U.S. patent application number 11/090419 was filed with the patent office on 2005-08-04 for compositions and methods involving direct write optical lithography.
This patent application is currently assigned to Affymetrix, Inc.. Invention is credited to Goldberg, Matrin J., Quate, Calvin F., Yamamoto, Melvin.
Application Number | 20050169589 11/090419 |
Document ID | / |
Family ID | 30118008 |
Filed Date | 2005-08-04 |
United States Patent
Application |
20050169589 |
Kind Code |
A1 |
Yamamoto, Melvin ; et
al. |
August 4, 2005 |
Compositions and methods involving direct write optical
lithography
Abstract
In one embodiment, fiber optic arrays or bundles are used as a
light guide to transmit ultraviolet light to the substrate surface
for photo-directed polymer synthesis Digital Micromirror Array
(DMA) is used as a switching device to reflect light onto the entry
side of the fiber optic array
Inventors: |
Yamamoto, Melvin; (Fremont,
CA) ; Goldberg, Matrin J.; (Saratoga, CA) ;
Quate, Calvin F.; (Menlo Park, CA) |
Correspondence
Address: |
AFFYMETRIX, INC
ATTN: CHIEF IP COUNSEL, LEGAL DEPT.
3380 CENTRAL EXPRESSWAY
SANTA CLARA
CA
95051
US
|
Assignee: |
Affymetrix, Inc.
Santa Clara
CA
|
Family ID: |
30118008 |
Appl. No.: |
11/090419 |
Filed: |
March 25, 2005 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
11090419 |
Mar 25, 2005 |
|
|
|
10318838 |
Dec 12, 2002 |
|
|
|
60319107 |
Jan 30, 2002 |
|
|
|
Current U.S.
Class: |
385/115 |
Current CPC
Class: |
G03F 7/70291 20130101;
G03F 7/70308 20130101; G03F 7/70275 20130101 |
Class at
Publication: |
385/115 |
International
Class: |
G02B 006/04 |
Claims
1-17. (canceled)
18. An optical lithography system comprising a light source; a
substrate mount; a switching device comprising a digital
micromirror array; and a light guide comprising a fiber optical
array wherein the light guide reflects light onto substrate.
19. The optical lithographic system of claim 18 wherein the fiber
optical array comprises a staggered array of fiber optic
elements.
20. The optical lithographic system of claim 19 further comprising
a scanning mechanism to translate the optical array across the
substrate.
Description
RELATED APPLICATIONS
[0001] This application claims the priority to U.S. Provisional
Application No. 60/319,107, filed on Jan. 30, 2002 This application
is also related to U.S. Pat. No. 6,271,957, issued Aug. 7, 2001 All
cited applications are incorporated herein by reference
BACKGROUND OF THE INVENTION
[0002] This invention relates to optical lithography and more
particularly to direct write optical lithography
[0003] Polymer arrays, such as the GeneChip.RTM. probe array
(Affymetrix, Inc, Santa Clara, Calif.), can be synthesized using
light-directed methods described, for example, in U.S. Pat. Nos.
5,424,186, 5,510,270, 5,800,992, 5,445,934, 5,744,305, 5,384,261
and 5,677,195 and PCT published application no WO 95/11995, which
are hereby incorporated by reference in their entireties In many
cases a different mask having a particular predetermined image
pattern is used for each separate photomasking step, and synthesis
of a wafer containing many chips requires a plurality of
photomasking steps with different image patterns For example,
synthesis of an array of 20 mers typically requires approximately
seventy photolithographic steps and related unique photomasks So,
using present photolithographic systems and methods, a plurality of
different image pattern masks must be pre-generated and changed in
the photolithographic system at each photomasking step Thus, a
photolithographic system and method that does not require such
masks may be useful in providing a more efficient and simplified
lithographic process
SUMMARY OF THE INVENTION
[0004] According to a second aspect of the invention, polymer array
synthesis is performed using a system with a transmissive spatial
light modulator and without a lens and photomask
[0005] According to another aspect of the invention, a Direct Write
System transmits image patterns to be formed on the surface of a
substrate (e g, a wafer) The image patterns are stored in a
computer The Direct Write System projects light patterns generated
from the image patterns onto a surface of the substrate for
light-directed polymer synthesis (e g, oligonucleotide) The light
patterns are generated by a spatial light modulator controlled by a
computer, rather than being defined by a pattern on a photomask
Thus, in the Direct Write System each pixel is illuminated with an
optical beam of suitable intensity and the imaging (printing) of an
individual feature on a substrate is determined dynamically by
computer control
[0006] According to a further aspect of the invention, polymer
array synthesis is accomplished using a class of devices known as
spatial light modulators to define the image pattern of the polymer
array to be deprotected
[0007] In another embodiment, fiber optic arrays or bundles are
used as a light guide to transmit ultraviolet light to the
substrate surface A Digital Micromirror Array (DMA) is used as a
switching device to reflect light onto the entry side of the fiber
optic array Since the DMA can selectively reflect light at
individual mirrors or pixels, only specific fiber elements will be
illuminated The light that exits the other end of the fiber array
will illuminate selected locations on the substrate
[0008] In some embodiments, the use of spherical lens on the entry
and exit ends of the fibers can enhance the collection and focus of
light as well On the entry end, the relative narrow collection
angle of a conventional fiber may not be efficient enough to
transmit sufficient light intensity to the substrate surface On the
exit end of the fiber a large angle of light scatter is typically
expected The addition of spherical lenses bonded to a concave
surface on the end of the fiber may be beneficial
BRIEF DESCRIPTION OF THE DRAWINGS
[0009] The accompanying drawings, which are incorporated in and
form a part of this specification, illustrate embodiments of the
invention and, together with the description, serve to explain the
principles of the invention
[0010] FIG. 1 shows a first embodiment of the invention having a
light source, a reflective spatial light modulator, such as a
micromirror array, and a lens
[0011] FIG. 2 is a diagrammatic representation of a second
embodiment of the invention employing an array of, for example,
micro-lenses
[0012] FIG. 3 illustrates a micro-lens array in the form of Fresnel
Zone Plates, which may be used in the invention
[0013] FIG. 4 shows a third embodiment of the invention having a
transmissive spatial light modulator
[0014] FIGS. 5A and 5B shows an exemplary photodirected synthesis
system with digital micromirror and fiberoptics
DETAILED DESCRIPTION OF THE INVENTION
[0015] The present invention has many preferred embodiments and
relies on many patents, applications and other references for
details known to those of the art Therefore, when a patent,
application, or other reference is cited or repeated below, it
should be understood that it is incorporated by reference in its
entirety for all purposes as well as for the proposition that is
recited
[0016] I. General
[0017] As used in this application, the singular form "a," "an,"
and "the" include plural references unless the context clearly
dictates otherwise For example, the term "an agent" includes a
plurality of agents, including mixtures thereof
[0018] An individual is not limited to a human being but may also
be other organisms including but not limited to mammals, plants,
bacteria, or cells derived from any of the above
[0019] Throughout this disclosure, various aspects of this
invention can be presented in a range format It should be
understood that the description in range format is merely for
convenience and brevity and should not be construed as an
inflexible limitation on the scope of the invention Accordingly,
the description of a range should be considered to have
specifically disclosed all the possible subranges as well as
individual numerical values within that range For example,
description of a range such as from 1 to 6 should be considered to
have specifically disclosed subranges such as from 1 to 3, from 1
to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc, as
well as individual numbers within that range, for example, 1, 2, 3,
4, 5, and 6 This applies regardless of the breadth of the range
[0020] The practice of the present invention may employ, unless
otherwise indicated, conventional techniques and descriptions of
organic chemistry, polymer technology, molecular biology (including
recombinant techniques), cell biology, biochemistry, and
immunology, which are within the skill of the art Such conventional
techniques include polymer array synthesis, hybridization,
ligation, and detection of hybridization using a label Specific
illustrations of suitable techniques can be had by reference to the
example herein below However, other equivalent conventional
procedures can, of course, also be used Such conventional
techniques and descriptions can be found in standard laboratory
manuals such as Genome Analysis A Laboratory Manual Series (Vols
I-IV), Using Antibodies A Laboratory Manual, Cells A Laboratory
Manual, PCR Primer A Laboratory Manual, and Molecular Cloning A
Laboratory Manual (all from Cold Spring Harbor Laboratory Press),
Stryer, L (1995) Biochemistry (4th Ed) Freeman, New York, Gait,
"Oligonucleotide Synthesis A Practical Approach" 1984, IRL Press,
London, Nelson and Cox (2000), Lehninger, Principles of
Biochemistry 3rd Ed, W H Freeman Pub, New York, N.Y. and Berg et al
(2002) Biochemisty, 5th Ed, W H Freeman Pub, New York, N.Y., all of
which are herein incorporated in their entirety by reference for
all purposes
[0021] The present invention can employ solid substrates, including
arrays in some preferred embodiments Methods and techniques
applicable to polymer (including protein) array synthesis have been
described in U.S. Ser. No. 09/536,841, WO 00/58516, U.S. Pat. Nos.
5,143,854, 5,242,974, 5,252,743, 5,324,633, 5,384,261, 5,405,783,
5,424,186, 5,451,683, 5,482,867, 5,491,074, 5,527,681, 5,550,215,
5,571,639, 5,578,832, 5,593,839, 5,599,695, 5,624,711, 5,631,734,
5,795,716, 5,831,070, 5,837,832, 5,856,101, 5,858,659, 5,936,324,
5,968,740, 5,974,164, 5,981,185, 5,981,956, 6,025,601, 6,033,860,
6,040,193, 6,090,555, 6,136,269, 6,269,846 and 6,428,752, in PCT
Applications Nos PCT/US99/00730 (International Publication Number
WO 99/36760) and PCT/US01/04285, which are all incorporated herein
by reference in their entirety for all purposes
[0022] Patents that describe synthesis techniques in specific
embodiments include U.S. Pat. Nos. 5,412,087, 6,147,205, 6,262,216,
6,310,189, 5,889,165, and 5,959,098 Nucleic acid arrays are
described in many of the above patents, but the same techniques are
applied to polypeptide arrays which are also described
[0023] Nucleic acid arrays that are useful in the present invention
include those that are commercially available from Affymetrix, Inc
(Santa Clara, Calif.) under the trademark GeneChip.RTM. Example
arrays are shown on the website at affymetrix com The present
invention also contemplates many uses for polymers attached to
solid substrates These uses include gene expression monitoring,
profiling, library screening, genotyping and diagnostics
Illustrative gene expression monitoring, and profiling methods are
shown in U.S. Pat. Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860,
6,040,138, 6,177,248 and 6,309,822 Illustrative genotyping and uses
therefore are shown in U.S. Ser. Nos. 60/319,253, 10/013,598, and
U.S. Pat. Nos. 5,856,092, 6,300,063, 5,858,659, 6,284,460,
6,361,947, 6,368,799 and 6,333,179 Other uses are embodied in U.S.
Pat. Nos. 5,871,928, 5,902,723, 6,045,996, 5,541,061, and
6,197,506
[0024] The present invention also contemplates sample preparation
methods in certain preferred embodiments Prior to or concurrent
with genotyping, the genomic sample may be amplified by a variety
of mechanisms, some of which may employ PCR See, e g, PCR
Technology Principles and Applications for DNA Amplification (Ed H
A Erlich, Freeman Press, NY, N.Y., 1992), PCR Protocols A Guide to
Methods and Applications (Eds Innis, et al, Academic Press, San
Diego, Calif., 1990), Mattila et al, Nucleic Acids Res 19, 4967
(1991), Eckert et al , PCR Methods and Applications 1, 17 (1991),
PCR (Eds McPherson et al, IRL Press, Oxford), and U.S. Pat. Nos.
4,683,202, 4,683,195, 4,800,159 4,965,188, and 5,333,675, and each
of which is incorporated herein by reference in their entireties
for all purposes The sample may be amplified on the array See, for
example, U.S. Pat. No. 6,300,070 and U.S. patent application Ser.
No. 09/513,300, which are incorporated herein by reference
[0025] Other suitable amplification methods include the ligase
chain reaction (LCR) (e g, Wu and Wallace, Genomics 4, 560 (1989),
Landegren et al, Science 241, 1077 (1988) and Barringer et al Gene
89 117 (1990)), transcription amphfication (Kwoh et al, Proc Natl
Acad Sci USA 86, 1173 (1989) and WO88/10315), self sustained
sequence replication (Guatelli et al, Proc Nat Acad Sci USA, 87,
1874 (1990) and WO90/06995), selective amplification of target
polynucleotide sequences (U.S. Pat. No. 6,410,276), consensus
sequence primed polymerase chain reaction (CP-PCR) (U.S. Pat. No.
4,437,975), arbitrarily primed polymerase chain reaction (AP-PCR)
(U.S. Pat. Nos. 5,413,909, 5,861,245) and nucleic acid based
sequence amplification (NABSA) (See, U.S. Pat. Nos. 5,409,818,
5,554,517, and 6,063,603, each of which is incorporated herein by
reference) Other amplification methods that may be used are
described in, U.S. Pat. Nos. 5,242,794, 5,494,810, 4,988,617 and in
U.S. patent application Ser. No. 09/854,317, each of which is
incorporated herein by reference
[0026] Additional methods of sample preparation and techniques for
reducing the complexity of a nucleic sample are described in Dong
et al, Genome Research 11, 1418 (2001), in U.S. Pat. Nos.
6,361,947, 6,391,592 and U.S. patent application Ser. Nos.
09/916,135, 09/920,491, 09/910,292, and 10/013,598, which are
incorporated herein by reference for all purposes
[0027] Methods for conducting polynucleotide hybridization assays
have been well developed in the art Hybridization assay procedures
and conditions will vary depending on the application and are
selected in accordance with the general binding methods known
including those referred to in Mamatis et al Molecular Cloning A
Laboratory Manual (2nd Ed Cold Spring Harbor, N Y, 1989), Berger
and Kimmel Methods in Enzymology, Vol 152, Guide to Molecular
Cloning Techniques (Academic Press, Inc, San Diego, Calif., 1987),
Young and Davism, P N A S, 80 1194 (1983) Methods and apparatus for
carrying out repeated and controlled hybridization reactions have
been described in U.S. Pat. Nos. 5,871,928, 5,874,219, 6,045,996,
6,386,749, and 6,391,623, each of which is incorporated herein by
reference
[0028] The present invention also contemplates signal detection of
hybridization between ligands in certain preferred embodiments See
U.S. Pat. Nos. 5,143,854, 5,578,832, 5,631,734, 5,834,758,
5,936,324, 5,981,956, 6,025,601, 6,141,096, 6,185,030, 6,201,639,
6,218,803, and 6,225,625, U.S. Patent Application No. 60/364,731,
and PCT Application PCT/US99/06097 (published as WO99/47964), each
of which also is hereby incorporated by reference in its entirety
for all purposes
[0029] Methods and apparatus for signal detection and processing of
intensity data are disclosed in, for example, U.S. Pat. Nos.
5,143,854, 5,547,839, 5,578,832, 5,631,734, 5,800,992, 5,834,758,
5,856,092, 5,902,723, 5,936,324, 5,981,956, 6,025,601, 6,090,555,
6,141,096, 6,185,030, 6,201,639, 6,218,803, and 6,225,625, in U.S.
Patent Application No. 60/364,731, and in PCT Application
PCT/US99/06097 (published as WO99/47964), each of which also is
hereby incorporated by reference in its entirety for all
purposes
[0030] The practice of the present invention may also employ
conventional biology methods, software and systems Computer
software products of the invention typically include computer
readable medium having computer-executable instructions for
performing the logic steps of the method of the invention Suitable
computer readable medium include floppy disk, CD-ROM/DVD/DVD-ROM,
hard-disk drive, flash memory, ROM/RAM, magnetic tapes and etc The
computer executable instructions may be written in a suitable
computer language or combination of several languages Basic
computational biology methods are described in, e g Setubal and
Meidanis et al, Introduction to Computational Biology Methods (PWS
Publishing Company, Boston, 1997), Salzberg, Searles, Kasif, (Ed),
Computational Methods in Molecular Biology, (Elsevier, Amsterdam,
1998), Rashidi and Buehler, Bioinformatics Basics Application in
Biological Science and Medicine (CRC Press, London, 2000) and
Ouelette and Bzevanis Bioinformatics A Practical Guide for Analysis
of Gene and Proteins (Wiley & Sons, Inc, 2nd ed, 2001)
[0031] The present invention may also make use of various computer
program products and software for a variety of purposes, such as
probe design, management of data, analysis, and instrument
operation See, for example, U.S. Pat. Nos. 5,593,839, 5,795,716,
5,733,729, 5,974,164, 6,066,454, 6,090,555, 6,185,561, 6,188,783,
6,223,127, 6,229,911 and 6,308,170, which are incorporated herein
by reference
[0032] Additionally, the present invention may have preferred
embodiments that include methods for providing genetic information
over networks such as the Internet as shown in U.S. patent
applications Ser. Nos. 10/197,621, 10/065,868, 10/065,856,
10/063,559, Provisionals 60/349,546, 60/376,003, 60/394,574,
60/403,381, each of which is incorporated herein by reference in
its entirety for all purposes
[0033] II Glossary
[0034] The following terms are intended to have the following
general meanings as used herein
[0035] Nucleic acids according to the present invention may include
any polymer or oligomer of pyrimidine and purine bases, preferably
cytosine (C), thymine (T), and uracil (U), and adenine (A) and
guanine (G), respectively See Albert L Lehninger, PRINCIPLES OF
BIOCHEMISTRY, at 793-800 (Worth Pub 1982) Indeed, the present
invention contemplates any deoxyribonucleotide, ribonucleotide or
peptide nucleic acid component, and any chemical variants thereof,
such as methylated, hydroxymethylated or glucosylated forms of
these bases, and the like The polymers or oligomers may be
heterogeneous or homogeneous in composition, and may be isolated
from naturally occurring sources or may be artificially or
synthetically produced In addition, the nucleic acids may be
deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), or a mixture
thereof, and may exist permanently or transitionally in
single-stranded or double-stranded form, including homoduplex,
heteroduplex, and hybrid states
[0036] An "oligonucleotide" or "polynucleotide", is a nucleic acid
ranging from at least 2, preferable at least 8, and more preferably
at least 20 nucleotides in length or a compound that specifically
hybridizes to a polynucleotide Polynucleotides of the present
invention include sequences of deoxyribonucleic acid (DNA) or
ribonucleic acid (RNA), which may be isolated from natural sources,
recombinantly produced or artificially synthesized and mimetics
thereof A further example of a polynucleotide of the present
invention may be peptide nucleic acid (PNA) in which the
constituent bases are joined by peptides bonds rather than
phosphodiester linkage, as described in Nielsen et al, Science 254
1497-1500 (1991), Nielsen Curr Opin Biotechnol, 10 71-75 (1999) The
invention also encompasses situations in which there is a
nontraditional base pairing such as Hoogsteen base pairing which
has been identified in certain tRNA molecules and postulated to
exist in a triple helix "Polynucleotide" and "oligonucleotide" are
used interchangeably in this application
[0037] An "array" is an intentionally created collection of
molecules which can be prepared either synthetically or
biosynthetically The molecules in the array can be identical or
different from each other The array can assume a variety of
formats, e g, libraries of soluble molecules, libraries of
compounds tethered to resin beads, silica chips, or other solid
supports
[0038] A nucleic acid library or array is an intentionally created
collection of nucleic acids which can be prepared either
synthetically or biosynthetically in a variety of different formats
(e g, libraries of soluble molecules, and libraries of
oligonucleotides tethered to resin beads, silica chips, or other
solid supports) Additionally, the term "array" is meant to include
those libraries of nucleic acids which can be prepared by
depositing, synthesizing, or otherwise placing or building nucleic
acids of essentially any length (e g, from 1 to about 1000
nucleotide monomers in length) onto a substrate The term "nucleic
acid" as used herein refers to a polymeric form of nucleotides of
any length, either ribonucleotides, deoxyribonucleotides or peptide
nucleic acids (PNAs), that comprise purine and pyrimidine bases, or
other natural, chemically or biochemically modified, non-natural,
or derivatized nucleotide bases (see, e g , U.S. Pat. No.
6,156,501, incorporated herein by reference) The backbone of the
polynucleotide can comprise sugars and phosphate groups, as may
typically be found in RNA or DNA, or modified or substituted sugar
or phosphate groups A polynucleotide may comprise modified
nucleotides, such as methylated nucleotides and nucleotide analogs
The sequence of nucleotides may be interrupted by non-nucleotide
components Thus the terms nucleoside, nucleotide, deoxynucleoside
and deoxynucleotide generally include analogs such as those
described herein These analogs are those molecules having some
structural features in common with a naturally occurring nucleoside
or nucleotide such that when incorporated into a nucleic acid or
oligonucleotide sequence, they allow hybridization with a naturally
occurring nucleic acid sequence in solution Typically, these
analogs are derived from naturally occurring nucleosides and
nucleotides by replacing and/or modifying the base, the ribose or
the phosphodiester moiety The changes can be tailor made to
stabilize or destabilize hybrid formation or enhance the
specificity of hybridization with a complementary nucleic acid
sequence as desired
[0039] "Solid support", "support", and "substrate" are used
interchangeably and refer to a material or group of materials
having a rigid or semi-rigid surface or surfaces In many
embodiments, at least one surface of the solid support will be
substantially flat, although in some embodiments it may be
desirable to physically separate synthesis regions for different
compounds with, for example, wells, raised regions, pins, etched
trenches, or the like According to other embodiments, the solid
support(s) will take the form of beads, resins, gels, microspheres,
or other geometric configurations
[0040] Combinatorial Synthesis Strategy A combinatorial synthesis
strategy is an ordered strategy for parallel synthesis of diverse
polymer sequences by sequential addition of reagents which may be
represented by a reactant matrix and a switch matrix, the product
of which is a product matrix A reactant matrix is a 1 column by m
row matrix of the building blocks to be added The switch matrix is
all or a subset of the binary numbers, preferably ordered, between
1 and m arranged in columns A "binary strategy" is one in which at
least two successive steps illuminate a portion, often half, of a
region of interest on the substrate In a binary synthesis strategy,
all possible compounds which can be formed from an ordered set of
reactants are formed In most preferred embodiments, binary
synthesis refers to a synthesis strategy which also factors a
previous addition step For example, a strategy in which a switch
matrix for a masking strategy halves regions that were previously
illuminated, illuminating about half of the previously illuminated
region and protecting the remaining half (while also protecting
about half of previously protected regions and illuminating about
half of previously protected regions) It will be recognized that
binary rounds may be interspersed with non-binary rounds and that
only a portion of a substrate may be subjected to a binary scheme A
combinatorial "masking" strategy is a synthesis which uses light or
other spatially selective deprotectmg or activating agents to
remove protecting groups from materials for addition of other
materials such as amino acids See, e g, U.S. Pat. No. 5,143,854
Monomer refers to any member of the set of molecules that can be
joined together to form an oligomer or polymer The set of monomers
useful in the present invention includes, but is not restricted to,
for the example of (poly)peptide synthesis, the set of L-amino
acids, D-amino acids, or synthetic amino acids As used herein,
"monomer" refers to any member of a basis set for synthesis of an
oligomer For example, dimers of L-amino acids form a basis set of
400 "monomers" for synthesis of polypeptides Different basis sets
of monomers may be used at successive steps in the synthesis of a
polymer The term "monomer" also refers to a chemical subunit that
can be combined with a different chemical subunit to form a
compound larger than either subunit alone
[0041] Biopolymer or biological polymer is intended to mean
repeating units of biological or chemical moieties Representative
biopolymers include, but are not limited to, nucleic acids,
oligonucleotides, amino acids, proteins, peptides, hormones,
oligosaccharides, lipids, glycolipids, lipopolysaccharides,
phosphohpids, synthetic analogues of the foregoing, including, but
not limited to, inverted nucleotides, peptide nucleic acids,
Meta-DNA, and combinations of the above "Biopolymer synthesis" is
intended to encompass the synthetic production, both organic and
inorganic, of a biopolymer
[0042] Related to a bioploymer is a "biomonomer" which is intended
to mean a single unit of biopolymer, or a single unit which is not
part of a biopolymer Thus, for example, a nucleotide is a
biomonomer within an oligonucleotide biopolymer, and an amino acid
is a biomonomer within a protein or peptide biopolymer, avidin,
biotin, antibodies, antibody fragments, etc, for example, are also
biomonomers Initiation Biomonomer or "initiator biomonomer" is
meant to indicate the first biomonomer which is covalently attached
via reactive nucleophiles to the surface of the polymer, or the
first biomonomer which is attached to a linker or spacer arm
attached to the polymer, the linker or spacer arm being attached to
the polymer via reactive nucleophiles
[0043] Complementary Refers to the hybridization or base pairing
between nucleotides or nucleic acids, such as, for instance,
between the two strands of a double stranded DNA molecule or
between an oligonucleotide primer and a primer binding site on a
single stranded nucleic acid to be sequenced or amplified
Complementary nucleotides are, generally, A and T (or A and U), or
C and G Two single stranded RNA or DNA molecules are the to be
complementary when the nucleotides of one strand, optimally aligned
and compared and with appropriate nucleotide insertions or
deletions, pair with at least about 80% of the nucleotides of the
other strand, usually at least about 90% to 95%, and more
preferably from about 98 to 100% Alternatively, complementarity
exists when an RNA or DNA strand will hybridize under selective
hybridization conditions to its complement Typically, selective
hybridization will occur when there is at least about 65%
complementarity over a stretch of at least 14 to 25 nucleotides,
preferably at least about 75%, more preferably at least about 90%
complementarity See, M Kanehisa Nucleic Acids Res 12 203 (1984),
incorporated herein by reference
[0044] The term "hybridization" refers to the process in which two
single-stranded polynucleotides bind non-covalently to form a
stable double-stranded polynucleotide The term "hybridization" may
also refer to triple-stranded hybridization The resulting (usually)
double-stranded polynucleotide is a "hybrid" The proportion of the
population of polynucleotides that forms stable hybrids is referred
to herein as the "degree of hybridization"
[0045] Hybridization conditions will typically include salt
concentrations of less than about 1M, more usually less than about
500 mM and less than about 200 mM Hybridization temperatures can be
as low as 5.degree. C., but are typically greater than 22.degree.
C., more typically greater than about 30.degree. C., and preferably
in excess of about 37.degree. C. Hybridizations are usually
performed under stringent conditions, i e conditions under which a
probe will hybridize to its target subsequence Stringent conditions
are sequence-dependent and are different in different circumstances
Longer fragments may require higher hybridization temperatures for
specific hybridization As other factors may affect the stringency
of hybridization, including base composition and length of the
complementary strands, presence of organic solvents and extent of
base mismatching, the combination of parameters is more important
than the absolute measure of any one alone Generally, stringent
conditions are selected to be about 5.degree. C. lower than the
thermal melting point (Tm) fro the specific sequence at a defined
ionic strength and pH The Tm is the temperature (under defined
ionic strength, pH and nucleic acid composition) at which 50% of
the probes complementary to the target sequence hybridize to the
target sequence at equilibrium.
[0046] Typically, stringent conditions include salt concentration
of at least 0 01 M to no more than 1 M Na ion concentration (or
other salts) at a pH 7 0 to 8 3 and a temperature of at least
25.degree. C. For example, conditions of 5.times.SSPE (750 mM NaCl,
50 mM NaPhosphate, 5 mM EDTA, pH 7 4) and a temperature of
25-30.degree. C. are suitable for allele-specific probe
hybridizations For stringent conditions, see for example, Sambrook,
Fritsche and Maniatis "Molecular Cloning A laboratory Manual" 2nd
Ed Cold Spring Harbor Press (1989) and Anderson "Nucleic Acid
Hybridization" 1st Ed , BIOS Scientific Publishers Limited (1999),
which are hereby incorporated by reference in its entirety for all
purposes above
[0047] Hybridization probes are nucleic acids (such as
oligonucleotides) capable of binding in a base-specific manner to a
complementary strand of nucleic acid Such probes include peptide
nucleic acids, as described in Nielsen et al, Science 254 1497-1500
(1991), Nielsen Curr Opin Biotechnol, 10 71-75 (1999) and other
nucleic acid analogs and nucleic acid mimetics See U.S. Pat. No.
6,156,501
[0048] Probe A probe is a molecule that can be recognized by a
particular target In some embodiments, a probe can be surface
immobilized Examples of probes that can be investigated by this
invention include, but are not restricted to, agonists and
antagonists for cell membrane receptors, toxins and venoms, viral
epitopes, hormones (e g, opioid peptides, steroids, etc ), hormone
receptors, peptides, enzymes, enzyme substrates, cofactors, drugs,
lectins, sugars, oligonucleotides, nucleic acids, oligosaccharides,
proteins, and monoclonal antibodies
[0049] Target A molecule that has an affinity for a given probe
Targets may be naturally-occurring or man-made molecules Also, they
can be employed in their unaltered state or as aggregates with
other species Targets may be attached, covalently or noncovalently,
to a binding member, either directly or via a specific binding
substance Examples of targets which can be employed by this
invention include, but are not restricted to, antibodies, cell
membrane receptors, monoclonal antibodies and antisera reactive
with specific antigenic determinants (such as on viruses, cells or
other materials), drugs, oligonucleotides, nucleic acids, peptides,
cofactors, lectins, sugars, polysaccharides, cells, cellular
membranes, and organelles Targets are sometimes referred to in the
art as anti-probes As the term targets is used herein, no
difference in meaning is intended A "Probe Target Pair" is formed
when two macromolecules have combined through molecular recognition
to form a complex
[0050] Ligand A ligand is a molecule that is recognized by a
particular receptor In particular, the agent bound by or reacting
with a receptor is called a "ligand," a term which is meaningful
only in terms of its counterpart receptor The term "ligand" does
not imply any particular molecular size or other structural or
compositional feature other than that the substance in question is
capable of binding or otherwise interacting with the receptor Also,
a ligand may serve either as the natural ligand to which the
receptor binds, or as a functional analogue that may act as an
agonist or antagonist Examples of ligands that can be investigated
by this invention include, but are not restricted to, agonists and
antagonists for cell membrane receptors, toxins and venoms, viral
epitopes, hormones (e g, opiates, steroids, etc ), hormone
receptors, peptides, enzymes, enzyme substrates, substrate analogs,
transition state analogs, cofactors, drugs, proteins, and
antibodies
[0051] Receptor A molecule that has an affinity for a given ligand
Receptors may be naturally-occurring or manmade molecules Also,
they can be employed in their unaltered state or as aggregates with
other species Receptors may be attached, covalently or
noncovalently, to a binding member, either directly or via a
specific binding substance Examples of receptors which can be
employed by this invention include, but are not restricted to,
antibodies, cell membrane receptors, monoclonal antibodies and
antisera reactive with specific antigenic determinants (such as on
viruses, cells or other materials), drugs, polynucleotides, nucleic
acids, peptides, cofactors, lectins, sugars, polysaccharides,
cells, cellular membranes, and organelles Receptors are sometimes
referred to in the art as anti-ligands As the term "receptors" is
used herein, no difference in meaning is intended A "Ligand
Receptor Pair" is formed when two macromolecules have combined
through molecular recognition to form a complex Other examples of
receptors which can be investigated by this invention include but
are not restricted to those molecules shown in U.S. Pat. No.
5,143,854, which is hereby incorporated by reference in its
entirety
[0052] Effective amount refers to an amount sufficient to induce a
desired result mRNA or mRNA transcripts as used herein, include,
but are not limited to, pre-mRNA transcript(s), transcript
processing intermediates, mature mRNA(s) ready for transcription
and translation of the gene or genes, or nucleic acids derived from
the mRNA transcript(s) Transcript processing may include splicing
(possibly in alternative forms), editing and degradation As used
herein, a nucleic acid derived from an mRNA transcript refers to a
nucleic acid for whose synthesis the mRNA transcript or a
subsequence thereof has ultimately served as a template Thus, a
cDNA reverse transcribed from an mRNA, a cRNA transcribed from that
cDNA, a DNA amplified from the cDNA, an RNA transcribed from the
amplified DNA, etc, are all derived from the mRNA transcript and
detection of such derived products is indicative of the presence
and/or abundance of the original transcript in a sample Thus, mRNA
derived samples include, but are not limited to, mRNA transcripts
of the gene or genes, cDNA reverse transcribed from the mRNA, cRNA
transcribed from the cDNA, DNA amplified from the genes, RNA
transcribed from amplified DNA, and the like
[0053] A fragment, segment, or DNA segment refers to a portion of a
larger DNA polynucleotide or DNA A polynucleotide, for example, can
be broken up, or fragmented into, a plurality of segments Various
methods of fragmenting nucleic acid are well known in the art These
methods may be, for example, either chemical or physical in nature
Chemical fragmentation may include partial degradation with a
DNase, partial depurination with acid, the use of restriction
enzymes, intron-encoded endonucleases, DNA-based cleavage methods,
such as triplex and hybrid formation methods, that rely on the
specific hybridization of a nucleic acid segment to localize a
cleavage agent to a specific location in the nucleic acid molecule,
or other enzymes or compounds which cleave DNA at known or unknown
locations Physical fragmentation methods may involve subjecting the
DNA to a high shear rate High shear rates may be produced, for
example, by moving DNA through a chamber or channel with pits or
spikes, or forcing the DNA sample through a restricted size flow
passage, e g , an aperture having a cross sectional dimension in
the micron or submicron scale Other physical methods include
sonication and nebulization Combinations of physical and chemical
fragmentation methods may likewise be employed such as
fragmentation by heat and ion-mediated hydrolysis See for example,
Sambrook et al, "Molecular Cloning A Laboratory Manual," 3rd Ed
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
(2001) ("Sambrook et al ) which is incorporated herein by reference
for all purposes These methods can be optimized to digest a nucleic
acid into fragments of a selected size range Useful size ranges may
be from 100, 200, 400, 700 or 1000 to 500, 800, 1500, 2000, 4000 or
10,000 base pairs However, larger size ranges such as 4000, 10,000
or 20,000 to 10,000, 20,000 or 500,000 base pairs may also be
useful See, e g, Dong et al, Genome Research 11, 1418 (2001), in
U.S. Pat. Nos. 6,361,947, 6,391,592, incorporated herein by
reference
[0054] A primer is a single-stranded oligonucleotide capable of
acting as a point of initiation for template-directed DNA synthesis
under suitable conditions e g , buffer and temperature, in the
presence of four different nucleoside triphosphates and an agent
for polymerization, such as, for example, DNA or RNA polymerase or
reverse transcriptase The length of the primer, in any given case,
depends on, for example, the intended use of the primer, and
generally ranges from 15 to 30 nucleotides Short primer molecules
generally require cooler temperatures to form sufficiently stable
hybrid complexes with the template A primer need not reflect the
exact sequence of the template but must be sufficiently
complementary to hybridize with such template The primer site is
the area of the template to which a primer hybridizes The primer
pair is a set of primers including a 5' upstream primer that
hybridizes with the 5' end of the sequence to be amplified and a 3'
downstream primer that hybridizes with the complement of the 3' end
of the sequence to be amplified
[0055] A genome is all the genetic material of an organism In some
instances, the term genome may refer to the chromosomal DNA A
genome may be multichromosomal such that the DNA is cellularly
distributed among a plurality of individual chromosomes For
example, in human there are 22 pairs of chromosomes plus a gender
associated XX or XY pair DNA derived from the genetic material in
the chromosomes of a particular organism is genomic DNA The term
genome may also refer to genetic materials from organisms that do
not have chromosomal structure In addition, the term genome may
refer to mitochondria DNA A genomic library is a collection of DNA
fragments that represents the whole or a portion of a genome
Frequently, a genomic libary is a collection of clones made from a
set of randomly generated, sometimes overlapping DNA fragments
representing the entire genome or a portion of the genome of an
organism
[0056] An allele refers to one specific form of a genetic sequence
(such as a gene) within a cell or within a population, the specific
form differing from other forms of the same gene in the sequence of
at least one, and frequently more than one, variant sites within
the sequence of the gene The sequences at these variant sites that
differ between different alleles are termed "variances",
"polymorphisms", or "mutations"
[0057] At each autosomal specific chromosomal location or "locus"
an individual possesses two alleles, one inherited from the father
and one from the mother An individual is "heterozygous" at a locus
if it has two different alleles at that locus An individual is
"homozygous" at a locus if it has two identical alleles at that
locus
[0058] Polymorphism refers to the occurrence of two or more
genetically determined alternative sequences or alleles in a
population A polymorphic marker or site is the locus at which
divergence occurs Preferred markers have at least two alleles, each
occurring at frequency of greater than 1%, and more preferably
greater than 10% or 20% of a selected population A polymorphism may
comprise one or more base changes, an insertion, a repeat, or a
deletion A polymorphic locus may be as small as one base pair
Polymorphlc markers include restriction fragment length
polymorphisms, variable number of tandem repeats (VNTR's),
hypervariable regions, minisatellites, dinucleotide repeats,
trinucleotide repeats, tetranucleotide repeats, simple sequence
repeats, and insertion elements such as Alu The first identified
allelic form is arbitrarily designated as the reference form and
other allelic forms are designated as alternative or variant
alleles The allelic form occurring most frequently in a selected
population is sometimes referred to as the wildtype form Diploid
organisms may be homozygous or heterozygous for allelic forms A
diallelic polymorphism has two forms A triallelic polymorphism has
three forms Single nucleotide polymorphisms (SNPs) are included in
polymorphisms
[0059] Single nucleotide polymorphism (SNPs) are positions at which
two alternative bases occur at appreciable frequency (>1%) in
the human population, and are the most common type of human genetic
variation The site is usually preceded by and followed by highly
conserved sequences of the allele (e g, sequences that vary in less
than {fraction (1/100)} or {fraction (1/1000)} members of the
populations) A single nucleotide polymorphism usually arises due to
substitution of one nucleotide for another at the polymorphic site
A transition is the replacement of one purine by another purine or
one pyrimidine by another pyrimidine A transversion is the
replacement of a purine by a pyrimidine or vice versa Single
nucleotide polymorphisms can also arise from a deletion of a
nucleotide or an insertion of a nucleotide relative to a reference
allele
[0060] Genotyping refers to the determination of the genetic
information an individual carries at one or more positions in the
genome For example, genotyping may comprise the determination of
which allele or alleles an individual carries for a single SNP or
the determination of which allele or alleles an individual carries
for a plurality of SNPs A genotype may be the identity of the
alleles present in an individual at one or more polymorphic
sites
[0061] Linkage disequilibrium or allelic association means the
preferential association of a particular allele or genetic marker
with a specific allele, or genetic marker at a nearby chromosomal
location more frequently than expected by chance for any particular
allele frequency in the population For example, if locus X has
alleles a and b, which occur equally frequently, and linked locus Y
has alleles c and d, wluch occur equally frequently, one would
expect the combination ac to occur with a frequency of 0 25 If ac
occurs more frequently, then alleles a and c are in linkage
disequilibrium Linkage disequilibrium may result from natural
selection of certain combination of alleles or because an allele
has been introduced into a population too recently to have reached
equilibrium with linked alleles A marker in linkage disequilibrium
can be particularly useful in detecting susceptibility to disease
(or other phenotype) notwithstanding that the marker does not cause
the disease For example, a marker (X) that is not itself a
causative element of a disease, but which is in linkage
disequilibrium with a gene (including regulatory sequences) (Y)
that is a causative element of a phenotype, can be detected to
indicate susceptibility to the disease in circumstances in which
the gene Y may not have been identified or may not be readily
detectable
[0062] III. Direct Write Optical Lithography System
[0063] Direct Write Optical Lithography System may provide
flexibility for polymer array synthesis by providing a maskless
optical lithography system and method where predetermined image
patterns can be dynamically changed during photolithographic
processing Maskless lithographic systems are particularly useful
for rapid product prototyping In such application, a polymer array
is designed and then synthesized using maskless lithography The
polymer array may be tested for its performance Several designs can
be compared If a design is acceptable, maskless can be made
according to the design to produce a large number of polymer
arrays
[0064] An optical lithography system is provided to include a means
for dynamically changing an intended image pattern without using a
photomask One such means includes a spatial light modulator that is
electronically controlled by a computer to generate unique
predetermined image patterns at each photolithographic step in
polymer array synthesis The spatial light modulators can be, for
example, micromachined mechanical modulators or microelectronic
devices (e g liquid crystal display (LCD)) The Direct Write System
of the present invention using such spatial light modulators is
particularly useful in the synthesis of polymer arrays, such as
polypeptide, carbohydrate, and nucleic acid arrays Nucleic acid
arrays typically include polynucleotides or oligonucleotides
attached to glass, for example, Deoxyribonucleic Acid (DNA)
arrays
[0065] Certain preferred embodiments of the invention involve use
of the micromachined mechanical modulators to direct the light to
predetermined regions (i e , known areas on a substrate predefined
prior to photolithography processing) of the substrate on which the
polymers are being synthesized The predetermined regions of the
substrate associated with, for example, one segment (referred to
herein as a pixel) of a micromachined mechanical modulator (e g , a
micro-mirror array) are referred to herein as features In each
predetermined region or feature a particular oligonucleotide
sequence, for example, is synthesized The mechanical modulators
come in a variety of types, two of which will be discussed in some
detail below
[0066] One type of mechanical modulator is a micro-mirror array
which uses small metal mirrors to selectively reflect a light beam
to particular individual features, thus causing the individual
features to selectively receive light from a light source (i e ,
turning light on and off of the individual features) An example is
the programmable micro-mirror array Digital Micromirror Device
(DMD.TM.) manufactured by Texas Instruments, Inc, Dallas, Tex., USA
Texas Instruments markets the arrays primarily for projection
display applications (e g, big-screen video) in which a highly
magnified image of the array is projected onto a wall or screen The
present invention shows, however, that with appropriate optics and
an appropriate light source, a programmable micro-mirror array can
be used for photolithographic synthesis, and in particular for
polymer array synthesis The Texas Instruments DLP.TM. technology
can be used to make digital micromirrors of different resolutions
Some arrays are designed to be illuminated 20 degrees off axis Each
mirror can be turned on (tilted 10 degrees in one direction) or off
(tilted 10 degrees in the other direction) A lens (on axis) images
the array onto a target When a micro-mirror is turned on, light
reflected by the micro-mirror passes through the lens and the image
of the micro-mirror appears bright When a micro-mirror is turned
off, light reflected by the micro-mirror misses the lens and the
image of the micro-mirror appears dark The array can be
reconfigured by software (i e , every micro-mirror in the array can
be turned on or off as desired) in a fraction of a second
[0067] An optical lithography system including a micro-mirror array
1 based spatial light modulator according to one embodiment of the
invention is shown in FIG. 1 This embodiment includes a spatial
light modulator made of a micro-mirror array 1, and arc lamp 3, and
a lens 2 to project a predetermined image pattern on a chip or
wafer (containing many chips) 4 In operation, collimated, filtered
and homogenized light 5 from the arc lamp 3 is selectively
reflected as a light beam 6 according to dynamically turned on
micro mirrors in the micro-mirror array 1 and transmitted through
lens 2 on to chip or wafer 4 as reflected light beam 8 Reflected
light from micro-mirrors that are turned off 7 is reflected in a
direction away from the lens 2 so that these areas appear dark to
the lens 2 and chip or wafer 4 Thus, the spatial light modulator,
micro-mirror array 1, modulates the direction of reflected light (6
and 7) so as to define a predetermined light image 8 projected onto
the chip or wafer 4 The direction of the reflected light alters the
light intensity transmitted from each pixel to each feature In
essence, the spatial light modulator operates as a directional and
intensity modulator The micro-mirror array 1 can be provided by,
for example, the micro-mirror array of the Texas Instruments(TI)
DMD, in particular, the TI SVGA DLP.TM. subsystem The Texas
Instruments SVGA DLP.RTM. subsystem with optics may be modified for
use in the present invention The Texas instruments SVGA DLP.TM.
subsystem includes a micro-mirror array (shown as micro-mirror
array 1 in FIG. 1), a light source, a color filter wheel, a
projection lens, and electronics for driving the array and
interfacing to a computer the color filter wheel is replaced with a
bandpass filter having, for example, a bandpass wavelength of
365-410 (wavelength dependent upon the type of photochemicals
selected for used in the process) for additional brightness at
wavelengths of, for example, 400-410the light source can be
replaced with arc lamp 3 and appropriate homogenizing and
collimating optics the lens included with the device is intended
for use at very large conjugate ratios and is replaced with lens 2
or set of lenses appropriate for imaging the micro-mirror array 1
onto chip or wafer 4 with the desired magnification selection of
the appropriate lens and bandpass filter is dependent on, among
other things, the requisite image size to be formed on the chip,
the type of spatial light modulator, the type of light source, and
the type of photoresist and photochemicals being used in the system
and process
[0068] A symmetric lens system (e g, lenses arranged by type
A-B-C-C-B-A) used at 1 1 magnification (object size is the same as
the image size) is desirable because certain aberrations
(distortion, lateral color, coma) are minimized by symmetry
Further, a symmetric lens system results in a relatively simple
lens design because there are only half as many variables as in an
asymmetric system having the same number of surfaces However, at 1
1 magnification the likely maximum possible chip size is 10 888
16with a VGA device, or 10 213 6 with an SVGA device Synthesis of,
for example, a standard GeneChip.RTM. 12 8 mm chip uses an
asymmetric optical system (e g, a magnification of about 1 25 1
with SVGA device) or a larger micro-mirror array (e g, 1 028
mirrors) if the mirror size is constant in essence, the lens
magnification can be greater than or less than 1 depending on the
desired size of the chip
[0069] In certain applications of the invention, a relatively
simple lens system, such as a back-to-back pair of achromats or
camera lens, is adequate A particularly useful lens for some
applications of the invention is the Rodenstock (Rockford, IL)
Apo-Rodagon D This lens is optimized for 1 1 imaging and gives good
performance at magnifications up to about 1.3 1 Similar lenses may
be available from other manufacturers with such lenses, either the
Airy disk diameter or the blur circle diameter will be rather large
(maybe 10 or larger) see Modern Optical Engineering, 2d Edition,
Smith, W J, ed, Mcgraw-Hill, Inc, New York (1990) For
higher-quality synthesis, the feature size is several times larger
than the airy disk or blur circle therefore, a custom-made lens
with resolution of about 1-2 over a 12 8 field is particularly
desirable
[0070] A preferred embodiment of synthesizing polymer arrays with a
programmable micro-mirror array using the DMT process with
photoresist takes place as follows First, a computer file is
generated and specifies, for each photolithography step, which
mirrors in the micro-mirror array 1 need to be on and which need to
be off to generate a particular predetermined image pattern Next,
the individual chip or the wafer from which it is made 4 is coated
with photoresist on the synthesis surface and is mounted in a
holder or flow cell (not shown) on the photolithography apparatus
so that the synthesis surface is in the plane where the image of
the micro-mirror array 1 will be formed The photoresist may be
either positive or negative thus allowing deprotection at locations
exposed to the light or deprotection at locations not exposed to
the light, respectively (example photoresists include negative tone
SU-8 epoxy resin (Shell Chemical) and those shown in the above
cited patents and U.S. Pat. No. 5,959,098) A mechanism for aligning
and focusing the chip or wafer is provided, such as a x-y
translation stage Then, the micro-mirror array 1 is programmed for
the appropriate configuration according to the desired
predetermined image pattern, a shutter in the arc lamp 3 is opened,
the chip or wafer 4 is illuminated for the desired amount of time,
and the shutter is closed if a wafer (rather than a chip) is being
synthesized, a stepping-motor-driven translation stage moves the
wafer by a distance equal to the desired center-to-center distance
between chips and the shutter of the arc lamp 3 is opened and
closed again, these two steps being repeated until each chip of the
wafer has been exposed
[0071] Next, the photoresist is developed and etched exposure of
the wafer 4 to acid then cleaves the DMT protecting groups from
regions of the wafer where the photoresist has been removed The
remaining photoresist is then stripped Then DMT-protected
nucleotides containing the desired base (adenine (A), cytosine (C),
guanine (G), or thymine (T)) are coupled to the deprotected
oligonucleotides
[0072] Subsequently, the chip or wafer 4 is re-coated with
photoresist The steps from mounting the photoresist coated chip or
wafer 4 in a holder through re-coating the chip or wafer 4 with
photoresist are repeated until the polymer array synthesis is
complete
[0073] As is clear from the above described method for polymer
array synthesis, no photomasks are needed This simplifies the
process by eliminating processing time associated with changing
masks in the optical lithography system and reduces the
manufacturing cost for polymer array synthesis by eliminating the
cost of the masks as well as processing defects associated with
using masks In addition, the process has improved flexibility
because reprogramming the optical lithography system to produce a
different image pattern can be done with relatively little lead
time compared with the time it takes to generate and verify new
photomasks, thus making it possible to transfer an image pattern
computer file directly from a CAD or similar system to the optical
lithography system or providing electronic signals directly from
the CAD system to drive the optical lithography system's means for
dynamically producing the desired light pattern (e g, spatial light
modulator) Therefore, the optical lithography system is simplified
and more efficient than conventional photomask based optical
lithography systems This is particularly valuable in complex
multiple step photolithography processing, for example polymer
array synthesis of GeneChip.RTM. probe arrays having upwards of
seventy or more cycles, especially when many different products are
made and revised
[0074] When synthesizing nucleic acid arrays, the photochemical
processes used to fabricate the arrays is preferably activated with
light having a wavelength greater than 365to avoid photochemical
degradation of the polynucleotides used to create the polymer
arrays Other wavelengths may be desirable for other probes Many
photoacid generators (PAGs) based on o -nitrobenzyl chemistry are
useful at 365 Further, when using the mirror array from Texas
Instruments discussed above, the PAG is preferably sensitive above
400to avoid damage to the mirror array to achieve this, p
-nitrobenzyl esters can be used in conjunction with a
photosensitizer for example, p -nitrobenzyltosylate and
2-ethyl-9,10-dimethoxy-anthracene can be used to photochemically
generate toluenesulfonic acid at 405 See S C Busman and J E Trend,
J Imag Technol , 1985, 11, 191, A T and O J Chem , 1988, 53, 3386
In this system, the sensitizer absorbs the light and then transfers
the energy to the p -nitrobenzyltosylate, causing dissociation and
the subsequent release of toluensulfonic acid Alternate
sensitizers, such as pyrene, N,N-dimethylnapthylamine, perylene,
phenothiazine, canthone, thiocanthone, actophenone, and
benzophenone that absorb light at other wavelengths are also
useful
[0075] A variety of photoresists sensitive to 436-nm light are
available for use in polymer array synthesis and will avoid
photochemical degradation of the polynucleotides
[0076] A second preferred mechanical modulator that may be used in
the invention is the Grating Light Valve.TM. (GLV.TM.) available
from Silicon LightMachines, Sunnyvale, Calif., USA The GLV.TM.
relies on micromachined pixels that can be programmed to be either
reflective or diffractive (Grating Light Valve.TM. technology)
Information regarding certain of the mechanical modulators
discussed herein is obtained at http //www ti com (Texas
instruments) and http //siliconlight com (Silicon
LightMachines)
[0077] Although preferred spatial light modulators include the
mechanical modulators DMD.TM. available from Texas Instruments and
the GLV.TM. available from Silicon LightMachines, various types of
spatial light modulators exist and may be used in the practice of
the present invention See Electronic Engineers Handbook, 3rd Ed,
Fink, D G and Christiansen, D Eds, Mcgraw-Hill Book Co, New York
(1989) Deformable membrane mirror arrays are available from Optron
Systems Inc (Bedford, Mass.) Liquid-crystal spatial light
modulators are available from Hamamatsu (Bridgewater, N.J.),
Spatialight (Novato, Calif.), and other companies However, one
skilled in the art must be careful to select the proper light
source and processing chemistries to ensure that the liquid-crystal
spatial light modulator is not damaged since these devices may be
susceptible to damage by various ultraviolet (uv) light
Liquid-crystal displays (LCD, e g, in calculators and notebook
computers) are also spatial light modulators useful for
photolithography particularly to synthesize large features However,
reduction optics would be required to synthesize smaller features
using LCDs
[0078] One embodiment that is particularly useful for extremely
high resolution involves imaging the micro-mirror array using a
system of the type shown in FIG. 2 In this system, a lens 12 images
the micro-mirror array 11 (e g, DMD.TM. or GLV.TM.) onto an array
10 having an array of micro-lenses 15 or non-imaging light
concentrators Each element of the array 10 focuses light onto the
chip or wafer, e g, Gene Chip array 14 Each micro-lens 15 produces
an image of one pixel of the micro-mirror array 11 Optics 16,
including a shaping lens 17 may be included to translate light from
a light source 13 onto the micro-mirror array 11
[0079] For example, if an SVGA DLP.TM. device is imaged with 1 1
magnification onto a micro-lens array 10, an appropriate micro-lens
array 10 can consist of 800600 lenses (micro-lenses 15) with 17
.mu.m center-to-center spacing Alternatively, the micro-lens array
can consist of 400.times.300 17 .mu.m diameter lenses with 34 .mu.m
center-to-center spacing, and with opaque material (e g, chrome)
between micro-lenses 15 One advantage of this alternative is that
cross-talk between pixels is reduced The light incident upon each
micro-lens 15 can be focused to a spot size of 1-2 .mu.m Because
the spot size is much less than the spacing between micro-lenses, a
2-axis translation stage (having, in these examples, a range of
travel of at least either 17 .mu.m.times.17 .mu.m or 34
.mu.m.times.34 .mu.m) is necessary if complete coverage of the chip
or wafer 14 is desired
[0080] Micro-lenses 15 can be diffractive, refractive, or hybrid
(diffractive and refractive) Refractive micro-lenses can be
conventional or gradient-index A portion of a diffractive
micro-lens array 10 is shown in Figureand has individual
micro-lenses formed as circles commonly known as Fresnel Zone
Plates 20 Alternatively an array of non-imaging light concentrators
can be employed An example of such an approach would include a
short piece of optical fiber which may be tapered to a small
tip
[0081] Furthermore, some spatial light modulators are designed to
modulate transmitted rather than reflected light An example of a
transmissive spatial light modulator is a liquid crystal display
(LCD) and is illustrated in another embodiment, shown in FIG. 4
This embodiment includes a light source 33 providing light 35,
transmissive spatial light modulator 31 and a computer 39 providing
electronic control signals to the transmissive spatial light
modulator 31 through cables 40 so as to transmit a desired light
image 38 on the chip or wafer 34 The computer 39 may be, for
example, a unique programmable controller, a personal computer
(PC), or a CAD system used to design the desired image pattern
Using a transmissive spatial light modulator has even additional
advantages over the conventional optical lithography system
Reflective spatial light modulators require a large working
distance between the modulator and the lens so that the lens does
not block the incident light Designing a high performance lens with
a large working distance is more difficult than designing a lens of
equivalent performance with no constraints on the working distance
With a transmissive spatial light modulator the working distance
does not have to be long and lens design is therefore easier In
fact, as show in FIG. 4, some transmissive spatial light modulators
31 might be useful for proximity or contact printing with no lens
at all, by locating the modulator very close to the chip or wafer
34 In fact, the transmissive spatial light modulator in the
embodiment of FIG. 4 could be replaced by an LED array or a
semiconductor laser arrays emitting light of the appropriate
wavelength, each of which not only may be operated to dynamically
define a desired image but also act as the light source Thus, as
modified, this embodiment would be simplified so as to not require
a separate light source
[0082] In another embodiment, the use of fiber optic arrays or
bundles as a light guide to transmit ultraviolet light to the
substrate surface FIGS. 5a and 5b shows a representation of an
exemplary lithography system using fiber optic arrays
[0083] The Digital Micromirror Array (DMA) is used as a switching
device to reflect light onto the entry side of the fiber optic
array since the DMA can selectively reflect light at individual
mirrors or pixels, only specific fiber elements will be illuminated
The light that exits the other end of the fiber array will
illuminate selected locations on the substrate
[0084] Even though the diameters of some commercially available
fiber elements, (5-10 um, with 20 um cladding) have relatively
large diameter (the density of the pixels from DMA devices is
considerably higher (14 um square)), if the substrate is positioned
very close to the end of the fiber optic arrays, 5-10 um features
can be produced
[0085] In some embodiments, the use of spherical lens on the entry
and exit ends of the fibers can enhance the collection and focus of
light as well On the entry end, the relative narrow collection
angle of a conventional fiber may not be efficient enough to
transmit sufficient light intensity to the substrate surface On the
exit end of the fiber a large angle of light scatter is typically
expected The addition of spherical lenses bonded to a concave
surface on the end of the fiber may be beneficial
[0086] Another consideration involves the relative density or
packing of features that can be possible with fiber optics with the
relatively large cladding diameters the closest adjoining features
may be 20 um apart However, if a staggered array of fiber elements
is created and a scanning technique is used to translate the fiber
bundle across the substrate, feature spacing can be reduced (5-10um
or smaller)
[0087] In exemplary embodiments for scanning include moving the
DMA, fiber optic array or substrate relative to each other FIG. 5b
shows one such embodiment in some embodiments, it may be beneficial
to control the sequence timing and spatial coordinates of the light
switching by the DMA relative to the other translating
components
[0088] It is to be understood that the above description is
intended to be illustrative and not restrictive Many variations of
the invention will be apparent to those of skill in the art upon
reviewing the above description The scope of the invention should
be determined with reference to the appended claims, along with the
full scope of equivalents to which such claims are entitled All
cited references, including patent and non-patent literature, are
incorporated herewith by reference in their entireties for all
purposes
* * * * *