U.S. patent number 9,809,844 [Application Number 13/107,400] was granted by the patent office on 2017-11-07 for method of dna analysis using micro/nanochannel.
This patent grant is currently assigned to Wisconsin Alumni Research Foundation. The grantee listed for this patent is Dalia M. Dhingra, Kyubong Jo, David C. Schwartz. Invention is credited to Dalia M. Dhingra, Kyubong Jo, David C. Schwartz.
United States Patent |
9,809,844 |
Schwartz , et al. |
November 7, 2017 |
Method of DNA analysis using micro/nanochannel
Abstract
Methods are provided for tagging, characterizing and sorting
double-stranded biomolecules while maintaining the integrity of the
biomolecules.
Inventors: |
Schwartz; David C. (Madison,
WI), Jo; Kyubong (Champaign, IL), Dhingra; Dalia M.
(Arlington Heights, IL) |
Applicant: |
Name |
City |
State |
Country |
Type |
Schwartz; David C.
Jo; Kyubong
Dhingra; Dalia M. |
Madison
Champaign
Arlington Heights |
WI
IL
IL |
US
US
US |
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|
Assignee: |
Wisconsin Alumni Research
Foundation (Madison, WI)
|
Family
ID: |
37943900 |
Appl.
No.: |
13/107,400 |
Filed: |
May 13, 2011 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20110275066 A1 |
Nov 10, 2011 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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11633232 |
Nov 29, 2006 |
7960105 |
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60740583 |
Nov 29, 2005 |
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60740693 |
Nov 30, 2005 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q
1/6816 (20130101); B82Y 15/00 (20130101); C12Q
1/6837 (20130101); B82Y 30/00 (20130101); C12Q
1/6869 (20130101); C12Q 1/6837 (20130101); C12Q
2537/143 (20130101); C12Q 1/6816 (20130101); C12Q
2565/631 (20130101); C12Q 2527/137 (20130101); C12Q
2521/307 (20130101); C12Q 1/6869 (20130101); C12Q
2565/631 (20130101); C12Q 2527/137 (20130101); C12Q
2521/307 (20130101); C12Q 1/6869 (20130101); C12Q
2565/631 (20130101); C12Q 2565/601 (20130101); C12Q
2521/307 (20130101); B01L 3/5027 (20130101); Y10S
436/80 (20130101) |
Current International
Class: |
B01L
3/00 (20060101); B82Y 30/00 (20110101); C12Q
1/68 (20060101); B82Y 15/00 (20110101) |
References Cited
[Referenced By]
U.S. Patent Documents
Other References
"Base Pair," LIMSWiki.org, accessed Feb. 8, 2017. cited by examiner
.
Roberts, Richard J., A nomenclature for restriction enzymes, DNA
methyltransferases, homing endonucleases and their genes, Nucleic
Acids Research 2003, vol. 31, No. 7, 1805-1812. cited by applicant
.
Samuelson, James C., The isolation of strand-specific nicking
endonucleases from a randomized Sapl expression library, Nucleic
Acids Research 2004, vol. 32, No. 12, 3661-3671. cited by applicant
.
Bousse L, et al., "Electrokinetically controlled microfluidic
analysis systems," Annu. Rev. Biophys. Biomol. Struct. 29:155-181
(2000). cited by applicant .
Heiter D, et al., "Site-specific DNA-nicking mutants of the
heterodimeric restriction endonuclease R.BbvCl," J. Mol. Biol.
348:631-640 (2005). cited by applicant .
Rye J, et al., "Stable fluorescent dye-DNA complexes in high
sensitivity detection of protein-DNA interactions. Application to
heat shock transcription factor," J. Biol. Chem. 268:25229-25238
(1993). cited by applicant .
Wabuyele B, et al., "Single molecule detection of double-stranded
DNA in poly(methylmethacrylate) and polycarbonate microfluidic
devices," Electrophoresis 22:3939-3948 (2001). cited by applicant
.
Mukai, T. et al., "Isolation of circular DNA molecules from whole
cellular DNA by use of APT-dependent deoxyribonuclease", 1973,
Proc. Natl. Acad. Sci. USA, vol. 71, No. 10, pp. 2884-2887. cited
by applicant .
Trifonov, E.N., "Curved DNA", 1985, CRC Critical Reviews in
Biochemistry, vol. 19, No. 2, pp. 89-106. cited by applicant .
Garcia, H.G. et al., "Biological consequences of tightly bent DNA:
The other life biological of a macromolecular celebrity", 2007,
Biopolymers, vol. 85, No. 2, pp. 115-130. cited by applicant .
Manning, G.S. "The persistence length of DNA is reached from the
persistence length of its null isomer through an internal
electrostatic stretching force." Biophysical Journal, 91:3607-3616.
cited by applicant.
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Primary Examiner: Dauner; Joseph G.
Attorney, Agent or Firm: Quarles & Brady LLP
Government Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under HG000225
awarded by the National Institutes of Health and 0425880 awarded by
the National Science Foundation. The government has certain rights
in the invention.
Parent Case Text
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation application of U.S. patent
application Ser. No. 11/633,232, filed Nov. 29, 2006 now U.S. Pat.
No. 7,960,105, which claimed the benefit of U.S. Provisional Patent
Application Nos. 60/740,583, filed Nov. 29, 2005; and 60/740,693,
filed Nov. 30, 2005. Each application is incorporated herein by
reference as if set forth in its entirety.
Claims
We claim:
1. A method of preparing a double-stranded DNA molecule for optical
analysis, the method comprising the steps of: ligating the DNA
molecule to remove inherent nicks; nicking at least one predefined
sequence position of one strand of the DNA molecule without
breaking the double-stranded DNA molecule into wholly separate
pieces, wherein at least one nicked position defines a
pattern-characteristic of the nucleotide sequence of the DNA
molecule; elongating the DNA molecule in a buffer having an ionic
strength sufficiently low to increase the persistence length of the
DNA molecule; labeling the DNA molecule with at least one
fluorescent label wherein the fluorescent label is specific to the
nicked position; and introducing the elongated and labeled DNA
molecule suspended in the buffer into a channel to maintain the
elongated and labeled DNA molecule in an elongated state capable of
being analyzed optically without fixation to the channel.
2. The method of claim 1, wherein the ionic strength of the buffer
is adjusted after the elongated DNA is introduced into the
channel.
3. The method of claim 1, wherein the DNA molecule adopts an
elongated form having a persistence length greater than 50 nm.
4. The method of claim 1, further comprising: detecting by optical
analysis using a microscope at least one nicked position in the
labeled DNA molecule maintained in an elongated state, whereby the
analyzed elongated and labeled DNA molecule is capable of being
sorted from a plurality of DNA molecules on the basis of the
pattern characteristic of the nucleotide sequence defined by the at
least one nicked position.
5. A method of providing an elongated and labeled DNA molecule in a
channel for optical analysis, the method comprising: (a) providing
the DNA molecule in a buffer having an ionic strength sufficiently
low that the molecule adopts an elongated form; (b) labeling the
DNA molecule with at least one fluorescent label; and (c)
introducing the elongated and labeled DNA molecule provided in the
buffer into a channel having a cross-sectional dimension that
constrains the elongated and labeled DNA which is at least as wide
as the elongated and labeled DNA molecule and is less than 1000
nanometers, whereby the elongated DNA is constrained in the channel
in the focal plane of a microscope objective, and wherein the
elongated DNA molecule remains in the elongated state suitable for
being analyzed optically without fixation to the channel.
6. The method of claim 5, further comprising adjusting the ionic
strength of the buffer in which the elongated and labeled DNA is
provided after the elongated and labeled DNA is introduced into the
channel.
7. The method of claim 5, wherein the elongated DNA has a
persistence length greater than 50 nm.
8. The method of claim 5, further comprising (d) detecting by
optical analysis using a microscope at least one nicked position in
the elongated and labeled DNA molecule in the channel, whereby the
analyzed elongated and labeled DNA molecule is capable of being
sorted from a plurality of DNA molecules on the basis of the
pattern characteristic of the nucleotide sequence of the DNA
molecule that is defined by the at least one nicked position.
Description
BACKGROUND OF THE INVENTION
The present invention relates to methods of presenting polymeric
biomolecules such as nucleic acids for analysis, and in particular,
to methods for tagging and elongating the biomolecules for
characterization, sorting and analysis or other use.
A single DNA molecule can be elongated, for example, by shear
forces of liquid flow, by capillary action or by convective flow,
and then fixed in an elongated form to a substrate by electrostatic
attraction. Sequence features of the fixed molecule can be
identified by cleaving the fixed molecule with one or more
restriction enzymes to produce gaps that can be marked by
fluoroscopic markers or the like and then visualized. See, e.g.,
U.S. Pat. Nos. 6,713,263; 6,610,256; 6,607,888; 6,509,158;
6,448,012; 6,340,567; 6,294,136; 6,221,592. See also, U.S.
Published Patent Application Nos. 2005/0082204; 2003/0124611;
2003/0036067. Each patent and published patent application is
incorporated herein by reference as if set forth in its entirety.
Although fixing the DNA to the substrate simplifies the analysis by
preserving the elongated state, stabilizing the position of the
molecule, and preventing fragment shuffling after cleavage, it is
difficult to control chemical interactions with the DNA because of
its close proximity to the substrate. Also, cleaved DNA may not be
not suited for subsequent use, especially where fragment shuffling
diminishes information content that can be obtained from an
uncleaved molecule.
One can avoid such surface effects by suspending the DNA molecule
in a "nanochannel" without attachment to the channel walls. A
nanochannel is a channel having a cross-sectional dimension less
than 1,000 nanometers and typically on the order of 30 nanometers.
The suspended DNA molecule is sufficiently spaced apart from the
channel walls to avoid surface interference in the reaction process
while still stabilizing the DNA molecule sufficiently for
analytical techniques.
Practical use of nanochannels faces a number of obstacles.
Nanochannels are extremely difficult to fabricate, thus costly, and
as a practical matter, are not reusable. In addition, the small
size of nanochannels makes the addition of chemical reagents,
especially enzymes, difficult. It is also difficult to encourage
DNA molecules to enter the small cross-sectional area of
nanochannels. Likewise, it can be difficult to remove interfering
reaction by-products from nanochannels. Finally, because DNA is not
under significant tension within nanochannels, restriction enzymes
cutting the DNA may not make visible gaps.
SUMMARY OF THE INVENTION
The present invention provides methods for marking individual
double-stranded polymeric nucleic acid molecules to yield intact,
marked polymeric nucleic acid molecules suitable for
characterization and for subsequent uses. In accord with the
method, a single strand of the double stranded molecule is broken
(nicked) but the integrity of the molecule is maintained. Because
the molecule is not cleaved in the nicking process, the nicking
process can be performed before the molecule is immobilized for
analysis in a nanochannel, and optionally characterized and sorted
for subsequent uses, including use in an array of sorted
molecules.
The invention also relates to methods for providing the nicked,
polymeric nucleic acid molecules in a low ionic strength buffer to
increase the stiffness of the molecules, thereby facilitating use
of devices having convenient geometries for characterization.
The third technique, rendered possible by the increased stiffness,
is to use a channel having a nanometer scale in height, but a
micrometer scale in width, relying on the greater stiffness of the
elongated DNA molecule to remain properly aligned within the larger
channels. The larger channel simplifies loading of the DNA, the
introduction of reagents, and greatly simplifies channel
construction, thereby reducing costs and making disposable channels
practical.
These simplified processes for preparing the individual DNA
molecules (which can include multiple copies of particular
individual molecules, where, e.g., multiple genome-equivalents are
analyzed) away from a surface and before introduction into the
nanochannel, also simplify marking of the DNA molecule with
multiple fluoroscopic materials. The use of fluorescence resonance
energy transfer (FRET), in which one fluorescent material produces
light exciting the other, allows dual color imaging and reduces the
effects of unincorporated dyes because of the limited range of this
effect. The profile of fluorescent labels on each imaged molecule,
referred to as its `barcode,` is characteristic of that molecule.
From the characteristic barcode, the location of the molecule can
be ascertained from an existing database of nucleic acid sequences
of the source organism, tissue or cell type, in a manner known to
the art. Individual molecules of interest can be flagged according
to a user-specified set of parameters for further collection,
analysis or other use.
In another aspect, the invention relates to sorting of nucleic
acids characterized in accord with the invention. In particular, a
nucleic acid molecule characterized in a nanochannel after
site-specific labeling on a single strand as described elsewhere
herein can be captured by, e.g., electrostatic attraction, to an
electrode activated to capture on the particular molecule (or,
e.g., a related class of molecules). The electrode can be provided
in a microchannel (i.e., a channel having width and height
dimensions greater than those of a nanochannel, e.g., 5 microns in
width and 10 microns in height) in electrical connection with and
under the logical control of a controller (such as a computer
having a suitable user interface for specifying user parameters)
that can also coordinate the process of matching the labeled
nucleic acids against a genomic sequence database to identify and
distinguish nucleic acid molecules of higher interest from those of
lesser interest. In turn, the controller can address the electrode
independently, thereby facilitating separate collection of one or
more molecules at defined positions in an array. A plurality of
electrodes, each under separate or coordinated control of one or
more controllers, can effectively capture and accumulate a
plurality of identical, related or distinct molecules characterized
as described. Electrodes can be provided in a matrix suited for
electrophoretic migration of nucleic acids, e.g., agarose or
polyacrylamide, such that captured molecules tend to remain at or
near the electrode until directed by the controller to release the
captured molecules. Alternatively or additionally, a ligand can be
provided at the capture site to fixedly or releasably retain the
captured molecules at the site. A suitable capture system can be
based upon the addressable electrode arrays described in various
patents assigned to Nanogen, Inc., such as U.S. Pat. Nos.
7,101,717; 7,045,097; and 6,867,048, each of which is incorporated
herein by reference as if set forth in its entirety. Other systems
for capturing and/or releasing nucleic acid can be envisioned.
After capture on one or a plurality of such electrodes, identical
or related captured molecules can be released from the electrodes
in an ordered manner by reversing charge on the electrodes. Again,
the release can be separately or coordinately controlled by the
controller or controllers. Upon release, the molecules can be
conveyed for subsequent analysis, such as sequencing analysis. The
powerful labeling and identification features of the invention,
coupled with the ability to selectively capture or discard
identified molecules, yield a system for high-throughput analysis
of nucleic acid molecules. One appropriate use for such released
molecule(s) is a conventional nucleotide-level sequence analysis of
the molecules to ascertain whether the obtained molecule(s) are
identical to or different from a reference sequence in a
pre-existing database. In a related embodiment, after the profile
of each molecule is determined in a nanochannel and its value
assessed, the molecule flows in a stream from the nanochannel into
a sorting microchannel-sized chamber whereupon the controller
instructs a microvalve in the chamber either (1) to open to reject
a molecule of low interest from the chamber into a waste chamber or
(2) to close so that a molecule of high interest is drawn (e.g., by
charge) into a downstream system, such as a sequencing platform or
amplification system. It will be understood that high throughput
can be achieved in any of these embodiments by providing a
plurality of nanochannels for sorting multiple molecules in
parallel from a single inlet source along with a controller network
and software having adequate facility to manage the parallel
sorting and disposition of the tagged molecules.
These and other features, aspects and advantages of the present
invention will become better understood from the description that
follows. In the description, reference is made to the accompanying
drawings, which form a part hereof and in which there is shown by
way of illustration, not limitation, embodiments of the invention.
The description of preferred embodiments is not intended to limit
the invention to cover all modifications, equivalents and
alternatives. Reference should therefore be made to the claims
recited herein for interpreting the scope of the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
The invention will be better understood and features, aspects and
advantages other than those set forth above will become apparent
when consideration is given to the following detailed description
thereof. Such detailed description makes reference to the following
drawings, wherein:
FIG. 1 is a graphical representation of the process of the present
invention in which DNA can be chemically manipulated before being
inserted in a nanochannel for optical mapping;
FIG. 2 is a cross-sectional view along line 2-2 of FIG. 1 through a
nanochannel having nano- and micro-scale features;
FIGS. 3a, 3b and 3c are simplified representations of DNA during
three stages of the present invention in which the DNA is repaired,
nicked, elongated, labeled and entrapped within a nanochannel;
FIG. 4 is a flow chart showing these principle steps of the present
invention; and
FIGS. 5a and b depicts a design of a suitable micro-nanochannel
device.
FIGS. 6a and b show the effect of buffer ionic strength on DNA
elongation.
FIG. 7 graphically depicts the impact of buffer dilution upon DNA
elongation.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
The present invention relates to the observation that when large
genomic DNA molecules are a primary analyte, a key issue becomes
how to unravel and mark DNA molecules for high-throughput
application. With respect to unraveling DNA molecules,
high-throughput methods and systems using nanochannels for
analyzing single, intact DNA molecules are possible at low buffer
ionic strength because persistence length of DNA molecules
inversely varies with ionic strength of a buffer. Likewise, and
with respect to marking of DNA molecules, labeled,
sequence-specific nucleotides can be added to DNA molecules nicked
at specific sites using endonucleases that do not catalyze double
strand cleavage of the molecules, thereby providing markers of
site-specific nicking. Using available genomic sequence
information, one can correlate the site-specific markers with
identifiable nucleic acid molecules. Desired nucleic acid molecules
so identified can be sorted and collected for subsequent use. It
will be appreciated that intact individual nucleic acid molecules
prepared for presentation and analysis as described herein can
alternatively be analyzed after being deposited on a surface, with
the understanding that difficulty in removing such deposited
molecules precludes subsequent analysis of such molecules, e.g. by
nucleic acid sequencing or other methods.
Referring to FIG. 1, per the present invention, DNA 10 can be
initially processed in a solution 12 without being affixed to a
surface such as may interfere with some chemical reactions. For
example, a DNA 10 can be dyed with a fluorescent marker, such as
YOYO-1 fluorescent dye (hereinafter, "YOYO-1").
Referring also to FIGS. 3a and 4, DNA 10 in solution, however, may
include a number of inherent or pre-existing nicks 14 in which one
strand 16 is broken. Such nicks 14 may result from damage from
mechanical damage, UV light, or temperature.
In a first step, as represented by process block 18 of FIG. 4,
incidental inherent nicks 14 are repaired to prevent confusion with
nicks made for marking purposes. That is, DNA ligase and dideoxy
nucleotides are added to the DNA 10 in solution to remove the
inherent nicks. In addition, or alternative, a nuclease-free DNA
polymerase (such as DNase-free DNA Polymerase I, available from
Roche Applied Science) and dideoxy nucleotides are added to the DNA
10 in solution.
As shown in FIG. 3b, and represented by process block 24 of FIG. 4,
the suspended DNA 10, as repaired, can be nicked at predefined base
pair sequences 20 by enzyme 22. For example, the enzyme 22 can be a
genetically engineered nicking endonuclease that cleaves only a
single strand of a double-stranded polynucleotide, such as an
enzyme of this class commercially available from New England
Biolabs, including Nb.BbvCI and others. Typically, 20 units of
Nb.BbvCI and deoxynucleotides are allowed to incubate with DNA 10
in solution at 37.degree. C. As indicated by FIG. 3c, and
represented by process block 36, the nicks 14 produced by enzyme 22
can be labeled by incorporating at the nicked site at least one
fluorochrome 28 labeled deoxynucleotide providing a given frequency
of light emission 30, and the remaining body of the DNA 10 can be
labeled with a second fluorochrome 32 having a second frequency of
emission 34. Fluorochrome 28 can be uniquely keyed to the point of
the nick 14 whereas the fluorochromes 32 can distribute themselves
uniformly over the remaining surface of the DNA 10. The nicked,
labeled DNA can thus be imaged using Fluorescence Resonance Energy
Transfer. These labeled nicks, when identified in position, will
reveal characteristic sequence properties of the DNA 10.
Per process block 26 of FIG. 4, salt then can be removed from the
DNA 10 by adjustment of the buffering solution 12 to cause an
elongation of the DNA 10 and a corresponding increased
rigidity.
The elongated and labeled DNA in solution may then be removed for
example, by a pipette 38 and transferred into a first chamber 40 of
a nanochannel assembly 42. The first chamber 40 provides one
electrode 44 of an electrophoresis device and communicates through
a set of nanochannels 50 with a second chamber 46 of the assembly
42 having a second electrode 51 of the electrophoresis device. As
will be understood in the art, operation of a voltage across
electrodes 44 and 51 will draw charged molecules such as DNA 10
from first chamber 40 to second chamber 46 through the nanochannels
50 extending therebetween. This step entraps the DNA within the
nanochannels 50 for analyses or subsequent processing, as
represented by process block 60 of FIG. 4.
Referring to FIG. 2, each nanochannel 50 may have a height 52 on
the order of 30 nanometers effectively constraining the DNA 10 from
substantial curvature in a vertical plane based on the
cross-sectional diameter of the DNA 10. This constraint ensures
that the DNA is maintained within the focal plane of a microscope
objective which may view the DNA 10 through a transparent top wall
56 of the nanochannels 50.
The width of the channel 58 can be on the order of 1,000 nanometers
(one micrometer) or less. This allows for simple fabrication of the
channel using elastomeric molding techniques, for example, and
improves the ability to draw the DNA into the nanochannels 50. The
increased stiffness of the DNA 10 preserves its orientation and
alignment in the nanochannels 50 despite the width of the
nanochannels 50.
The DNA 10 may then be characterized or manipulated in other ways
within the nanochannels 50 per process block 62. One wall of the
nanochannels 50 can be semi-permeable to perform reactions on or
otherwise affect the DNA 10, for example, restoring salt to the
DNA.
Upon exit from the nanochannel, characterized molecules can be
sorted or selected on the basis of user-specified parameters, as
described. For example, the molecules can be sorted onto an array
on the basis of chromosomal heritage (i.e., only DNA from a
particular chromosome or set of chromosomes can be retained, if
desired, by providing appropriate capture ligands. Alternatively,
related sequences of, e.g., DNA encoding closely related genes can
be retained with each capture ligand retaining a single unique
version of the gene. Similarly, members of a single gene family can
be sorted away from other related or unrelated genes. Also,
molecules evidencing known aberrations or mutations can be sorted
for further analysis. It will be apparent that the sorting
possibilities are extensive.
Unless defined otherwise, all technical and scientific terms used
herein have the same meaning as commonly understood by one of
ordinary skill in the art to which the invention belongs. Although
any methods and materials similar to or equivalent to those
described herein can be used in the practice or testing of the
present invention, the preferred methods and materials are
described herein.
As used herein, persistence length refers to basic mechanical
property quantifying the stiffness of a macromolecule of a polymer,
reflecting the relative directional orientation of several
infinitesimal segments. Under common laboratory conditions, DNA
molecules have a persistence length of .about.50 nm.
Example 1: Construction of Nanochannel Devices
Fabrication of nanochannel devices followed standard soft
lithography techniques known to one skilled in the art. Whitesides
G, et al., "Soft lithography in biology and biochemistry," Annu.
Rev. Biomed. Eng. 3:335-373 (2001). To begin, a chrome mask,
created with e-beam lithography at the University of Wisconsin
Center for nanotechnology, was used as a mask in photolithography
on negative photoresist spin-coated onto silicon wafers, creating
an array of 1 .mu.m channels. The wafer was etched to a depth of
100 nm by CF4 gas. Photoresist was lifted off by piranha solution.
The height of the pattern was determined by an alpha step
profilometer and the width of the pattern was measured under
scanning electron microscope. After fabrication of the
nanochannels, a microchannel array was overlaid on the
nanopatterned wafer. SU-8 2005 photoresist was used to create
channels 5 .mu.m high and 100 .mu.m wide. FIG. 5 shows the
nanochannels (diagonal lines; 100 nm high.times.1 .mu.m wide)
overlaid with microchannels (horizontal lines; 3 .mu.m
high.times.100 .mu.m wide).
Next, the devices were formed by molding polydimethylsiloxane
(PDMS; Dow Corning; Midland, Mich.) onto the wafer described above.
PDMS replicas were formed by curing the PDMS for 24 hours at
65.degree. C. A short curing time (i.e. less than 24 hours), is not
enough to make stable, PDMS nanochannel devices. An O.sub.2 plasma
treatment (O.sub.2 pressure of .about.0.67 millibars; load coil
power 100 W; 36 seconds; Technics Plasma GMBH 440; Florence, Ky.)
of the PDMS nanochannel devices was used to render the devices
hydrophilic. Plasma-treated devices were stored in ultrapure water
for twenty-four hours, as PDMS surfaces are reactive right after
plasma treatment. Long-time storage in pure water makes the
surfaces less reactive. In addition, the PDMS nanochannel devices
were washed with 0.5 M EDTA (pH 8.5) three times to extract
platinum ions, which was a catalyst for PDMS polymerization.
Finally, the PDMS nanochannel devices were mounted on acid cleaned
glass, prepared as described previously. Dimalanta E, et al., "A
microfluidic system for large DNA molecule arrays," Anal. Chem.
76:5293-5301 (2004).
Example 2: Sequence-Specific Labeling of Nicked DNA
Sequence-specific labeled DNA was the result of the following
steps: (1) linearization, (2) ligation, (3) nick site blocking, (4)
nick translation, and (5) protein digestion. Linearization is
required only when using circular DNA. Regardless of whether
linearization was required, DNA ligase was used to remove inherent
nicks in DNA. A DNA ligase reaction with T4 DNA ligase was
performed at room temperature overnight. An overnight reaction
ensures that ligation is complete and kills DNA ligase activity. To
further ensure that and all inherent nicks were removed, DNA
polymerase I (10 units) was added with dideoxy nucleotides (ddNTPs;
0.2 .mu.M each) for 30 minutes at 37.degree. C. ddNTPs incorporated
into nicks block additional polymerase reaction and avoid random
labeling. A nicking enzyme (Nb.BbvCI, 20 units; GC^ATGAGG) was then
added with deoxynucleotides (dNTPs), such as ALEXA FLUOR
647-aha-dCTP fluorescent marker (2 .mu.M), ALEXA FLUOR 647-aha-dUTP
fluorescent marker (2 .mu.M), dATP (20 .mu.M), dCTP (1 .mu.M), dGTP
(20 .mu.M) and dTTP (1 .mu.M). Because DNA polymerase was added
previously, no additional DNA polymerase was added during nick
translation. The nick translation reaction was performed for 30
minutes at 37.degree. C. EDTA (pH 8.0, 20 .mu.M) was added to
quench reactions. Proteinase K (100 ng/.mu.l) and lauroyl sarcosine
(0.1% w/v) were added to remove all enzymes.
Following sequence-specific labeling, DNA was counterstained with
YOYO-1 (25 .mu.M; Molecular Probes; Eugene, Oreg.). DNA base pairs
to YOYO-1 in a ratio of 6:1 for .lamda. DNA and a ratio of 5:1 to
T4 DNA. Final DNA samples containing DNA (1 ng/.mu.l of .lamda. DNA
or 0.78 ng/.mu.l of T4 DNA), Tris-EDTA buffer (pH 8.0),
.beta.-mercaptoethanol and POP6 (0.1% w/v; Applied Biosystems;
Foster City, Calif.) were then loaded into the microchannels by
capillary action and subsequently entered the nanochannels by
application of an electric field. Tris-EDTA buffer concentration
varied from 1.times.TE (10 mM Tris and 1 mM EDTA) to 0.01.times.TE
(100 .mu.M Tris and 10 .mu.M EDTA). The ionic strength of the
buffer can be varied both before or after entry into the
nanochannels to affect elongation of the DNA.
An argon ion laser-illuminated inverted ZEISS 135M microscope was
used to image DNA molecules. The microscope was equipped with a
63.times.ZEISS Plan-Neofluar oil immersion objective, a DAGE
SIT68GL low-light level video camera connected to a SONY monitor
for visual inspection of DNA molecules, and a charge-couple device
(CCD) camera for acquiring focus and high-resolution images. A LUDL
ELECTRONICS x-y stage and focus motor with 0.1-m resolution was
used for x-y-z translation. Two emission filters were installed in
the microscope, YOYO-1 emission filter XF3086 and ALEXA FLUOR 647
emission filter. The YOYO-1 filter was used to take images of DNA
backbones; whereas the ALEXA FLUOR 647 filter was used to take
fluorescence resonance energy transfer (FRET) images.
Example 3: Elongation of Labeled DNA
As shown in FIGS. 6a and 6b, diminished ionic strength buffer
conditions increased intrachain electrostatic repulsion of DNA in
the nanochannels, thereby increasing persistence length.
Specifically, FIGS. 6a and 6b show typical images of T4 DNA (166
kbp; polymer contour length, 74.5 .mu.m) and .lamda. DNA (48.5 kbp;
polymer length, 21.8 .mu.m) elongated within nanochannels under low
ionic strength buffer conditions (0.05.times.TE and 0.01.times.TE)
showing apparent lengths of 40.9.+-.8.4 .mu.m (T4 DNA) and
13.0.+-.2.4 .mu.m (.lamda. DNA).
As shown in FIG. 7, DNA elongation is a function of the dilution of
TE (1/TE) reported as "stretch," and defined as the average
apparent length, X, divided by the dye adjusted polymer contour
length, L (e.g., L=21.8 for .lamda. DNA); a stretch value of 1.0
indicates complete elongation. FIG. 7 also shows that the degree of
DNA elongation is size independent and inversely related to salt
concentration or ionic strength used for the calculation of
persistence by the following equation:
P=P.sub.o+P.sub.el=P.sub.o+1/(4.kappa..sup.2l.sub.b)=P.sub.o+0.324I.sup.--
1 .ANG.; where P.sub.o is the non-electrostatic intrinsic
persistence length due to base stacking, P.sub.el is the
electrostatic persistence length due to intrachain repulsion,
.kappa..sup.-1 is the Debye-Huckel screening length, and l.sub.b is
the Bjerrum length (7 .ANG. in water).
The invention has been described in connection with what are
presently considered to be the most practical and preferred
embodiments. However, the present invention has been presented by
way of illustration and is not intended to be limited to the
disclosed embodiments. Accordingly, those skilled in the art will
realize that the invention is intended to encompass all
modifications and alternative arrangements within the spirit and
scope of the invention as set forth in the appended claims.
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