U.S. patent application number 09/460316 was filed with the patent office on 2001-07-05 for method and apparatus for analyzing nucleic acids.
Invention is credited to FOOTE, ROBERT S., RAMSEY, J. MICHAEL.
Application Number | 20010006785 09/460316 |
Document ID | / |
Family ID | 25303613 |
Filed Date | 2001-07-05 |
United States Patent
Application |
20010006785 |
Kind Code |
A1 |
RAMSEY, J. MICHAEL ; et
al. |
July 5, 2001 |
METHOD AND APPARATUS FOR ANALYZING NUCLEIC ACIDS
Abstract
A method and apparatus for analyzing nucleic acids includes
immobilizing nucleic probes at specific sites within a microchannel
structure and moving target nucleic acids into proximity to the
probes in order to allow hybridization and fluorescence detection
of specific target sequences.
Inventors: |
RAMSEY, J. MICHAEL;
(KNOXVILLE, TN) ; FOOTE, ROBERT S.; (OAK RIDGE,
TN) |
Correspondence
Address: |
DANN DORFMAN HERRELL & SKILLMAN
SUITE 720
1601 MARKET STREET
PHILADELPHIA
PA
19103-2307
US
|
Family ID: |
25303613 |
Appl. No.: |
09/460316 |
Filed: |
December 14, 1999 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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09460316 |
Dec 14, 1999 |
|
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08848553 |
Apr 28, 1997 |
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Current U.S.
Class: |
435/6.19 ;
436/94 |
Current CPC
Class: |
B01J 19/0093 20130101;
B01L 2400/0421 20130101; B01L 2300/0636 20130101; B01L 2300/0816
20130101; Y10T 436/143333 20150115; B01J 2219/00831 20130101; B01L
2300/0867 20130101; B01L 2400/0415 20130101; B01L 2400/0418
20130101; B01L 2400/0487 20130101; B01L 2300/0864 20130101; B01L
3/5027 20130101 |
Class at
Publication: |
435/6 ;
436/94 |
International
Class: |
C12Q 001/68 |
Goverment Interests
[0001] This invention was made with government support under
Contract No. DE-AC05-840R21400 awarded by the U.S. Department of
Energy to Lockheed Martin Energy Systems, Inc. and the government
has certain rights in this invention.
Claims
What is claimed is:
1. A method for analyzing nucleic acids comprising the steps of: a)
providing a substrate having a microchannel structure which
includes at least one microchannel therein; b) immobilizing a
number of different nucleic acid probes within at least a portion
of said microchannel structure, at least one said microchannel
having a probe-containing portion with a like number of probe
sites, wherein each of said different nucleic acid probes is
immobilized at a discrete probe site; c) moving a target nucleic
acid sample under the influence of an electrokinetic force into the
probe-containing portion of said microchannel; d) subjecting said
target nucleic acid sample in said probe-containing portion of said
microchannel to hybridization conditions; e) labelling with a
fluorescent substance one member selected from the group consisting
of said target nucleic acid sample or any hybrids formed in step d;
and f) detecting fluorescence emission from said fluorescent
substances.
Description
BACKGROUND OF THE INVENTION
[0002] 1. Field of The Invention
[0003] The present invention relates generally to medical and/or
biological testing and devices for performing same, and more
particularly, to a method and apparatus for analyzing minute
amounts of nucleic acids for the presence of specific nucleotide
sequences. Single-strand DNA probes are bound to specific regions
of microchannels in a glass microchip device. Sub-microliter
volumes of nucleic acid solutions, buffers and other reagents are
transported through the channels under electrokinetic or hydraulic
control. Hybridization of target nucleic acid sequences to
complementary probes is detected using either fluorescent labels or
intercalating fluorescent dyes.
[0004] 2. Description of the Related Art
[0005] Hybridization analysis is typically performed in microtiter
plate wells or on planar surfaces that contain arrays of DNA
probes. Chemical manipulations are required to bring about a
hybridization test and to detect the results. These manipulations
presently include washing or dipping planar arrays into the
appropriate chemicals.
[0006] The aforementioned procedures suffer from many drawbacks.
For example, they are wasteful of expensive reagents and limited
sample volumes. Moreover, they are generally not compatible with
efficient automation strategies and thus tend to be time
consuming.
[0007] A continuing need exists for methods and apparatuses that
limit the use of expensive reagents and priceless samples, while
simplifying the overall procedures to require smaller samples and
fewer processing steps.
SUMMARY OF THE INVENTION
[0008] An object of the present invention is to provide a method
and apparatus for analyzing nucleic acids which simplifies chemical
manipulations required to bring about a hybridization test when
performing DNA diagnostics in biomedical, forensic, and research
applications.
[0009] Another object of the present invention is to provide a
method and apparatus for analyzing nucleic acids which minimizes
the use of expensive reagents and limited sample volumes.
[0010] Another object of the present invention is to provide a
method and apparatus for analyzing nucleic acids which avoids the
necessity of pre-labeling a target DNA and increases the
sensitivity of hybrid detection by reducing background fluorescence
due to non-specific surface adsorption of labeled target DNA.
[0011] Still another object of the present invention is to provide
a method and apparatus for analyzing nucleic acids which
significantly extend the usefulness of hybridization diagnostics by
allowing its application to much smaller samples and facilitating
automated processing.
[0012] These and other objects are met by providing an apparatus
for analyzing nucleic acids which includes a microchip having a
microchannel structure formed therein, at least one portion of the
microchannel structure having at least one site capable of affixing
thereto a probe, and a plurality of reservoirs in communication
with the microchannel structure for introducing at least one of, or
a mixture of, a reagent, analyte solution, and buffer.
[0013] In another aspect of the invention, a method of analyzing
nucleic acids includes bonding oligonucleotide probes to a
microchannel formed in a microchip, adding target nucleic acids and
fluorescent stains to the microchannel, and detecting hybridization
by fluorescence staining of double-stranded DNA.
[0014] These together with other objects and advantages which will
be subsequently apparent, reside in the details of construction and
operation as more fully hereinafter described and claimed, with
reference being had to the accompanying drawings forming a part
hereof, wherein like numerals refer to like elements
throughout.
BRIEF DESCRIPTION OF THE DRAWINGS
[0015] FIG. 1 is a schematic view of an apparatus for analyzing
nucleic acids according to a preferred embodiment of the present
invention;
[0016] FIGS. 2 and 3 are schematic views of different arrangements
of nucleic acid hybridization probes in microchannels;
[0017] FIG. 4 is a schematic view of a microchip and microchannel
structure according to another preferred embodiment of the present
invention;
[0018] FIG. 5 is a schematic view of a microchip of the present
invention;
[0019] FIG. 6 is a photomicrograph showing discrimination of target
and non-target DNA at the intersection of microchannels in the
inset area of FIG. 5 after dsDNA staining with fluorescent dye;
[0020] FIG. 7 is a schematic view of another apparatus for
analyzing nucleic acids according to a preferred embodiment of the
present invention; and
[0021] FIG. 8 shows fluorescence image profiles of two probe
channels after ds-DNA staining with fluorescent dye.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0022] Referring to FIG. 1, a microchip 16 includes a glass
substrate 18 and a cover plate 20 which covers a microchannel
structure 22 formed in the upper surface of the substrate 16. The
cover plate 20 is permanently bonded to the substrate 18. Both the
substrate 18 and cover plate 20 are preferably made of clear glass,
and the substrate may preferably be made from a standard microscope
slide. Alternative construction materials could include plastics
(such as polypropylene, polycarbonate, or polymethylmethacrylate),
silicon, or sapphire.
[0023] The microchannel structure 22 is formed using standard
photolithographic techniques, and includes a longitudinal
microchannel manifold portion 24, a first transverse microchannel
portion 26 forming an intersection 28 with the longitudinal portion
24, and a second transverse microchannel portion 30 forming an
intersection 32 with the longitudinal portion 24.
[0024] First and second reservoirs 34 and 36 are in fluid
communication with opposite ends of the longitudinal portion 24.
The opposite ends act as ports to introduce the contents of the
reservoirs 34 and 36 into the microchannel structure 22. Each
reservoir can be a cylindrical container open at its opposite axial
ends, with the ends of the longitudinal portion 24 being in fluid
communication with the bottom of the container.
[0025] Third and fourth reservoirs 38 and 40 are in fluid
communication with opposite ends of the first transverse portion
26. The opposite ends act as ports to introduce the contents of the
reservoirs 38 and 40 into the microchannel structure 22. Each
reservoir 38 and 40 is similar in construction to the other
reservoirs, with the ends of the first transverse portion being in
fluid communication with the bottom of each respective reservoir 38
and 40.
[0026] Fifth and sixth reservoirs 42 and 44 are in fluid
communication with opposite ends of the second transverse portion
30. The opposite ends act as ports to introduce the contents of the
reservoirs 42 and 44 into the microchannel structure 22. Each
reservoir 42 and 44 is similar in construction to the other
reservoirs, with the ends of the second transverse portion being in
fluid communication with the bottom of each respective reservoir 42
and 44.
[0027] One or more types of single-stranded DNA probes 46 are
attached at individual sites within the microchannel portion 24 of
the microchannel structure 22. The design and fabrication of
microchips and the electrokinetic transport of fluids through the
microchannels is described in U.S. Ser. No. 08/283,769, filed Aug.
1, 1994, hereby incorporated by reference. The microchips described
therein include planar, glass substrates into which the
microchannels are etched photolithographically. The reservoirs
typically hold analyte solutions, buffers, reagents, etc. Typical
microchannel dimensions are 10 .mu.m by 50 .mu.m
(depth.times.width), although channel widths of 1 .mu.m to >100
.mu.m and channel depths of <1 .mu.m to >100 .mu.m may be
used. Voltages are applied to solutions as described in the
aforementioned application to produce electroosmotic flow of fluids
or electrophoretic migration of charged species through the
channels. Alternatively, pressure (or vacuum) may be applied to one
or more fluid reservoirs to cause reagent flow through the
channels.
[0028] The individual DNA probes may be arranged in a linear
pattern, as shown in FIG. 2. An alternative embodiment is shown in
FIG. 3, wherein the 46' are arranged in a two-dimensional array in
a widened area 48 of the channel portion 24'. Fluid flow is in the
direction indicated by arrows.
[0029] Typically, oligonucleotide probes ten to thirty nucleotides
long are used for hybridization analysis, although much longer
probes, such as DNA restriction fragments or cDNA sequences of
>100 nucleotide length, may be used in certain applications.
[0030] Oligonucleotide probes may be immobilized by covalent
chemical linkage to the surface. In general, such linkage involves
derivatization of the glass surface with a silane coupling agent,
such as 3-aminopropyltriethoxysilane or
3-glycidoxypropyltrimethoxysilane. An oligonucleotide probe bearing
an alkylamine group at the 5' or 3' end may then be linked to the
surface by direct reaction of its terminal amine with a silane
epoxy group or by cross linking the silane and oligonucleotide
amines using glutaraldehyde or other amine-reactive bifunctional
compounds.
[0031] Other immobilization method may also be used. For example,
surface-immobilized avidin or streptavidin may be used to bind
biotinylated probes. Non-covalently adsorbed oligonucleotides on
glass surfaces have also been shown to hybridize to target
sequences.
[0032] In the preferred fabrication method, the probes are attached
to the open microchip channels and the cover plate is then bound to
the substrate by a low temperature technique which does not damage
the biomolecules. Such a low temperature bonding technique is
described in copending application Ser. No. ______, entitled "Low
Temperature Material Bonding Technique" by J. M. Ramsey, R. S.
Foote, and H. Wang, which is incorporated herein by reference.
Individual probes may be applied to specific sites in the channels
by micro-pipeting or other means, such as ink-jet printing. The
separation of individual probes may be facilitated by preparing the
surface with a pattern of reactive, hydrophilic sites separated by
non-reactive, hydrophobic areas. For example, the glass surface may
be treated with an alkyltrialkoxysilane to produce a non-reactive,
hydrophobic surface. Photolithography and chemical etching or laser
ablation may be used to remove the silane layer and expose the
glass substrate in a pattern of separated spots. These spots may
then be treated with a silane coupling agent as described above to
produce reactive, hydrophilic spots. An aqueous probe solution
applied to an individual spot would be confined to its hydrophilic
site and thus prevented from mixing with different probe solutions
in adjacent spots. The intervening hydrophobic regions would also
prevent probe mixing in the case of the other immobilization
methods described above.
[0033] Alternatively, the probes may be attached to specific sites
in the channels after standard high-temperature cover plate
bonding. Three methods of achieving this are provided as
examples:
[0034] (1) The functional group of the silane linker (e.g., the
amino function of 3-aminopropylsilane) may be blocked with a
photolabile protective group. The silane linkers are then
de-protected at specific positions in the channel by exposure to
light through the cover plate using a photolithographic mask or
focused beam. Cross linkers and probes passed through the channel
would react only at de-protected sites. A series of separate
de-protection and addition steps are used to attach a number of
different probes to individual sites.
[0035] (2) An array of oligonucleotide probes may be
photochemically synthesized in situ in a parallel fashion.
[0036] (3) A channel manifold may be designed to allow the addition
of an individual probe to a given branch or segment of the manifold
by controlling fluid flows.
[0037] In the preferred methodology, nucleic acids, buffers and
dyes are electrokinetically driven through the microchannels
containing the immobilized probes. For example, the following
sequence of operations can be used with the device schematically
illustrated in FIG. 4. As seen in FIG. 4, a microchip 50 includes a
microchannel structure 52 connected to a nucleic acid sample
reservoir 54, a buffer reservoir 56, a dye reservoir 58, dye buffer
reservoir 60, and waste reservoir 62. A hybridization chamber 64 is
disposed in the microchannel structure 52 between first and second
transverse portions 66, 68 of the microchannel structure.
[0038] A voltage is applied between reservoir 54 which contains the
nucleic acid sample being analyzed and reservoir 56 containing
nucleic acid buffer. For buffers containing a high NaCl
concentration (desirable for rapid nucleic hybridization) the
polarity of reservoir 56 is positive relative to reservoir 54 and
the negatively charged nucleic acids electrophoretically migrate
from reservoir 54 to reservoir 56, passing through the
hybridization chamber 64. Alternatively, a nucleic acid solution
containing a low salt concentration may be electroosmotically
transported into the hybridization chamber by applying a positive
voltage at reservoir 54 relative to reservoir 56. Because
electroosmotic flow toward reservoir 56 is high relative to
electrophoretic migration toward the positive electrode, the net
movement of nucleic acids will be toward reservoir 56 in the later
case. The use of electroosmotic flow versus electrophoretic
migration will depend on a number of factors, and may vary
depending on the type of sample being analyzed. The term
"electrokinetic transport" includes both electroosmotic flow and
electrophoretic migration.
[0039] After the DNA sample reaches equilibrium over the probe
sites, the voltage may be discontinued while hybridization occurs.
A double-strand-DNA-specific (dsDNA-specific) fluorescent dye is
then electrokinetically transported through the hybridization
chamber 64 by applying voltages to fluid reservoir 58 which
contains a dye and reservoir 60 containing a dye buffer. Because
high salt concentrations are not normally required or desirable for
this step, electroosmotic flow is the preferred method of dye
addition and the polarity of reservoir 58 will normally be positive
relative to reservoir 60. Several fluorescent
double-strand-specific nucleic acid stains are commercially
available. Many of these stains are positively charged so that
their electrophoretic migration will be in the same direction as
the electroosmotic flow.
[0040] Alternatively, the nucleic acids being analyzed may be
pre-labeled with fluorescent groups by well known procedures.
Although this later method can lead to higher background
fluorescence, it may be preferred in cases where probes contain
self-complementary sequences that can result in stable duplex
formation and dye binding by the probe itself.
[0041] Variations in the chip design and analysis procedure are
possible. For example, electrokinetically driven washing steps may
be included before and/or after the dye addition step by applying
appropriate voltages between the buffer reservoirs and a waste
reservoir 62. Nucleic acid and dye solutions might also be added
simultaneously to the hybridization chamber. As an alternative to
electrokinetically driven fluid manipulation, hydraulic pressure or
vacuum may be applied to appropriate reservoirs to control the flow
of solutions through the microchannels.
[0042] After completion of the hybridization and dsDNA staining
steps, if used, the hybridization chamber is examined for the
presence of fluorescently labeled sites by illumination with
exciting light through the cover plate. An epifluorescence
microscope and CCD camera may be used, as described below, to
obtain a fluorescence image of the entire chamber or portion
thereof. Scanning confocal fluorescence microscopy may also be
used.
[0043] The following examples incorporate the apparatus and
methodology of the present invention. Each involves the steps of
(1) covalently bonding oligonucleotide probes to microchannels, (2)
adding target nucleic acids and fluorescent stains to microchannels
by electrokinetic flow, (3) detecting hybridization by fluorescence
staining of double-stranded DNA, and (4) discriminating target and
non-target nucleic acids.
EXAMPLE 1
[0044] A 16-mer oligodeoxynucleotide probe sequence containing a
5'-(6-aminohexyl)phosphate
[H.sub.2N--CH.sub.2).sub.6-5'-pCGGCACCGAGTTTAG- C-3'] was
covalently attached to the hybridization chamber of a prototype
microchip similar to that shown in FIG. 4 by glutaraldehyde cross
linking with the 3-aminopropylsilane-derivatized glass surface. A
complementary 16-mer (target sequence) oligodeoxynucleotide in
6.times. SSC buffer was then electrophoretically added to the
hybridization chamber by applying 0.5 kV between reservoir 56 and
reservoir 54 (positive electrode at reservoir 54) for thirty
minutes. A dsDNA-specific fluorescent dye (TOTO-1, Molecular
Probes) in 10 mM Tris-borate buffer, pH 9.2, was then
electroosmotically added to the chamber by applying 1.0 kV between
reservoir 60 and reservoir 58 for 30 minutes. The chip was examined
by video microscopy using laser excitation (514 nm) of
fluorescence. Bright fluorescence due to the dsDNA-bound dye was
observed in the hybridization chamber relative to channels not
exposed to the target DNA. The image was recorded on video
tape.
[0045] In a subsequent similar experiment using the dsDNA specific
dye, PicoGreen (Molecular Probes), quantification by CCD imaging
and analysis showed a 10-fold increase in fluorescence intensity
when staining was carried out after hybridization of the target
DNA, relative to the intensity observed by staining prior to the
hybridization step.
EXAMPLE 2
[0046] The 16-mer oligonucleotide probe of Example 1 was uniformly
bound to the channels of a cross-channel chip shown schematically
in FIG. 5 by glutaraldehyde cross-linking. Solutions (50 .mu.M) of
the complementary (target sequence) 16-mer oligodeoxynucleotide (T)
and a non-complementary (non-target sequence) 16-mer
oligodeoxynucleotide (N) in phosphate-buffered saline (PBS) were
then added to separate channels as indicated in FIG. 5, by applying
suction at W for 10 minutes. The channels were then washed with
buffer and dsDNA-specific dye solution (PicoGreen, Molecular
Probes) was added to all channels for five minutes. The
cross-channel intersection was examined by epifluorescence
microscopy using a mercury lamp illumination source and FITC
filters. A 1.0 second CCD exposure, shown in FIG. 6 as the insert
of the broken line area of FIG. 5, showed intense fluorescence
(dark regions) in the channel exposed to target DNA relative to
that of channels exposed to non-target DNA or buffer.
[0047] In a similar experiment using laser induced fluorescence
imaging, as described in co-pending application Ser. No. ______,
entitled "Method and Apparatus for Staining Immobilized Nucleic
Acids" by J. M. Ramsey and R. S. Foote, incorporated herein by
reference, signal intensity from channels exposed to target DNA was
10-fold greater than from channels exposed to non-target DNA or
buffer.
EXAMPLE 3
[0048] Two 16-mer probes [H.sub.2N-
(CH.sub.2).sub.6-5'-GCTAAACTCGGTGCCG-3- ' (Probe 1)] and
[H.sub.2N-(CH.sub.2).sub.5-5'-pCGGCACCGAGTTTAGC-3' (Probe 2)] were
immobilized in separate channels of a cross-channel chip as
indicated in FIG. 7. In FIG. 7, the "T" reservoir is for target
DNA, "B" is for PBS buffer and "W" is for waste.
[0049] A solution of 16-mer oligonucleotide (50 nM oligonucleotide
in PBS) complementary to Probe 1 was induced to flow through both
channels for a total of 15 minutes by applying a vacuum at W. The
channels were then washed with buffer and treated with a ds-DNA
specific dye solution (PicoGree, Molecular Probes) for two minutes.
After washing with 10 mM Tris-HCL (pH 8), one mM EDTA (TE) buffer
for one minute, the channels were examined for laser-induced
fluorescence using an argon ion laser at 488 nm and 100 milliwatts
power. Quantitation by CCD imaging, shown in FIG. 8, shows a 4 to
5-fold greater fluorescence in the Probe 1 channel than in the
Probe 2 channel after subtraction of the background signal.
[0050] According to the above methods and apparatuses,
hybridization analysis can be performed in a microchip structure
that requires low instrumentation space and extremely low
sample/reagent volumes. The electrokinetic transport of samples and
reagents facilitates automation of sample/reagent manipulations.
Moreover, the detection of hybridization using double-strand
DNA-specific fluorescent dyes eliminates the target DNA labeling
step associated with prior art techniques and increases detection
sensitivity.
[0051] While the examples referred to above describe nucleic acid
probes, the methodology and apparatuses could also be used for
other uses including, but not limited to, immobilized antibodies
for micro-immunoassays. Numerous biomedical applications can be
envisioned.
[0052] While the various embodiments have referred to specific
reservoirs containing specific reagents, buffers or samples,
mixtures of two or more substances can be contained in individual
reservoirs. For example, a reservoir can contain a mixture of
reagent and buffer, buffer and sample, etc.
[0053] The many features and advantages of the invention are
apparent from the detailed specification, and thus, it is intended
by the appended claims to cover all such features and advantages of
the invention which fall within the true spirit and scope of the
invention. Further, since numerous modifications and variations
will readily occur to those skilled in the art, it is not desired
to limit the invention to the exact construction and operation
illustrated and described and accordingly, all suitable
modifications and equivalents may be resorted to, falling within
the scope of the invention.
* * * * *