as
to provide a thin layer of PDMS across the mold. Fourth layer 184
can include openings, recesses, or other voids that at least
partially form or define interface channel 160. After fourth layer
184 is sufficiently cured, the combined first layer 181, second
layer 182, and third layer 183 can be aligned and contacted with
the fourth layer. The fourth layer can adhere with the third layer,
and all four layers can be peeled off mold 190e simultaneously.
Optionally, the four layers can be placed on or contacted with a
fifth layer 186 as shown in FIG. 1A. The fifth layer can include a
laminate or tape, or a similarly suitable material, which operates
to seal a recess in the fourth layer, so as to form or seal
interface channel 160. In this way, the combined first, second,
third, and fourth layers can then be placed on or contacted with
the fifth layer, which may be a solid spin layer. The fifth layer
can act as a sealing layer. According to some embodiments, the
fifth layer may include an elastomeric material, such as PDMS. In
some cases, the fifth layer can include a rigid or hard material
such as glass, silicon, or a plastic such as polystyrene. The fifth
layer may, for example, seal recesses formed in bottom of the
fourth layer, so as to provide channels in the fourth layer. The
sealing layer can include a film which may be attached to the
fourth layer via an adhesive. Hence, the sealing layer can form
channels from recesses molded or machined into an adjacent layer.
The sealing layer can be a transparent material, for example,
polystyrene, polycarbonate, or polypropylene. Relatedly, the
sealing layer can be flexible, such as an adhesive tape, and may be
suitable for attachment to a substrate by bonding, such as with
adhesive or heat sealing, or mechanically attached such as by
compression. Often, materials used to fabricate a sealing layer are
compliant to form fluidic seals with each recess to form a fluidic
channel with minimal leakage. A sealing layer may further be
supported by an additional support layer that is rigid (not shown).
In some cases, a sealing layer is rigid.
[0081] In some cases, passages or vias can be formed between
channels or chambers at one layer and channels or chambers at
another layer. For example, it is possible to create a via 131
through second layer 182 to provide fluid communication between
first chamber 140 in first layer 181 and reaction channel 170 in
third layer 183. Similarly, it is possible to create a via 111
through second layer 182 to provide fluid communication between
second chamber 120 in first layer 181 and second channel 110 and
reaction channel 170 in third layer 183. In some instances,
creation of these vias can enlarge the volume of the reaction
chambers. In some cases, the vias can be formed by using a laser
punch to remove or ablate portions of elastomeric membrane. As
shown in FIG. 1A, for example, reaction chambers 120, 140 can have
an interior space that extends above a plane defined by the top of
first channel 130. This interior space can also extend above a
plane defined by the top of second channel 110, and above a plane
defined by the top of reaction channel 170. Hence, during loading
of the unit cell, fluid can flow through first channel 130 and
upward into the interior of first chamber 140. Similarly, during
loading, fluid can flow through second channel 110 and upward into
the interior of second chamber 120, optionally through a via formed
in the second layer. Relatedly, during a mixing operation, fluid
can flow from the interior of first chamber 140 and downward into
reaction channel 170, optionally through a via 131 formed in the
second layer. Similarly, during a mixing operation fluid can flow
from reaction channel 170 and upward into the interior of second
chamber 120, optionally through a via 111 formed in the second
layer.
[0082] According to embodiments of the present invention, the
second, third, fourth, and fifth layers can be processed or laser
punched as part of a procedure that forms a loading passage to
first channel 130 in first layer 181. Relatedly, the fourth and
fifth layers can be processed or laser punched as part of a
procedure that forms a loading passage to second channel 110 in
third layer 183. Loading passages, vias, and the like can be formed
using a drilling or ablation mechanism. For example, a loading
passage or via can be fabricated by ablating a portion of the
elastomeric block. Excimer lasers are well suited for such ablation
techniques, as they can produce a laser beam which removes a
portion of the elastomeric block. In some cases, loading passages
or vias, or portions thereof, can be formed before one or more of
the individual layers are adhered together. For example, a portion
of a loading passage or via can be formed in a layer during the
molding process, or after the molding process and before the
adhesion process. Optionally, formation of at least a portion of
the loading passage or via can involve etching one or more
elastomeric layers prior to forming the complete multilayer
elastomeric block.
[0083] Accordingly, in some embodiments fabrication methods include
forming a first elastomeric layer on top of a first micromachined
mold, where the first micromachined mold has one or more raised
protrusions that form one or more recesses along a bottom surface
of the first elastomeric layer. Methods may also include forming a
second elastomeric layer on top of a second micromachined mold,
where the second micromachined mold has one or more raised
protrusions that form one or more recesses along a bottom surface
of the second elastomeric layer. Methods may include bonding or
adhering the bottom surface of the first elastomeric layer onto a
top surface of the second elastomeric layer such that a channel or
chamber forms in a recess between the first and second elastomeric
layers. Any desired number of layers can be fabricated in this way.
Methods also include positioning the last or final elastomeric
layer on top of a planar substrate such that a channel or chamber
forms in a recess between the final elastomeric layer and the
planar substrate. Embodiments of the present invention encompass
multilayer microfluidic devices having any desired elastomeric
valve or pump configuration which includes such channels or
chambers. Exemplary elastomeric valve and pump fabrication
techniques are described in U.S. Pat. No. 6,408,878, the content of
which is incorporated herein by reference.
[0084] Microfluidic device embodiments of the invention can be
constructed out of any material or combination of materials that
can be fabricated to have microfluidic channels and chambers, and
valves that regulate flow through channels and into chambers.
Materials from which a device can be fabricated include, without
limitation, elastomers, silicon, glass, metal, polymer, ceramic,
inorganic materials, and/or combinations of these materials.
[0085] The methods used in fabrication of a microfluidic device may
vary with the materials used, and include soft lithography methods,
microassembly, bulk micromachining methods, surface micro-machining
methods, standard lithographic methods, wet etching, reactive ion
etching, plasma etching, stereolithography and laser chemical
three-dimensional writing methods, modular assembly methods,
replica molding methods, injection molding methods, hot molding
methods, laser ablation methods, combinations of methods, and other
methods known in the art or developed in the future. A variety of
exemplary fabrication methods are described in Fiorini and Chiu,
2005, "Disposable microfluidic devices: fabrication, function, and
application" Biotechniques 38:429-46; Beebe et al., 2000,
"Microfluidic tectonics: a comprehensive construction platform for
microfluidic systems." Proc. Natl. Acad. Sci. USA 97:13488-13493;
Rossier et al., 2002, "Plasma etched polymer microelectrochemical
systems" Lab Chip 2:145-150; Becker et al., 2002, "Polymer
microfluidic devices" Talanta 56:267-287; Becker et al., 2000,
"Polymer microfabrication methods for microfluidic analytical
applications" Electrophoresis 21:12-26; U.S. Pat. No. 6,767,706 B2,
e.g., Section 6.8 "Microfabrication of a Silicon Device"; Terry et
al., 1979, A Gas Chromatography Air Analyzer Fabricated on a
Silicon Wafer, IEEE Trans. on Electron Devices, v. ED-26, pp.
1880-1886; Berg et al., 1994, Micro Total Analysis Systems, New
York, Kluwer; Webster et al., 1996, Monolithic Capillary Gel
Electrophoresis Stage with On-Chip Detector in International
Conference On Micro Electromechanical Systems, MEMS 96, pp. 491496;
and Mastrangelo et al., 1989, Vacuum-Sealed Silicon Micromachined
Incandescent Light Source, in Intl. Electron Devices Meeting, IDEM
89, pp. 503-506. Each of these references are incorporated herein
by reference for all purposes.
[0086] In preferred embodiments, the device is fabricated using
elastomeric materials. Fabrication methods using elastomeric
materials and methods for design of devices and their components
have been described in detail in the scientific and patent
literature. See, e.g., Unger et al., 2000, Science 288:113-16; U.S.
Pat. Nos. 6,960,437 (Nucleic acid amplification utilizing
microfluidic devices); U.S. Pat. No. 6,899,137 (Microfabricated
elastomeric valve and pump systems); 6,767,706 (Integrated active
flux microfluidic devices and methods); 6,752,922 (Microfluidic
chromatography); 6,408,878 (Microfabricated elastomeric valve and
pump systems); 6,645,432 (Microfluidic systems including
three-dimensionally arrayed channel networks); U.S. Patent
Application publication Nos. 2004/0115838, 2005/0072946;
2005/0000900; 2002/0127736; 2002/0109114; 2004/0115838;
2003/0138829; 2002/0164816; 2002/0127736; and 2002/0109114; PCT
patent publications WO 2005/084191; WO 05030822A2; and WO 01/01025;
Quake & Scherer, 2000, "From micro to nanofabrication with soft
materials" Science 290: 1536-40; Xia et al., 1998, "Soft
lithography" Angewandte Chemie-International Edition 37:551-575;
Unger et al., 2000, "Monolithic microfabricated valves and pumps by
multilayer soft lithography" Science 288:113-116; Thorsen et al.,
2002, "Microfluidic large-scale integration" Science 298:580-584;
Chou et al., 2000, "Microfabricated Rotary Pump" Biomedical
Microdevices 3:323-330; Liu et al., 2003, "Solving the
"world-to-chip" interface problem with a microfluidic matrix"
Analytical Chemistry 75, 4718-23," Hong et al, 2004, "A
nanoliter-scale nucleic acid processor with parallel architecture"
Nature Biotechnology 22:435-39; Fiorini and Chiu, 2005, "Disposable
microfluidic devices: fabrication, function, and application"
Biotechniques 38:429-46; Beebe et al., 2000, "Microfluidic
tectonics: a comprehensive construction platform for microfluidic
systems." Proc. Natl. Acad. Sci. USA 97:13488-13493; Rolland et
al., 2004, "Solvent-resistant photocurable "liquid Teflon" for
microfluidic device fabrication" J. Amer. Chem. Soc. 126:2322-2323;
Rossier et al., 2002, "Plasma etched polymer microelectrochemical
systems" Lab Chip 2:145-150; Becker et al., 2002, "Polymer
microfluidic devices" Talanta 56:267-287; Becker et al., 2000, and
other references cited herein and found in the scientific and
patent literature. Each of these references are incorporated herein
by reference for all purposes.
[0087] Embodiments of the present invention further encompass
aspects of microfluidic fabrication and production, as well as
microfluidic device operation and use, as disclosed in U.S. patent
application Ser. No. 12/018,138 filed Jan. 22, 2008, the content of
which is incorporated herein by reference for all purposes.
[0088] Any of a variety of ablation, etching, or similar techniques
can be used to form vias or passages in an elastomeric block,
membrane, or layer. Such etching procedures are well suited for
creating elastomeric layers having multiple holes or apertures, for
example. In an exemplary process, an elastomeric material is placed
on a wafer or mold, and allowed to cure. The elastomeric material
can include one or more polymers incorporating materials such as
chlorosilanes or methyl-, ethyl-, and phenylsilanes, and
polydimethylsiloxane (PDMS) such as Dow Chemical Corp. Sylgard 182,
184 or 186, or aliphatic urethane diacrylates such as (but not
limited to) Ebecryl 270 or Irr 245 from UCB Chemical may also be
used. In some cases, the elastomeric material is deposited on the
wafer or mold in a spin coating process, a spray coating process, a
dip coating process, a screen printing process, an inkjet
deposition process, or the like. The curing procedure can involve
baking or room temperature vulcanizing (RTV), photocuring, and the
like.
[0089] An elastomeric composition may include multiple parts, which
can be mixed together at various ratios to obtain desired bond
properties. For example, an elastomeric material may include a Part
A and a Part B, which when mixed together in prescribed amounts
facilitates the desired bond parameters. In some cases, the parts
may be mixed in a ratio within a range from about 3:1 to about
30:1. For example, an elastomeric PDMS composition is baked to
provide a 10:1 RTV layer.
[0090] In some cases, a photoresist material can be placed on the
cured elastomeric material. For example, an SU-8 resist (available
from MicroChem Corp., Newton Mass.) can be applied to the
elastomer. Exemplary SU-8 resists include SU-8 2000, SU-8 3000,
SU-8 2007, SU-8 3005, and the like. The photoresist can be
deposited on the elastomeric material in a spin coating procedure,
at a desired rotational speed and duration. In some cases, the spin
coating can be performed at a rotational speed within a range from
about 1000 to about 10,000 rpm, and for a duration within a range
from about 20 seconds to about 2,000 seconds. For example, the spin
coating can be performed at 5000 rpm for 200 seconds. Following
this deposition, the photoresist mask can have a thickness or depth
within a range from about 0.5 to about 50 microns. In some cases,
the thickness is about 5 microns. The thickness of the mask can be
selected for facile via opening formation, and the selected spin
time can eliminate or inhibit beading of the photoresist material.
The photoresist material can be used as an etch mask.
[0091] Additional procedures can be performed to prepare the
photoresist for lithography exposure. For example, the photoresist
can be processed at a selected temperature for a selected time
duration. In some embodiments, the photoresist is soft baked at a
temperature within a range from about 45.degree. C. to about
85.degree. C. Relatedly, the photoresist can be baked for a
duration within a range from about 1 minute to about 10 minutes. In
some cases, the soft bake is performed for 5 minutes at 65.degree.
C. Such preparation techniques can help to eliminate or inhibit
photoresist mask cracking at exposure. The preparation procedure
may also include cooling the photoresist. For example, the
photoresist may be cooled at room temperature or at a temperature
within a range from about 18.degree. C. to about 37.degree. C., and
for a duration within a range from about 3 minutes to about 300
minutes. In some cases, the photoresist is cooled for about 30
minutes.
[0092] The lithography procedure can involve multiple exposure
steps. For example, a first exposure step can be performed with a
first exposure mask, and a second subsequent exposure step can be
performed with a second exposure mask. An exposure step can involve
the application of radiation or energy, through an exposure mask,
toward a photoresist. Exposure radiation can include ultraviolet
light, near ultraviolet light, deep ultraviolet light, visible
light, infrared light, or energy at any desired wavelength along
the electromagnetic spectrum. In some cases, exposure radiation is
delivered at one or more wavelengths within a range from about 10
to about 10.sup.-9 cm. In some cases, the type of radiation or
energy is selected based on the composition of the photoresist. For
example, specific types of radiation or energy can be applied to
I-line photoresists, G-line photoresists, H-line photoresists, and
the like.
[0093] The use of multiple masks can help to prevent or inhibit the
effect of contaminants on a mask from replicating on the
photoresist. For example, if there is an unwanted particle on the
first mask at a certain location, exposure with a second mask can
help to ensure exposure of the photoresist at that location. The
exposure process can be followed with a post-exposure bake (PEB)
procedure. In some cases, a PEB procedure is performed for a
duration within a range from about 0 to about 200 minutes, and at a
temperature within a range from about 50.degree. C. to about
80.degree. C. For example, a PEB can be performed for 2 minutes at
65.degree. C. In some cases, the PEB can operate to cross-link the
photoresist mask material, rendering the material nonsoluble.
Thereafter, the exposed photoresist can be allowed to cool. An
exemplary cooling process is performed at a temperature within a
range from about 18.degree. C. to about 37.degree. C. for a
duration within a range from about 1 hour to about 40 hours. In
some cases, the exposed photoresist is cooled at room temperature
for about 18 hours.
[0094] A development process can be performed following exposure.
In some cases, the photoresist mask is developed for a duration
within a range from about 10 seconds to about 10 minutes. During
the development process a developer is applied to the exposed
photoresist. The developer can include, for example, an organic
solvent such as acetate. It is understood that the developer or
solvent may be selected based on the composition of the
photoresist. The developer can operate to dissolve or degrade areas
or locations of the photoresist layer that were unexposed or masked
during the exposure process. Following development, the photoresist
mask is subject to a drying procedure. For example, the mask can be
spin-dried. The mask may also be allowed to relax for a desired
period of time. In some cases, the mask is allowed to relax at or
near room temperature for a duration within a range from about 1
minute to about 48 hours.
[0095] Optionally, additional elastomeric layers can be spin-coated
or otherwise applied onto the developed photoresist. For example,
an RTV coating have a thickness or depth within a range from about
0.3 microns to about 30 microns can be deposited on the photoresist
mask. The elastomeric coating can be baked for a duration within a
range from about 5 minutes to about 3 hours, at a temperature
within a range from about 40.degree. C. to about 80.degree. C. In
some cases, a 3 micron RTV coating is spin-coated on an SU-8 mask,
and baked for 1 hour at 60.degree. C. Such techniques can help to
minimize lateral etch, and reduce via size non-uniformity. The RTV
layer can be deposited on a patterned photoresist layer, to help
prevent or inhibit the formation of pinholes in the underlying
elastomer.
[0096] Typically, etching involves removing certain areas of the
elastomeric material that are not protected by the photoresist
following development. In an exemplary procedure, etching can be
performed for a duration within a range from about 1 minute to
about 20 minutes and at a temperature within a range from about
50.degree. C. to about 90.degree. C. For example, etching can be
carried out in an 80% tetrabutylammonium fluoride (TBAF) etchant
solution for 6-8 minutes at 70 degrees .degree. C. In some cases,
etching is performed in an ultrasonic bath tank, optionally in
degas mode. Such procedures can help to ensure a uniform etching
depth, with minimum damage to a photoresist mask during the etching
procedure. Etching can be followed with a deionized water wash. In
some cases, a hot water wash is performed for three minutes. The
photoresist mask can be removed with adhesive tape. A deionized
water wash can be applied again, optionally for 3 minutes. Stacking
procedures can provide additional layers to the elastomer. In some
cases, adjacent layers adhere to one another by way of interlayer
bonding.
[0097] FIG. 2 illustrates another perspective view of unit cell
100. As shown here with reference to the "A" arrows, the first
material can flow from first reaction chamber 140, through via 131,
through reaction channel 170, past interface valve 162, through via
111, and into second reaction chamber 120, where the first material
can contact the second material. It is understood that in some
embodiments, the second material can flow from second reaction
chamber 120, through via 111, through reaction channel 170, past
interface valve 162, through via 131, and into first reaction
chamber. To allow such flow through reaction channel 170, the
interface channel 160 can be activated so as to transform interface
valve 162 from a closed valve state to an open valve state. Under
such conditions, the first and second reaction chambers 140, 120
are in open fluid communication by way of the reaction channel and
the vias. When, for example, material contained in first reaction
chamber 140 is more highly pressurized relative to material
contained in second reaction chamber 120, the pressure differential
can help to release or open interface valve 162. Relatedly, such a
pressure differential can facilitate mixing between the first
material and the second material, as the first material is
forcefully expelled from first chamber and into second chamber,
thus squirting a stream of first material into a second material
contained in the second chamber, where the first material can
diffuse into or permeate through the second material. Often, the
presence, absence, or extent of any reaction between the first and
second materials, or involving either or both of the first and
second materials, within the second reaction chamber can be
characterized, confirmed, detected, or quantified by inspection,
for example with a reader, sensor, or imaging device 190. An
imaging device 190 can include a camera, optionally having a
charge-coupled device (CCD), that detects or monitors energy that
emits from the chamber. In some cases, the imaging device can
detect emission intensity output. Exemplary imaging devices and
reader techniques suitable for use with embodiments of the present
invention are described in U.S. Pat. No. 7,307,802 issued Dec. 11,
2007, the content of which is incorporated herein by reference. In
some cases, a reaction within a chamber is facilitated by a thermal
cycler. Embodiments of the present invention encompass systems and
methods for mixing or reacting materials within chambers, where
such mixing or reacting procedures involve any of a variety of
desired thermal cycling heating protocols or thermal gradient
modalities.
[0098] FIG. 3 illustrates a perspective view of a matrix 300 having
four unit cells 300.sub.(1,1), 300.sub.(1,2), 300.sub.(2,1), and
300.sub.(2,2) arranged in two rows and two columns. Matrix 300
includes a plurality of first channels 330.sub.(1), 330.sub.(2), a
plurality of first isolation valves 332.sub.(1,1), 332.sub.(1,2),
332.sub.(2,1), 332.sub.(2,2), a plurality of first chambers
340.sub.(1,1), 340.sub.(1,2), 340.sub.(2,1), 340.sub.(2,2), a
plurality of second channels 310.sub.(1), 310.sub.(2), a plurality
of second isolation valves 312.sub.(1,1), 312.sub.(1,2),
312.sub.(2,1), 312.sub.(2,2), a plurality of second chambers
320.sub.(1,1), 320.sub.(1,2), 320.sub.(2,1), 320.sub.(2,2), a
plurality of control channels 350.sub.(1), 350.sub.(2), a plurality
of interface channels 360.sub.(1), 360.sub.(2), and a plurality of
reaction channels 370.sub.(1,1), 370.sub.(1,2), 370.sub.(2,1),
370.sub.(2,2). It is appreciated that the unit cell architecture
embodiments disclosed herein can be scaled to provide a matrix
having any number of desired unit cells. For example, a matrix can
include 9216 unit cells arranged in 96 rows and 96 columns. Hence,
embodiments of the present invention provide a high density format
for reacting a plurality of samples with a plurality of reagents,
for example, ninety-six (96) samples with ninety-six (96)
reagents.
[0099] Microfluidic device features such as channels, valves,
chambers, are often at least partially contained, embedded, or
formed by or within one or more layers of an elastomeric block 380.
As shown here with reference to the "A1" arrows, a first material
such as a reagent can flow through a first channel 330.sub.(1),
past or through a plurality of first isolation valves
332.sub.(1,1), 332.sub.(1,2), and into a plurality of first
chambers 340.sub.(1,1), 340.sub.(1,2), respectively. Likewise, with
reference to the "A2" arrows, a second material such as a reagent
can flow through a first channel 330.sub.(2), past or through a
plurality of first isolation valves 332.sub.(2,1), 332.sub.(2,2),
and into a plurality of first chambers 340.sub.(2,1),
340.sub.(2,2), respectively. In some embodiments, materials flow
through first channel 330.sub.(1) and first channel 330.sub.(2) in
the same direction. In some embodiments, material flowing through
first channel 330.sub.(1) travels in a direction opposite from
material flowing through first channel 330.sub.(2). With reference
to the "B1" arrows, a third material such as a sample can flow
through a second channel 310.sub.(1), past or through a plurality
of second isolation valves 312.sub.(1,1), 312.sub.(2,1), and into a
plurality of second chambers 320.sub.(1,1), 320.sub.(2,1),
respectively. Hence, embodiments of the present invention provide
microfluidic techniques whereby a material can be flowed through a
common passage or trunk of a channel, such as second channel
310.sub.(1), and into a plurality of individual branches stemming
from the common trunk, such as those branch channels which
individually feed into second chambers 320.sub.(1,2),
320.sub.(2,2). Similarly, with reference to the "B2" arrows, a
fourth material such as a sample can flow through a second channel
310.sub.(2), past or through a plurality of second isolation valves
312.sub.(1,2), 312.sub.(2,2), and into a plurality of second
chambers 320.sub.(1,2), 320.sub.(2,2), respectively. In some
embodiments, materials flow through second channel 310.sub.(1) and
second channel 310.sub.(2) in the same direction. In some
embodiments, material flowing through second channel 310.sub.(1)
travels in a direction opposite from material flowing through
second channel 310.sub.(2). As shown in FIG. 3, material flowing
through second channel 310.sub.(1) and material flowing through
second channel 310.sub.(2) travel in opposing directions "B1" and
"B2", respectively. Hence, when loading multiple samples into an
elastomeric layered block, some samples can be introduced through
routing lines on one side of the block, and some samples can be
introduced through routing lines on an opposing side of the block.
This allows for an even distribution or placement of sample loading
route lines on opposite sides of the block, instead of placing all
or most sample loading route lines on the same side of the block.
Because the sum total of the sample routing lines are divided
between different sides of the block, more sample routing lines can
be introduced into the block. Consequently, a greater number of
samples can be analyzed within the block during a single
procedure.
[0100] To allow flow from the plurality of first channels
330.sub.(1), 330.sub.(2) into the plurality of first reaction
chambers 340.sub.(1,1), 340.sub.(1,2), 340.sub.(2,1),
340.sub.(2,2), each of the plurality of first isolation valves
332.sub.(1,1), 332.sub.(1,2), 332.sub.(2,1), 332.sub.(2,2) is in an
open valve state. To allow flow from the plurality of second
channels 310.sub.(1), 310.sub.(2) into the plurality of second
reaction chambers 320.sub.(1,1), 320.sub.(1,2), 320.sub.(2,1),
320.sub.(2,2), each of the plurality of second isolation valves
312.sub.(1,1), 312.sub.(1,2), 312.sub.(2,1), 312.sub.(2,2) is in an
open valve state. To prevent or inhibit flow between each of the
plurality of first reaction chambers 340.sub.(1,1), 340.sub.(1,2),
340.sub.(2,1), 340.sub.(2,2) and their corresponding counterpart of
the plurality of second reaction chambers 320.sub.(1,1),
320.sub.(1,2), 320.sub.(2,1), 320.sub.(2,2) through their
corresponding counterpart of the plurality of reaction channels
370.sub.(1,1), 370.sub.(1,2), 370.sub.(2,1), 370.sub.(2,2),
respectively, each of the plurality of interface valves
362.sub.(1,1), 362.sub.(1,2), 362.sub.(2,1), 362.sub.(2,2),
respectively, is in a closed valve state. Under such conditions,
first channel 330.sub.(1) is in fluid communication with first
reaction chambers 340.sub.(1,1), 340.sub.(1,2), first channel
330.sub.(2) is in fluid communication with first reaction chambers
340.sub.(2,1), 340.sub.(2,2), second channel 310.sub.(1) is in
fluid communication with second reaction chambers 320.sub.(1,1),
320.sub.(2,1), and second channel 310.sub.(2) is in fluid
communication with second reaction chambers 320.sub.(1,2),
320.sub.(2,2). Fluid communication between first chambers
340.sub.(1,1), 340.sub.(1,2), 340.sub.(2,1), 340.sub.(2,2) and
second chambers 320.sub.(1,1), 320.sub.(1,2), 320.sub.(2,1),
320.sub.(2,2), respectively, is interrupted.
[0101] A first material can be loaded into first reaction chambers
340.sub.(1,1), 340.sub.(1,2) via first channel 330.sub.(1). A
second material can be loaded into first reaction chambers
340.sub.(2,1), 340.sub.(2,2) via first channel 330.sub.(2). A third
material can be loaded into second reaction chambers 320.sub.(1,1),
320.sub.(2,1) via second channel 310.sub.(1). A fourth material can
be loaded into second reaction chambers 320.sub.(1,2),
320.sub.(2,2) via second channel 310.sub.(2). Optionally, such
materials can be loaded into the chambers under a desired or
selected pressure. Control channel 350.sub.(1) can be activated so
as to transform each of first isolation valves 332.sub.(1,1),
332.sub.(2,1) and second isolation valves 312.sub.(1,1),
312.sub.(2,1) from an open valve state to a closed valve state.
Similarly, control channel 350.sub.(2) can be activated so as to
transform each of first isolation valves 332.sub.(1,2),
332.sub.(2,2) and second isolation valves 312.sub.(1,2),
312.sub.(2,2) from an open valve state to a closed valve state. In
this way the materials can be confined or maintained, optionally
under pressure, within the reaction chambers.
[0102] FIG. 4 illustrates another perspective view of matrix 300
having four unit cells 300.sub.(1,1), 300.sub.(1,2), 300.sub.(2,1),
300.sub.(2,2). As shown here with reference to the "A" arrows, the
first material can flow from first reaction chamber 340.sub.(1,1),
through reaction channel 370.sub.(1,1), past interface valve
362.sub.(1,1), and into second reaction chamber 320.sub.(1,1),
where the first material can contact the third material. To allow
such flow through reaction channel 370.sub.(1,1), the interface
channel 360.sub.(1) can be activated so as to transform interface
valve 362.sub.(1,1) from a closed valve state to an open valve
state. Under such conditions, first reaction chamber 340.sub.(1,1)
and second reaction chamber 320.sub.(1,1) are in fluid
communication via reaction channel 370.sub.(1,1). Often, the
presence, absence, or extent of any reaction between the first and
third materials within second reaction chamber 320.sub.(1,1) can be
confirmed, detected, or quantified by inspection, for example with
a reader or sensor 390.
[0103] With reference to the "B" arrows, the first material can
flow from first reaction chamber 340.sub.(1,2), through reaction
channel 370.sub.(1,2), past interface valve 362.sub.(1,2), and into
second reaction chamber 320.sub.(1,2), where the first material can
contact the fourth material. To allow such flow through reaction
channel 370.sub.(1,2), the interface channel 360.sub.(1) can be
activated so as to transform interface valve 362.sub.(1,2) from a
closed valve state to an open valve state. Under such conditions,
first reaction chamber 340.sub.(1,2) and second reaction chamber
320.sub.(1,2) are in fluid communication via reaction channel
370.sub.(1,2). Often, the presence, absence, or extent of any
reaction between the first and third materials within second
reaction chamber 340.sub.(1,2) can be confirmed, detected, or
quantified by inspection, for example with a reader or sensor
390.
[0104] With reference to the "C" arrows, the second material can
flow from first reaction chamber 340.sub.(2,1), through reaction
channel 370.sub.(2,1), past interface valve 362.sub.(2,1), and into
second reaction chamber 320.sub.(2,1), where the second material
can contact the third material. To allow such flow through reaction
channel 370.sub.(2,1), the interface channel 360.sub.(2) can be
activated so as to transform interface valve 362.sub.(2,1) from a
closed valve state to an open valve state. Under such conditions,
first reaction chamber 340.sub.(2,1) and second reaction chamber
320.sub.(2,1) are in fluid communication via reaction channel
370.sub.(2,1). Often, the presence, absence, or extent of any
reaction between the first and third materials within second
reaction chamber 320.sub.(2,1) can be confirmed, detected, or
quantified by inspection, for example with a reader or sensor
390.
[0105] With reference to the "D" arrows, the second material can
flow from first reaction chamber 340.sub.(2,2), through reaction
channel 370.sub.(2,2), past interface valve 362.sub.(2,2), and into
second reaction chamber 320.sub.(2,2), where the second material
can contact the fourth material. To allow such flow through
reaction channel 370.sub.(2,2), the interface channel 360.sub.(2)
can be activated so as to transform interface valve 362.sub.(2,2)
from a closed valve state to an open valve state. Under such
conditions, first reaction chamber 340.sub.(2,2) and second
reaction chamber 320.sub.(2,2) are in fluid communication via
reaction channel 370.sub.(2,2). Often, the presence, absence, or
extent of any reaction between the fourth and second materials
within second reaction chamber 320.sub.(2,2) can be confirmed,
detected, or quantified by inspection, for example with a reader or
sensor 390.
[0106] In some embodiments, the terms isolation valve and
containment valve may be used interchangeably. Similarly, the terms
interface valve and reaction valve may be used interchangeably.
Such valves can be actuated or activated or otherwise controlled by
any of a variety of valve operation methods or configurations.
Exemplary valve systems and techniques which are well suited for
use with embodiments of the present invention are described, for
example, in U.S. Pat. No. 6,408,878, the content of which is
incorporated herein by reference. Often, such valves include an
elastomeric portion that, when actuated, deflects into a recess.
For example, FIG. 5A shows a side view or cross section of a
microfluidic device unit cell 500. The unit cell includes a first
channel 530 and first sample chamber 540 in a first layer 581 of an
elastomeric block 580, control channel 550 and via 511a in a second
layer 582, and a reaction channel 570 in a third layer 583. An
isolation valve 532 can be actuated, so as to inhibit or prevent
flow through first channel 530. Actuation of isolation valve 532
can involve the deflection of an elastomeric portion 532a into a
recess 531 of first channel 530. Fourth layer 584 includes
interface channel 560. FIG. 5B shows another side view or cross
section of microfluidic device unit cell 500. The unit cell
includes a sample chamber 520 in a first layer 581, a control
channel 550 and via 531b in a second layer 582, and a second
channel 510 in a third layer 583. Isolation valve 512 can be
actuated, so as to inhibit or prevent flow through second channel
510. Actuation of isolation valve 512 can involve the deflection of
an elastomeric portion 512a into a recess 511 of second channel
510. FIG. 5C shows a side view or cross section which is orthogonal
to the side views of FIGS. 5A and 5B. As depicted here, actuation
of control channel 550 can operate to activate both isolation valve
532 and isolation valve 512. For example, by changing the pressure
of fluid within control channel or containment line 550, it is
possible to simultaneously deflect a first elastomeric portion
upward into first channel 530 and a second elastomeric portion
downward into second channel 510. Optionally this can result in the
containment or isolation of a first material within a first chamber
and a second material within a second chamber. As shown in FIG. 5C,
first channel 530 and second channel 510 each present a rectangular
cross section. In some instances, either or both of these channels
can present a dome shaped cross section, where the dome is upright
with regard to first channel 530 and inverted with regard to second
channel 510.
[0107] FIG. 6A illustrates a microfluidic device 699 according to
embodiments of the present invention. Materials can be delivered
from wells 605 toward elastomeric block 608 through passages or
routing lines 601. FIG. 6B depicts microfluidic device 699 in a
plan view. Microfluidic device 699 includes a substrate 600 with
integrated pressure accumulator wells 601 and 602, each having a
receptacle 603, 604 that contains a valve, such as a check valve.
Microfluidic device 699 also includes one or more wells 605 for
receiving materials such as samples or reagents, and one or more
channels or routing lines disposed between wells 605 and an
elastomeric block location 607 of substrate 600. An elastomeric
block 608 can be coupled with substrate 600 at elastomeric block
location 607. Elastomeric block can include one or more layers of
elastomeric material having microfabricated recesses or channels
formed therein. Elastomeric block 608 can be coupled with substrate
600 in any of a variety of ways. For example, the elastomeric block
can be attached or bonded with the substrate. In some cases, the
block is directly bonded to the substrate. In some cases, the block
is coupled with the substrate without the use of an adhesive. In
some cases, the block is coupled with the substrate with an
adhesive. Within elastomeric block 608 are one or more channels in
fluid communication with one or more vias 614, which in turn
provide fluid communication between the elastomeric block channels
and the substrate channels. Hence, the substrate channels can
provide fluid communication between wells 605 and channels within
the elastomeric block.
[0108] Accumulator wells 601, 602 often include valves 611, 612,
respectively, which can be check valves for introducing and holding
gas of fluid under pressure into accumulator chambers 615 and 616.
Valves 611 and 612 are situated inside of receptacles 604 and 603,
respectively, which can keep liquid, when present in accumulator
chambers 615 and 616, from contacting valves 611 and 612. In some
embodiments, valves 611 and 612 may be mechanically opened by
pressing a shave, pin or the like, within a check valve to overcome
a self closing force of the check valve, thereby permitting release
of pressure from the accumulator chamber, or reducing fluid
pressure contained within the accumulator chamber.
[0109] Substrate 600 and associated components may be fabricated
from polymers, such as polypropylene, polyethylene, polycarbonate,
high-density polyethylene, polytetrafluoroethylene PTFE or
Teflon.RTM., glass, quartz, transparent materials, polysilicon,
metals, such as aluminum, or the like. Any of a variety of gases,
liquids, or fluids can be introduced into accumulator chambers 615
and 616. In some cases, valves 611 and 612 can be actuated to
release fluid pressure otherwise held inside of accumulator
chambers 615 and 616. Optionally, a portion of substrate 600
beneath the elastomeric block region 607 can be transparent. In
some cases, the portion may be opaque or reflective. Accumulator
chambers 601 and 602 can be in fluid communication with channels
contained in elastomeric block region 607, and ultimately, with
channels contained in elastomeric block 608. Accumulator operation
is described in U.S. Patent Publication No. 2007/0196912, the
content of which is incorporated herein by reference. In some
cases, operation of a channel, such as a control channel 150 as
shown in FIG. 1, can be modulated or controlled by an
accumulator.
[0110] FIG. 7 illustrates a microfluidic device 700 according to
embodiments of the present invention. Device 700 includes a carrier
710 coupled with a chip or block 750. Carrier or frame 710 includes
a plurality of routing lines 712 configured to allow flow from
carrier wells toward chip 750. For example, routing lines disposed
on the "S" side of the carrier can provide for the passage of
sample, and routing lines disposed on the "R" side of the carrier
can provide for the passage of reagent. In some cases, chip 750 can
also include a plurality of routing lines 752. For example, routing
lines on the chip can provide material transport on the chip from
location A to location B, and from location C to location D. In
this way, a portion of the samples loaded onto the carrier can be
transported to location E of the chip, and another portion of the
samples loaded onto the carrier can be transported to locations D
and B of the chip, such that some sample is loaded at one side of
the block, and some sample is loaded at an opposing side of the
block, as further discussed herein with reference to FIG. 3.
[0111] FIG. 8 illustrates a microfluidic device 800 according to
embodiments of the present invention. Device 800 includes a carrier
810 coupled with a chip or block 850. Carrier or frame 810 includes
a plurality of routing lines 812 configured to allow flow from
carrier wells toward chip 850. For example, routing lines disposed
on the "S" side of the carrier can provide for the passage of
sample, and routing lines disposed on the "R" side of the carrier
can provide for the passage of reagent. As shown in this
illustration, 24 samples loaded into wells at zone S.sub.1 flow to
the left side of the chip (upper half), 24 samples loaded into
wells at zone S.sub.2 flow to the upper side of the chip (left
half), 24 samples loaded into wells at zone S.sub.3 flow to the
upper side of the chip (right half), and 24 samples loaded into
wells at zone S.sub.4 flow to the right side of the chip (upper
half). Thereafter, through another set of routing lines optionally
disposed at or within the elastomeric block, the S.sub.1 samples
flow to the left side of the chip (lower half), the S.sub.2 samples
flow to the left side of the chip (upper half), the S.sub.3 samples
flow to the right side of the chip (upper half), and the S.sub.4
samples flow to the right side of the chip (lower half). Further,
24 reagent portions loaded into wells at zone R.sub.1 flow to the
left side of the chip (lower half), 24 reagent portions loaded into
wells at zone R.sub.2 flow to the lower side of the chip (left
half), 24 reagent portions loaded into wells at zone R.sub.3 flow
to the lower side of the chip (right half), and 24 reagent portions
loaded into wells at zone R.sub.4 flow to the right side of the
chip (lower half). Thereafter, through another set of routing lines
optionally disposed at or within the elastomeric block, the R.sub.1
reagent portions flow to the lower side of the chip (left half),
the R.sub.2 reagent portions flow to the lower side of the chip
(left half), the R.sub.3 reagent portions flow to the lower side of
the chip (right half), and the R.sub.4 samples flow to the lower
side of the chip (right half). Hence, routing lines on or in the
chip can provide material transport on or through the chip from one
location to another. In this way, a portion of the samples loaded
at one end of the carrier (e.g. the "S" end) can be transported
such that some sample is loaded at one side of the block, and some
sample is loaded at an opposing side of the block, as further
discussed herein with reference to FIG. 3.
[0112] In some embodiments, microfluidic devices may contain blind
flow channels which include a region that functions as a reaction
chamber or reaction site. Blind flow, or blind fill, can refer to
the filling of a dead-end tube or lumen with a liquid where a head
of gas is pushed in front of the liquid bolus, and where that head
of gas is vented or otherwise released from the lumen, allowing the
dead-end lumen to fill fully with the liquid. In some embodiments,
polydimethylsiloxane (PDMS) can be used as an elastomeric material.
PDMS is sufficiently gas permeable that liquid pressurized at a few
psi can drive the gas out of the channels, leaving them completely
filled with liquid.
[0113] Table 1 provides an exemplary experimental design where
various materials can be loaded or introduced into a microfluidic
device that includes four unit cells. According to this table,
sample can be flowed through first channels and reagent can be
flowed through second channels. It is understood that
alternatively, reagent can be flowed through first channels and
sample can be flowed through second channels. Embodiments of the
present invention encompass techniques were sample is flowed
through a set of first channels and a set of second channels, and
reagent is flowed through a set of first channels and a set of
second channels.
TABLE-US-00001 TABLE 1 channel material chamber first channel
330.sub.(1) DNA sample from person A first chambers 340.sub.(1, 1),
340.sub.(1, 2) first channel 330.sub.(2) DNA sample from person B
first chambers 340.sub.(2, 1), 340.sub.(2, 2) second channel
310.sub.(1) disease X gene primers/probes second chambers
320.sub.(1, 1), 320.sub.(2, 1) second channel 310.sub.(2) disease Y
gene primers/probes second chambers 320.sub.(1, 2), 320.sub.(2,
2)
[0114] Table 2 shows the mixtures occurring in the microfluidic
device reaction chambers, and the experimental inquiries which can
be answered, for example, by conducting a PCR reaction where the
sample contains patient DNA and the reagent contains an
oligonucleotide primer and probe set.
TABLE-US-00002 TABLE 2 reaction chamber materials mixed inquiry
second chamber 320.sub.(1, 1) DNA sample from person A person A has
gene for disease X? disease X gene primer/probe second chamber
320.sub.(1, 2) DNA sample from person A person A has gene for
disease Y? disease Y gene primer/probe second chamber 320.sub.(2,
1) DNA sample from person B person B has gene for disease X?
disease X gene primer/probe second chamber 320.sub.(2, 2) DNA
sample from person B person B has gene for disease Y? disease Y
gene primer/probe
[0115] It is understood that any of a variety of materials may be
mixed or reacted in according to embodiments of the present
invention. For example, genotyping applications may involve
detecting the presence or absence of a target in a sample. Gene
expression applications may involve measuring or quantifying
amounts of materials contained in a sample. Such applications may
benefit from the enhanced mixing function provided by embodiments
of the present invention. Further, microfluidic devices and methods
can be used to crystallize a protein. In one embodiment a method
includes providing a microfluidic device having a first chamber
having a dimension between 1000 .mu.m and 1 .mu.m, a second chamber
having a dimension between 1000 .mu.m and 1 .mu.m, and one or more
flow or control channels each having a dimension between 1000 .mu.m
and 1 .mu.m. The first and second chambers can be in fluid
communication with each other through a channel. A valve can be
disposed along a channel which, when actuated to open or close,
controls fluid communication between the first and second chambers,
or into or out of the first or second chamber, or both. The method
can include introducing a crystallization reagent into the first
chamber, introducing the protein in a solution into the second
chamber, opening a valve so that the solution containing the
protein in the second chamber becomes in fluid communication with
the crystallization reagent in the first chamber, and closing the
valve after a period of time to interrupt fluid communication
between the first and second chambers.
[0116] In some embodiments, a valve can be under the control of an
automated valve actuating device, which in turn may be further
under control of a computer or processor. A multilayer microfluidic
device can include at least one elastomeric layer, and a valve can
include a deflectable membrane. In some cases, a deflectable
membrane of a valve can be deflectable into one or more channels to
control fluid movement along the channels. Multiple elastomeric
membranes may be bonded or adhered together to form an elastomeric
block. In some cases, portions of channels or chambers can overlap
with portions of other channels or chambers at an overlap region.
Such channels or chambers can be in fluid communication through a
via located at the overlap region.
[0117] FIGS. 9-13 disclose additional aspects of microfluidic
systems and methods according to embodiments of the present
invention. FIG. 9 shows a photomicrograph, with scale bar, of an
exemplary microfluidic device. FIGS. 10-12 each show reader images
of exemplary microfluidic devices and experimental results provided
by the devices. FIG. 13 illustrates an exemplary microfluidic
device, showing channel connections between input wells and an
elastomeric block. As shown in FIG. 13, a microfluidic system can
include a microfluidic device having a multiwell plate, optionally
referred to as a carrier or frame. Often, the multiwell plate
includes a plastic material, such as an injection molded plastic.
The multiwell plate can include channel connections or passages for
providing fluid communication between input wells and an
elastomeric block. U.S. Patent Application No. 61/030,887 filed
Feb. 22, 2008, (Integrated Carrier for Microfluidic Device) which
is incorporated herein by reference, describes carrier or frame
configurations which are suitable for use with microfluidic systems
and methods of the instant application. FIG. 14 shows further
aspects of microfluidic systems and methods according to
embodiments of the present invention.
[0118] Additional embodiments of the invention include methods for
detecting nucleic acid analytes through their interactions with a
nucleic acid probe, such as a hydrolysis probe, a hairpin probe, a
padlock probe (PLP) or a hybridization probe. The methods of the
invention combine the features of using the high throughput
microfluidic device as described herein, labeled nucleic acid
probes, and homogenous assays to detect and/or quantify nucleic
acid analytes with high PCR and probe specificity. Certain methods
described herein may allow for the detection of low copy number
nucleic acid analyte per cell, have low fluorescence background
yielding a high signal to noise ratio. The homogeneous assays of
the invention may have a dynamic range of at least about 3 orders
of magnitude, more often at least about 4, even more often at least
about 5, even more often at least about 6, often at least about 7,
and sometimes at least about 8 orders of magnitude.
[0119] According to an embodiment of the invention, the detection
and/or quantification of a plurality of nucleic acid analytes from
a sample may generally be carried out by obtaining a pre-amplified
sample, aliquoting the sample and distributing the pre-amplified
sample into reaction chambers of a microfluidic device containing
the appropriate buffers, primers, probes and enzymes, performing a
homogenous assay for the target nucleic analytes of interest, and
querying the aliquots for the presence of nucleic acid
analytes.
[0120] In a first embodiment, a sample is obtained which is
suspected of containing the target nucleic acid analyte of
interest. The sample may be first reversed transcribed into cDNA
and subjected to a preliminary amplification reaction to generate a
pre-amplified sample. In the preliminary amplification reaction,
the reverse transcribed sample is subjected to 14 cycles of PCR in
order to increase the nucleic acid analytes by about 16,000
fold.
[0121] In a second embodiment, aliquots of the pre-amplified sample
are distributed into separated compartments of a microfluidic
device and combined with the appropriate reagents. In particular,
the aliquot may have a volume of in the range of about 1 picoliter
to about 500 nanoliters, more often in the range of about 100
picoliters to about 20 nanoliters, even more often in the range of
about 1 nanoliter to about 20 nanoliters, and most often in the
range of about 5 nanoliters to about 15 nanoliters. The reagents
may include a labeled nucleic acid probe, PCR primers (e.g.,
forward primers and reverse primers), a thermostable DNA
polymerase, GT buffer, an aqueous buffer, magnesium chloride and
deoxynucleotide truphosphates, and may also include other
non-reactive ingredients. In a specific aspect, a pre-sample mix
may be prepared which may include TaqMan Universal PCR master Mix,
AmpliTaq-Gold (about 5 units/.mu.l), 20.times.GT buffer, and
H.sub.2O. The pre-sample mix may be combined with the nucleic acid
of interest, and appropriate primers.
[0122] In one aspect of the invention, a 1.times.GT buffer may
contain betaine in a range of about 0.1 M to about 0.8 M, BSA in a
range of about 1 mg/ml to about 4 mg/ml, glycerol in a range of
about 1% to about 5%, PEG 20,000 in a range of about 1% to about
5%, PEG MME550 in a range of about 0.05% to about 5%, MME5000 in a
range of 1% about to about 5%, Superblock.RTM. in PBS in a range of
about 1% to about 15%, Superblock.RTM. T20 in a range of about 1%
to about 10%, and Tween 20 in a range of 0.1% about to about 3%. In
a specific aspect, the 1.times.GT buffer may contain about 0.4 M
betaine, 2 mg/ml BSA, about 2.5% glycerol, about 2% PEG 20,000,
about 1% PEG MME550, about 2.5% MME5000, about 10% Superblock.RTM.
in PBS, about 5% Superblock.RTM. T20, and about 0.5% Tween 20. In a
more specific embodiment, the 1.times.GT buffer may contain about
0.4 M betaine, 4 mg/ml BSA, about 5% glycerol, about 2% PEG 20,000,
about 1% PEG MME550, about 2.5% MME5000, about 10% Superblock.RTM.
in PBS, about 10% Superblock.RTM. T20, and about 1% Tween 20.
[0123] In another aspect of the invention, a 20.times.GT buffer may
be prepared and may be diluted to a final concentration of 1.times.
when used in the dynamic arrays. For example, a 20.times.GT buffer
may include betaine in a range of about 1M to about 10M, BSA in a
range of about 5 mg/ml to about 15 mg/ml, and Superblock.RTM. T20
(in TBS) in a range of about 20% to about 65%. In a particular
aspect, the GT buffer may include about 5 M betaine, about 10 mg/ml
BSA, and about 57% Superblock.RTM.T20 in TBS. As one skilled in the
art appreciates, the 20.times.GT buffer would be diluted to
1.times. in the final reaction mix.
[0124] The PCR primers must be sufficiently long to prime the
synthesis of extension products in the presence of the agent for
polymerization. The exact length and composition of the primer will
depend on many factors, including temperature of the annealing
reaction, source and composition of the primer, proximity of the
probe annealing site to the primer annealing site, and ratio of
primer:probe concentration. For example, depending on the
complexity of the target sequence, the oligonucleotide primer
typically contains in the range of about 15 to about 30
nucleotides, although it may contain more or fewer nucleotides. The
primers should be sufficiently complementary to selectively anneal
to their respective strands and form stable duplexes. One skilled
in the art appreciates how to select appropriate PCR primer pairs
to amplify the target nucleic acid analyte of interest.
[0125] In a third embodiment, a homogenous assay may be performed
such as real-time PCR, for example. In this assay, the labeled
nucleic acid probe contains a stretch of nucleic acid sequences
that are capable of recognizing 8-mer and 9-mer motifs in the
target nucleic acid analyte, as described above. FRET quenching of
the labeled nucleic acid probe is irrevocably eliminated when the
Taq polymerase reaches the region where the labeled probe is
annealed to the target nucleic acid analyte, recognizes the
probe-template hybrid as a substrate, and subsequently hydrolyzes
phosphodiester bonds of the probe during primer-directed DNA
amplification. The hydrolysis reaction irrevocably releases the
quenching effect of the quencher dye on the reporter dye, thus
resulting in increasing detector fluorescence with each successive
PCR cycle. It will be appreciated that the invention is not limited
to the use of real-time PCR, and that other variations of PCR,
described above, may be used to detect and/or quantify the analyte
of interest.
[0126] The homogenous assay of the invention should not be
construed to be limited to PCR-based detection methods, but may
employ any method of detection and/or quantification to detect
and/or quantify a target nucleic acid analyte. In one aspect, PCR
may be used to amplify a target. In another aspect, other
amplification systems or detection systems may be used, including
systems described in U.S. Pat. No. 7,118,910, which is incorporated
herein by reference in its entirety. In a further aspect, a
detection system other than PCR may be used such as an Invader.RTM.
assay (Third Wave, Madison, Wis.). In one aspect, real time
quantification methods may be used to determine the quantity of a
target nucleic acid analyte present in a sample by measuring the
amount of amplification product formed during or after the
amplification process itself. Fluorogenic nuclease assays are one
specific example of a real time quantification method that may be
used successfully with the matrix-type microfluidic devices
described herein. This method of monitoring the formation of
amplification product involves the continuous measurement of PCR
product accumulation using a dual-labeled nucleic acid probe, such
as a hydrolysis probe. It will be appreciated that the invention is
not limited to use of these probes and any tag-specific probe may
be used.
[0127] In a fourth embodiment, the aliquots in the reaction
chambers may be queried for the presence of the targeted nucleic
acid analyte, which is accomplished by the use of the labeled
probes. The fluorescent signal may be monitored and quantified with
fluorescence detectors, such as fluorescence spectrophotometers and
commercial systems that allow the monitoring of fluorescence in PCR
reactions.
[0128] Alternatively, however, the probe may be unlabeled, but may
be detectable by specific binding with a ligand which is labeled,
either directly or indirectly. Suitable labels, and method for
labeling probes and ligands are well known in the art, and include,
for example, radioactive labels which may be incorporated by known
methods (e.g., nick translation, random priming or kinasing),
biotin, fluorescent groups, chemiluminescent groups (e.g.,
dioxetanes) enzymes, antibodies, gold nanoparticles and the like.
Variations of this basic scheme are known in the art, and include
those variations that facilitate separation of the hybrids to be
detected from extraneous materials and/or that amplify the signal
from the labeled moiety.
[0129] It will be appreciated that specifically at least about 10,
more often at least about 25, still more often at least about 50,
even more often at least about 100, in some cases at least about
500 and sometimes at least about 1000 targets may be detected using
the methodology of the invention. Thus, the method may make use of
at least about 10, more often at least about 25, still more often
at least about 50, even more often at least about 100, in some
cases at least about 500 and sometimes at least about 1000
target-specific probes.
[0130] All publications and patent documents (patents, published
patent applications, and unpublished patent applications) cited
herein are incorporated herein by reference as if each such
publication or document was specifically and individually indicated
to be incorporated herein by reference. Citation of publications
and patent documents is not intended as an admission that any such
document is pertinent prior art, nor does it constitute any
admission as to the contents or date of the same.
[0131] While the exemplary embodiments have been described in some
detail, by way of example and for clarity of understanding, those
of skill in the art will recognize that a variety of modification,
adaptations, and changes may be employed. Hence, the scope of the
present invention should be limited solely by the claims.
* * * * *