U.S. patent application number 10/997136 was filed with the patent office on 2005-08-25 for combinatorial strategies for polymer synthesis.
This patent application is currently assigned to Affymetrix, Inc.. Invention is credited to Aldwin, Lois, Buchko, Christopher J., Fodor, Stephen P.A., Modlin, Douglas N., Ross, Debra A., Winkler, James L..
Application Number | 20050186683 10/997136 |
Document ID | / |
Family ID | 34916589 |
Filed Date | 2005-08-25 |
United States Patent
Application |
20050186683 |
Kind Code |
A1 |
Winkler, James L. ; et
al. |
August 25, 2005 |
Combinatorial strategies for polymer synthesis
Abstract
A method and device for forming large arrays of polymers on a
substrate (401). According to a preferred aspect of the invention,
the substrate is contacted by a channel block (407) having channels
(409) therein. Selected reagents are delivered through the
channels, the substrate is rotated by a rotating stage (403), and
the process is repeated to form arrays of polymers on the
substrate. The method may be combined with light-directed
methodolgies.
Inventors: |
Winkler, James L.; (San
Diego, CA) ; Fodor, Stephen P.A.; (Palo Alto, CA)
; Buchko, Christopher J.; (Palo Alto, CA) ; Ross,
Debra A.; (Arnold, CA) ; Aldwin, Lois; (San
Mateo, CA) ; Modlin, Douglas N.; (Palo Alto,
CA) |
Correspondence
Address: |
BANNER & WITCOFF LTD.,
ATTORNEYS FOR AFFYMETRIX
1001 G STREET , N.W.
ELEVENTH FLOOR
WASHINGTON
DC
20001-4597
US
|
Assignee: |
Affymetrix, Inc.
Santa Clara
CA
AFFYMAX TECHNOLOGIES N.V.
Curacao
|
Family ID: |
34916589 |
Appl. No.: |
10/997136 |
Filed: |
November 24, 2004 |
Related U.S. Patent Documents
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Application
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Filing Date |
Patent Number |
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10997136 |
Nov 24, 2004 |
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09579982 |
May 26, 2000 |
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09579982 |
May 26, 2000 |
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09498554 |
Feb 4, 2000 |
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09498554 |
Feb 4, 2000 |
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09129463 |
Aug 4, 1998 |
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6040193 |
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09129463 |
Aug 4, 1998 |
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08426202 |
Apr 21, 1995 |
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6136269 |
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08426202 |
Apr 21, 1995 |
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07980523 |
Nov 20, 1992 |
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5677195 |
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07980523 |
Nov 20, 1992 |
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07874849 |
Apr 24, 1992 |
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5412087 |
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07980523 |
Nov 20, 1992 |
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07796243 |
Nov 22, 1991 |
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5384261 |
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Current U.S.
Class: |
436/174 |
Current CPC
Class: |
B01J 2219/00432
20130101; B01J 2219/00619 20130101; B01J 2219/0059 20130101; C07H
21/00 20130101; Y10T 436/2575 20150115; B01J 2219/00686 20130101;
Y10T 436/255 20150115; B01J 2219/00527 20130101; B01J 2219/00612
20130101; B01J 2219/00626 20130101; B01J 2219/00722 20130101; C40B
60/14 20130101; Y10T 436/143333 20150115; B01J 2219/00475 20130101;
B01J 2219/00637 20130101; C07B 2200/11 20130101; C40B 40/06
20130101; B01J 2219/00378 20130101; C07K 1/045 20130101; B01J
19/0046 20130101; B01J 2219/00725 20130101; B82Y 30/00 20130101;
B01J 2219/0061 20130101; G01N 35/1072 20130101; B01J 2219/00531
20130101; B01J 2219/00659 20130101; B01J 2219/00702 20130101; B01J
2219/00536 20130101; B01J 2219/00711 20130101; C40B 40/10 20130101;
B01J 2219/005 20130101; B01J 2219/00416 20130101; B01J 2219/00621
20130101; B01J 2219/00367 20130101; Y10S 436/809 20130101; B01J
2219/0043 20130101; B01J 2219/00369 20130101; B01J 2219/00389
20130101; C07K 1/047 20130101; Y10T 436/25 20150115; B01J
2219/00608 20130101; B01J 2219/00585 20130101; B01J 2219/00596
20130101; B01J 2219/00605 20130101; B01J 2219/00364 20130101; B01J
2219/00529 20130101 |
Class at
Publication: |
436/174 |
International
Class: |
G01N 001/00 |
Claims
1. A method of forming polymers having diverse monomer sequences on
a single substrate, said substrate comprising a surface with a
plurality of selected regions, said method comprising the steps of:
a) forming a plurality of channels adjacent said surface, said
channels at least partially having a wall thereof defined by a
portion of said selected regions; b) placing selected monomers in
said channels to synthesize polymers at said portion of said
selected regions, said portion of said selected regions comprising
polymers with a sequence of monomers different from polymers in at
least one other of said selected regions; and c) repeating steps a)
and b) with said channels formed along a second portion of said
selected regions.
2-47. (canceled)
Description
BACKGROUND OF THE INVENTION
[0001] This application is a continuation-in-part of U.S. Ser. No.
796,243 (filed Nov. 22, 1991) which is incorporated herein by
reference for all purposes. This application is also a
continuation-in-part of U.S. Ser. No. 874,849 (filed Apr. 24,
1992), which is incorporated herein by reference for all
purposes.
[0002] The present invention relates to the field of polymer
synthesis and screening. More specifically, in one embodiment the
invention provides an improved method and system for synthesizing
arrays of diverse polymer sequences. According to a specific aspect
of the invention, a method of synthesizing diverse polymer
sequences such as peptides or oligonucleotides is provided. The
diverse polymer sequences may be used, for example, in screening
studies for determination of binding affinity.
[0003] Methods of synthesizing desired polymer sequences such as
peptide sequences are well known to those of skill in the art.
Methods of synthesizing oligonucleotides are found in, for example,
Oligonucleotide Synthesis: A Practical Approach, Gate, ed., IRL
Press, oxford (1984), incorporated herein by reference in its
entirety for all purposes. The so-called "Merrifield" solid phase
peptide synthesis has been in common use for several years and is
described in Merrifield, J. Am. Chem. Soc. (1963) 85:2149-2154,
incorporated herein by reference for all purposes. Solid-phase
synthesis techniques have been provided for the synthesis of
several peptide sequences on, for example, a number of "pins." See
e.g., Geysen et al., J. Immun. Meth. (1987) 102:259-274,
incorporated herein by reference for all purposes. Other
solid-phase techniques involve, for example, synthesis of various
peptide sequences on different cellulose disks supported in a
column. See Frank and Doring, Tetrahedron (1988) 44:6031-6040,
incorporated herein by reference for all purposes. Still other
solid-phase techniques are described in U.S. Pat. No. 4,728,502
issued to Hamill and WO 90/00626 (Beattie, inventor).
[0004] Each of the above techniques produces only a relatively low
density array of polymers. For example, the technique described in
Geysen et al. is limited to producing 96 different polymers on pins
spaced in the dimensions of a standard microtiter plate.
[0005] Improved methods of forming large arrays of peptides,
oligonucleotides, and other polymer sequences in a short period of
time have been devised. Of particular note, Pirrung et al., U.S.
Pat. No. 5,143,854 (see also PCT Application No. WO 90/15070) and
Fodor et al., PCT Publication No. WO 92/10092, all incorporated
herein by reference, disclose methods of forming vast arrays of
peptides and other polymer sequences using, for example,
light-directed synthesis techniques. See also, Fodor et al.,
Science (1991) 251:767-777, also incorporated herein by reference
for all purposes.
[0006] Some work has been done to automate synthesis of polymer
arrays. For example, Southern, PCT Application No. WO 89/10977
describes the use of a conventional pen plotter to deposit three
different monomers at twelve distinct locations on a substrate.
These monomers were subsequently reacted to form three different
polymers, each twelve monomers in length. The Southern Application
also mentions the possibility of using an ink-jet printer to
deposit monomers on a substrate. Further, in the above-referenced
Fodor et al., PCT application, an elegant method is described for
using a computer-controlled system to direct a VLSIPS.TM.
procedure. Using this approach, one heterogenous array of polymers
is converted, through simultaneous coupling at a number of reaction
sites, into a different heterogenous array. This approach is
referred to generally as a "combinatorial" synthesis.
[0007] The VLSIPS.TM. techniques have met with substantial success.
However, in some cases it is desirable to have alternate/additional
methods of forming polymer sequences which would not utilize, for
example, light as an activator, or which would not utilize light
exclusively.
SUMMARY OF THE INVENTION
[0008] Methods and devices for synthesizing high-density arrays of
diverse polymer sequences such as diverse peptides and
oligonucleotides are provided by virtue of the present invention.
In addition, methods and devices for delivering (and, in some
cases, immobilizing) available libraries of compounds on specific
regions of a substrate are provided by this invention. In preferred
embodiments, various monomers or other reactants are delivered to
multiple reaction sites on a single substrate where they are
reacted in parallel.
[0009] According to a preferred embodiment of the invention, a
series of channels, grooves, or spots are formed on or adjacent a
substrate. Reagents are selectively flowed through or deposited in
the channels, grooves, or spots, forming an array having different
compounds--and in some embodiments, classes of compounds--at
selected locations on the substrate.
[0010] According to the first specific aspect of the invention, a
block having a series of channels, such as grooves, on a surface
thereof is utilized. The block is placed in contact with a
derivatized glass or other substrate. In a first step, a pipettor
or other delivery system is used to flow selected reagents to one
or more of a series of apertures connected to the channels, or
place reagents in the channels directly, filling the channels and
"striping" the substrate with a first reagent, coupling a first
group of monomers thereto. The first group of monomers need not be
homogenous. For example, a monomer A may be placed in a first group
of the channels, a monomer B in a second group of channels, and a
monomer C in a third group of channels. The channels may in some
embodiments thereafter be provided with additional reagents,
providing coupling of additional monomers to the first group of
monomers. The block is then translated or rotated, again placed on
the substrate, and the process is repeated with a second reagent,
coupling a second group of monomers to different regions of the
substrate. The process is repeated until a diverse set of polymers
of desired sequence and length is formed on the substrate. By
virtue of the process, a is number of polymers having diverse
monomer sequences such as peptides or oligonucleotides are formed
on the substrate at known locations.
[0011] According to the second aspect of the invention, a series of
microchannels or microgrooves are formed on a substrate, along with
an appropriate array of microvalves. The channels and valves are
used to flow, selected reagents over a derivatized surface. The
microvalves are used to determine which of the channels are opened
for any particular coupling step.
[0012] Accordingly, one embodiment of the invention provides a
method of forming diverse polymer sequences on a single substrate,
the substrate comprising a surface with a plurality of selected
regions. The method includes the steps of forming a plurality of
channels adjacent the surface; the channels at least partially
having a wall thereof defined by a portion of the selected regions;
and placing selected reagents in the channels to synthesize polymer
sequences at the portion of the selected regions, the portion of
the selected regions comprising polymers with a sequence of
monomers different from polymers in at least one other of the
selected regions. In alternative embodiments, the channels or flow
paths themselves constitute the selected reaction regions. For
example, the substrate may be a series of adjoining parallel
channels, each having reaction sites therein.
[0013] According to a third aspect of the invention, a substrate is
provided which has an array of discrete reaction regions separated
from one another by inert regions. In one embodiment, a first
monomer solution is spotted on a first set of reaction regions of a
suitably derivatized substrate. Thereafter, a second monomer
solution is spotted on a second set of regions, a third monomer
solution is spotted on a third set and so on, until a number of the
regions each have one species of monomer located therein. These
monomers are reacted with the surface, and the substrate is
subsequently washed and prepared for reaction with a new set of
monomers. Dimers, trimers, and larger polymers of controlled length
and monomer sequence are prepared by repeating the above steps with
different groupings of the reaction regions and monomer solutions.
In alternative embodiments, the polymers or other compounds of the
array are delivered to the regions as complete species, and thus
the above polymer synthesis steps are unnecessary.
[0014] In a preferred embodiment, a plurality of reaction regions
on the substrate surface are surrounded by a constraining region
such as a non-wetting region which hinders the transport of
reactants between adjacent reaction regions. Thus, the reactants in
one region cannot flow to other regions where they could
contaminate the reaction. In certain preferred embodiments, the
regions of the array are defined by selective irradiation of a
substrate surface containing photolabile hydrophobic protecting
groups. In areas where the surface is irradiated, the hydrophobic
protecting groups are removed to define reaction regions. When an
aqueous or other polar reactant solution is deposited. in the
reaction region, it will have a relatively large wetting angle with
the substrate surface so that by adjusting the amount deposited,
one can ensure no flow to adjacent regions.
[0015] A further understanding of the nature and advantages of the
inventions herein may be realized by reference to the remaining
portions of the specification and the attached drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIG. 1 is a generalized diagram illustrating the
invention;
[0017] FIG. 2 is a flow chart illustrating the treatment steps
performed in synthesizing an array of various polymers;
[0018] FIG. 3 is a mapping of a resulting array of polymers;
[0019] FIG. 4a to 4c illustrate the arrangement of three channel
block templates in six process steps employed to synthesize 64
million hexapeptides from a 20 amino acid basis set;
[0020] FIG. 5a is a top view and FIG. 5b is a cross-sectional view
of a first embodiment of a device used to synthesize arrays of
polymer sequences;
[0021] FIG. 6 is a cross-sectional view of an embodiment containing
a pressure chamber for holding a substrate against a channel
block;
[0022] FIGS. 7a and 7b are top views of two of two different
"fanned array" channel blocks;
[0023] FIG. 8 is a cross-sectional view of a channel block and
associated flow ports according to one embodiment of the
invention;
[0024] FIG. 9 is a detailed cross-sectioal view of the flow ports
in a channel block;
[0025] FIG. 10 is a diagram of a flow system used to deliver
coupling compounds and reagents to a flow cell;
[0026] FIGS. 11a and 11b show an apparatus used to transfer a
substrate from one channel block to another;
[0027] FIG. 12 is a diagram of a multichannel solid-phase
synthesizer;
[0028] FIGS. 13a and 13b illustrate alternative arrangements of the
grooves in a channel block;
[0029] FIG. 14 is a schematic illustration of reaction pathways
used to prepare some hydrophobic groups of the present
invention;
[0030] FIGS. 15a and 15b illustrate a microvalve device;
[0031] FIGS. 16a and 16b illustrate an alternative embodiment of
the invention;
[0032] FIG. 17 is a mapping of expected fluorescent intensities
with a substrate selectively exposed to fluorescent dye;
[0033] FIG. 18 is a mapping of actual fluorescence intensity versus
location;
[0034] FIG. 19 is a mapping of fluorescence intensity versus
location on a slide having four different peptides synthesized
thereon;
[0035] FIG. 20 is a mapping of fluorescence intensity versus
location indicating fluorescein binding on 400 micron wide
photolyzed regions perpendicular to 100 micron flow paths;
[0036] FIG. 21 is a mapping of fluorescence intensity versus
location for a substrate containing octanucleotides,
heptanucleotides, and hexanucleotides and incubated with an
oligonucleotide complimentary to the octanucleotide; and
[0037] FIG. 22 is a magnified version of FIG. 21.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
Contents
[0038] I. Glossary
[0039] II. General
[0040] III. Methods for Mechanical Delivery of Reagents
[0041] IV. Flow Channel Embodiments
[0042] V. Spotting Embodiments
[0043] VI. Alternative Embodiments
[0044] VII. Examples
[0045] A. Leak Testing
[0046] B. Formation of YGGFL
[0047] C. 100 Micron Channel Block
[0048] D. Channel Matrix Hybridization Assay
[0049] VIII. Conclusion
I. GLOSSARY
[0050] The following terms are intended to have the following
general meanings as they are used herein:
[0051] 1. Ligand: A ligand is a molecule that is recognized by a
receptor. 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, opiates, steroids, peptides, enzyme substrates,
cofactors, drugs, lectins, sugars, oligonucleotides, nucleic acids,
oligosaccharides, and proteins.
[0052] 2. Monomer: A monomer is a member of the set of small
molecules which are or can be joined together to form a polymer or
a compound composed of two or more members. The set of monomers
includes but is not restricted to, for example, the set of common
L-amino acids, the set of D-amino acids, the set of synthetic
and/or natural amino acids, the set of nucleotides and the set of
pentoses and hexoses. The particular ordering of monomers within a
polymer is referred to herein as the "sequence" of the polymer. As
used herein, monomers refers to any member of a basis set for
synthesis of a polymer. For example, dimers of the 20 naturally
occurring 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.
Furthermore, each of the sets may include protected members which
are modified after synthesis. The invention is described herein
primarily with regard to the preparation of molecules containing
sequences of monomers such as amino acids, but could readily be
applied in the preparation of other polymers. Such polymers
include, for example, both linear and cyclic polymers of nucleic
acids, polysaccharides, phospholipids, and peptides having either
.alpha.-, .beta.- or .omega.-amino acids, heteropolymers in which a
known drug is covalently bound to any of the above,
polynucleotides, polyurethanes, polyesters, polycarbonates,
polyureas, polyamides, polyethyleneimines, polyarylene sulfides,
polysiloxanes, polyimides, polyacetates, or other polymers which
will be apparent upon review of this disclosure. Such polymers are
"diverse" when polymers having different monomer sequences are
formed at different predefined regions of a substrate. Methods of
cyclization and polymer reversal of polymers are disclosed in
copending application Ser. No. 796,727, filed Nov. 22, 1991,
entitled "POLYMER REVERSAL ON SOLID SURFACES," incorporated herein
by reference for all purposes.
[0053] 3. Peptide: A peptide is a polymer in which the monomers are
alpha amino acids and are joined together through amide bonds,
alternatively referred to as a polypeptide. Amino acids may be the
L-optical isomer or the D-optical isomer. Peptides are two or more
amino acid monomers long and are often more than 20 amino acid
monomers long. Standard abbreviations for amino acids are used
(e.g., P for proline). These abbreviations are included in Stryer,
Biochemistry, Third Ed., 1988, which is incorporated herein by
reference for all purposes.
[0054] 4. Receptor: A receptor is a molecule that has an affinity
for a ligand. Receptors may be naturally-occurring or manmade
molecules. They can be employed in their unaltered state or as
aggregates with other species. Receptors maybe 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, viruses,
cells, drugs, polynucleotides, nucleic acids, peptides, cofactors,
lectins, sugars, polysaccharides, 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
molecules have combined through molecular recognition to form a
complex.
[0055] Specific examples of receptors which can be investigated by
this invention include but are not restricted to:
[0056] a) Microorganism receptors: Determination of ligands that
bind to microorganism receptors such as specific transport proteins
or enzymes essential to survival of microorganisms would be a
useful tool for discovering new classes of antibiotics. Of
particular value would be antibiotics against opportunistic fungi,
protozoa, and bacteria resistant to antibiotics in current use.
[0057] b) Enzymes: For instance, a receptor can comprise a binding
site of an enzyme such as an enzyme responsible for cleaving a
neurotransmitter; determination of ligands for this type of
receptor to modulate the action of an enzyme that cleaves a
neurotransmitter is useful in developing drugs that can be used in
the treatment of disorders of neurotransmission.
[0058] c) Antibodies: For instance, the invention may be useful in
investigating a receptor that comprises a ligand-binding site on an
antibody molecule which combines with an epitope of an antigen of
interest; determining a sequence that mimics an antigenic epitope
may lead to the development of vaccines in which the immunogen is
based on one or more of such sequences or lead to the development
of related diagnostic agents or compounds useful in therapeutic
treatments such as for autoimmune diseases (e.g., by blocking the
binding of the "self" antibodies).
[0059] d) Nucleic Acids: Sequences of nucleic acids may be
synthesized to establish DNA or RNA binding sequences that act as
receptors for synthesized sequence.
[0060] e) Catalytic Polypeptides: Polymers, preferably antibodies,
which are capable of promoting a chemical reaction involving the
conversion of one or more reactants to one or more products. Such
polypeptides generally include a binding site specific for at least
one reactant or reaction intermediate and an active functionality
proximate to the binding site, which functionality is capable of
chemically modifying the bound reactant. Catalytic polypeptides and
others are described in, for example, PCT Publication No. WO
90/05746, WO 90/05749, and WO 90/05785, which are incorporated
herein by reference for all purposes.
[0061] f) Hormone receptors: Determination of the ligands which
bind with high affinity to a receptor such as the receptors for
insulin and growth hormone is useful in the development of, for
example, an oral replacement of the daily injections which
diabetics must take to relieve the symptoms of diabetes or a
replacement for growth hormone. Other examples of hormone receptors
include the vasoconstrictive hormone receptors; determination of
ligands for these receptors may lead to the development of drugs to
control blood pressure.
[0062] g) Opiate receptors: Determination of ligands which bind to
the opiate receptors in the brain is useful in the is development
of less-addictive replacements for morphine and related drugs.
[0063] 5. Substrate: A material having a rigid or semi-rigid
surface. In many embodiments, at least one surface of the substrate
will be substantially flat, although in some embodiments it may be
desirable to physically separate synthesis regions for different
polymers with, for example, wells, raised regions, etched trenches,
or the like. In some embodiments, the substrate itself contains
wells, trenches, flow through regions, etc. which form all or part
of the synthesis regions. According to other embodiments, small
beads may be provided on the surface, and compounds synthesized
thereon may be released upon completion of the synthesis.
[0064] 6. Channel Block: A material having a plurality of grooves
or recessed regions on a surface thereof. The grooves or recessed
regions may take on a variety of geometric configurations,
including but not limited to stripes, circles, serpentine paths, or
the like. Channel blocks may be prepared in a variety of manners,
including etching silicon blocks, molding or pressing polymers,
etc.
[0065] 7. Protecting Group: A material which is bound to a monomer
unit and which may be selectively removed therefrom to expose an
active site such as, in the specific example of an amino acid, an
amine group. Specific examples of photolabile protecting groups are
discussed in Fodor et al., PCT Publication No. WO 92/10092
(previously incorporated by reference) and U.S. Ser. No. ______
filed Nov. 2, 1992 (attorney docket No. 11509-68) incorporated
herein by reference for all purposes.
[0066] 8. Predefined Region: A predefined region is a localized
area on a substrate which is, was, or is intended to be used for
formation of a selected polymer and is otherwise referred to herein
in the alternative as "reaction" region, a "selected" region, or
simply a "region." The predefined region may have any convenient
shape, e.g., circular, rectangular, elliptical, wedge-shaped, etc.
In some embodiments, a predefined region and, therefore, the area
upon which each distinct polymer sequence is synthesized is smaller
than about 1 cm.sup.2, more preferably less than 1 mm.sup.2, and
still more preferably less than 0.5 mm.sup.2. In most preferred
embodiments the regions have an area less than about 10,000
.mu.m.sup.2 or, more preferably, less than 100 .mu.m.sup.2. Within
these regions, the polymer synthesized therein is preferably
synthesized in a substantially pure form.
[0067] 9. Substantially Pure: A polymer is considered to be
"substantially pure" within a predefined region of a substrate when
it exhibits characteristics that distinguish it from other
predefined regions. Typically, purity will be measured in terms of
biological activity or function as a result of uniform sequence.
Such characteristics will typically be measured by way of binding
with a selected ligand or receptor. Preferably the region is
sufficiently pure such that the predominant species in the
predefined region is the desired sequence. According to preferred
aspects of the invention, the polymer is at least 5% pure, more
preferably more than 10% to 20% pure, more preferably more than 80%
to 90% pure, and most preferably more than 95% pure, where purity
for this purpose refers to the ratio of the number of ligand
molecules formed in a predefined region having a desired sequence
to the total number of molecules formed in the predefined
region.
II. GENERAL
[0068] The invention can be used in variety of applications. For
example, the invention can be used as a synthesis tool (as for
example in peptide syntheses), as a screening tool (as for example
in screening compound libraries for drug activity), or as a
monitoring/diagnostic tool (as for example in medical or
environmental testing). In one specific embodiment, the invention
is used for nucleic acid-based diagnostics.
[0069] As a synthesis tool, the present invention provides for the
formation of arrays of large numbers of different polymer
sequences. According to a preferred embodiment, the invention
provides for the synthesis of an array of different peptides or
oligonucleotides in selected regions of a substrate. Such
substrates having the diverse sequences formed thereon may be used
in, for example, screening studies to evaluate their interaction
with receptors such as antibodies and nucleic acids. For example,
in preferred embodiments the invention provides for screening of
peptides to determine which if any of a diverse set of peptides has
a strong binding affinity with a receptor and, in most preferred
embodiments, to determine the relative binding affinity of various
peptides with a receptor of interest.
[0070] Such diverse polymer sequences are preferably synthesized on
a single substrate. By synthesizing the diverse polymer sequences
on a single substrate, processing of the sequences to evaluate
characteristics such as relative binding affinity is more easily
conducted. By way of example, when an array of peptide sequences
(or a library of other compounds) is to be evaluated to determine
the peptides' relative binding affinity to a receptor, the entire
substrate and, therefore, all or a group of the polymer sequences
may be exposed to an appropriately labelled receptor and evaluated
simultaneously.
[0071] In some embodiments, the present invention can be employed
to localize and, in some cases, immobilize vast collections of
synthetic chemical compounds or natural product extracts. In such
methods, compounds are deposited on predefined regions of a
substrate. The reaction of the immobilized compound (or compounds)
with various test compositions such as the members of the chemical
library or a biological extract are tested by dispensing small
aliquots of each member of the library or extract to a different
region. Competitive assays or other well-known techniques can be
used to identify a desired activity. As an example, a large
collection of human receptors is deposited on a substrate, one in
each region to form an array. A plant/animal extract is then
screened for binding to various receptors of the array.
[0072] The present invention has certain features in common with
the "light directed" methods described in U.S. Pat. No. 5,143,854,
previously incorporated by reference. The light directed methods
discussed in the '854 patent involve activating predefined regions
of the substrate and then contacting the substrate with a
preselected monomer solution. The predefined regions can be
activated with a light source shown through a mask (much in the
manner of photolithography techniques used in integrated circuit
fabrication). Other regions of the substrate remain inactive
because they are blocked by the mask from illumination. Thus, a
light pattern defines which regions of the substrate react with a
given monomer. By repeatedly activating different sets of
predefined regions and contacting different monomer solutions with
the substrate, a diverse array of polymers is produced on the
substrate. Of course, other steps such as washing unreacted monomer
solution from the substrate can be used as necessary.
[0073] In the present invention, a mechanical device or physical
structure defines the regions which are available to react with a
given monomer. In some embodiments, a wall or other physical
barrier is used to block a given monomer solution from contacting
any but a few selected regions of a substrate. In other
embodiments, the amount of the monomer (or other) solution
deposited and the composition of the substrate act to separate
different monomer solutions on the substrate. This permits
different monomers to be delivered and coupled to different regions
simultaneously (or nearly simultaneously) and reduces the number of
separate washing and other reaction steps necessary to form an
array of polymers. Further, the reaction conditions at different
activated regions can be controlled independently. Thus, the
reactant concentrations and other parameters can be varied
independently from reaction site to reaction site, to optimize the
procedure.
[0074] In alternative preferred embodiments of the present
invention, light or another activator is used in conjunction with
the physical structures to define reaction regions. For example, a
light source activates various regions of the substrate at one time
and then a mechanical system directs monomer solutions to different
activated regions, in parallel.
III. METHODS FOR MECHANICAL DELIVERY OF REAGENTS
[0075] In preferred embodiments of the present invention, reagents
are delivered to the substrate by either (1) flowing within a
channel defined on predefined regions or (2) "spotting" on
predefined regions. However, other approaches, as well as
combinations of spotting and flowing, may be employed. In each
instance, certain activated regions of the substrate are
mechanically separated from other regions when the monomer
solutions are delivered to the various reaction sites.
[0076] A typical "flow channel" method of the present invention can
generally be described as follows. Diverse polymer sequences are
synthesized at selected regions of a substrate by forming flow
channels on a surface of the substrate through which appropriate
reagents flow or in which appropriate reagents are placed. For
example, assume a monomer "A" is to be bound to the substrate in a
first group of selected regions. If necessary, all or part of the
surface of the substrate in all or a part of the selected regions
is activated for binding by, for example, flowing appropriate
reagents through all or some of the channels, or by washing the
entire substrate with appropriate reagents. After placement of a
channel block on the surface of the substrate, a reagent having the
monomer A flows through or is placed in all or some of the
channel(s). The channels provide fluid contact to the first
selected regions, thereby binding the monomer A on the substrate
directly or indirectly (via a linker) in the first selected
regions.
[0077] Thereafter, a monomer B is coupled to second selected
regions, some of which may be included among the first selected
regions. The second selected regions will be in fluid contact with
a second flow channel(s) through translation, rotation, or
replacement of the channel block on the surface of the substrate;
through opening or closing a selected valve; or through deposition
of a layer of photoresist. If necessary, a step is performed for
activating at least the second regions. Thereafter, the monomer B
is flowed through or placed in the second flow channel(s), binding
monomer B at the second selected locations. In this particular
example, the resulting sequences bound to the substrate at this
stage of processing will be, for example, A, B, and AB. The process
is repeated to form a vast array of sequences of desired length at
known locations on the substrate.
[0078] After the substrate is activated, monomer A can be flowed
through some of the channels, monomer B can be flowed through other
channels, a monomer C can be flowed through still other channels,
etc. In this manner, many or all of the reaction regions are
reacted with a monomer before the channel block must be moved or
the substrate must be washed and/or reactivated. By making use of
many or all of the available reaction regions simultaneously, the
number of washing and activation steps can be minimized.
[0079] Various embodiments of the invention will provide for
alternative methods of forming channels or otherwise protecting a
portion of the surface of the substrate. For example, according to
some embodiments, a protective coating such as a hydrophilic or
hydrophobic coating (depending upon the nature of the solvent) is
utilized over portions of the substrate to be protected, sometimes
in combination with materials that facilitate wetting by the
reactant solution in other regions. In this manner, the flowing
solutions are further prevented from passing outside of their
designated flow paths.
[0080] The "spotting" embodiments of the present invention can be
implemented in much the same manner as the flow channel
embodiments. For example, a monomer A can be delivered to and
coupled with a first group of reaction regions which have been
appropriately activated. Thereafter, a monomer B can be delivered
to and reacted with a second group of activated reaction regions.
Unlike the flow channel embodiments described above, reactants are
delivered by directly depositing (rather than flowing) relatively
small quantities of them in selected regions. In some steps, of
course, the entire substrate surface can be sprayed or otherwise
coated with a solution. In preferred embodiments, a dispenser moves
from region to region, depositing only as much monomer as necessary
at each stop. Typical dispensers include a micropipette to deliver
the monomer solution to the substrate and a robotic system to
control the position of the micropipette with respect to the
substrate. In other embodiments, the dispenser includes a series of
tubes, a manifold, an array of pipettes, or the like so that
various reagents can be delivered to the reaction regions
simultaneously.
IV. FLOW CHANNEL EMBODIMENTS
[0081] FIG. 1 illustrates an example of the invention. In this
particular example, monomers and dimers of the monomer group A, B,
C, and D are to be bound at selected regions of the substrate. The
substrate may be biological, nonbiological, organic, inorganic, or
a combination of any of these, existing as particles, strands,
precipitates, gels, sheets, tubing, spheres, containers,
capillaries, pads, slices, films, plates, slides, etc. The
substrate may have any convenient shape, such as a disc, square,
sphere, circle, etc. The substrate is preferably flat but may take
on a variety of alternative surface configurations. For example,
the substrate may contain raised or depressed regions on which the
synthesis takes place.
[0082] The substrate and its surface form a support on which to
carry out the reactions described herein. These monomers are bound
using first flow channel paths x.sub.1, x.sub.2, x.sub.3, and
x.sub.4 which are formed or placed on or adjacent the substrate in
a first orientation, and second flow channel paths y.sub.1,
y.sub.2, y.sub.3, and y.sub.4 which are formed or placed on or
adjacent the substrate in a second orientation. The second flow
channel paths intersect at least a part of the first flow channel
paths. The flow channels are formed according to techniques which
are described in greater detail elsewhere herein.
[0083] Initially the substrate is subjected to one or more
preliminary treatments such as, for example, cleaning and the
optional placement of "linker" molecules on the surface thereof.
The substrate may also be provided with various active groups,
common monomer sequences which will form a part of the polymers, or
the like.
[0084] Thereafter, in a first coupling step, one or more of the
flow channels are provided with the first monomer A, which binds
through covalent bonds or otherwise to the substrate (directly or
indirectly) where the flow channel contacts the substrate. In the
particular example shown in FIG. 1, the flow channels x.sub.1 and
x.sub.2 are utilized, binding the monomer A to the substrate along
the entire length of the substrate adjacent to the x.sub.1 and
x.sub.2 channels. Each coupling step may in some embodiments be
composed of a variety of substeps. For example, each coupling step
may include one or more substeps for washing, chemical activation,
or the like.
[0085] Thereafter or concurrently therewith, as shown in FIG. 2, a
second monomer B is provided to selected flow channels and the
monomer B binds to the substrate where the second flow channels
provide contact therewith. In the particular example shown in FIG.
2, monomer B is bound along channels x.sub.3 and x.sub.4. When the
monomers A and B flow through their respective flow channels
simultaneously, only a single process step is required to perform
two coupling steps simultaneously. As used herein, a "process step"
refers to the injection of one or more channels with one or more
reagents. A "coupling step" refers to the addition of a monomer in
a polymer.
[0086] Processing thereafter continues in a similar manner with
monomers C and D in the manner shown in the flow diagram of FIG. 2,
with monomer C being bound in the flow channels y.sub.1 and
y.sub.2, and D being bound in the flow channels y.sub.3 and
y.sub.4. Preferably, monomers C and D are directed through the flow
channels y.sub.1 to y.sub.4 simultaneously whereby two coupling
steps are performed with a single process step. Light regions in
FIG. 1 indicate the intersections of the resulting flow paths.
[0087] FIG. 3 illustrates the mapping of sequences formed using the
above illustrated steps. As shown therein, the sequences A, B, C,
D, AD, BD, AC, and BC have been formed using only two process
steps. Accordingly, it is seen that the process provides for the
synthesis of vast arrays of polymer sequences using only a
relatively few process steps. By way of further example, it is
necessary to use only two process steps to form all of the
4.sup.2=16 dimers of a four-monomer basis set. By way of further
example, to form all 4.sup.8 octomers of a four-monomer basis set,
it is necessary to provide only 256 flow channels oriented in the
"x" direction, and 256 flow channels oriented in the "y" direction,
with a total of eight coupling steps.
[0088] The power of the technique is further illustrated by
synthesizing the complete array of six hexamer peptides from a 20
amino acid basis set. This array will include 206 or 64,000,000
regions defining 64,000,000 different peptides and can be formed in
only six process steps. Further, the method requires only three
different templates, one having 20 parallel channels, a second
having 400 channels each {fraction (1/20)}th as wide as the first,
and a third having 8000 channels each {fraction (1/20)}th as wide
as the second. Each template will be used in two process steps,
each at an orientation at 90 degrees with respect to the other as
illustrated in FIG. 4. With the first template, the substrate is
activated and then solutions of each of the 20 amino acid basis set
(or other 20 member basis set) are flowed over and reacted on a
different predefined stripe in a first orientation. This is the
first process step and includes 20 coupling or attachment steps,
which can be performed simultaneously. Next, the entire substrate
is again activated and the first template is placed in a second
orientation, perpendicular to the first (FIG. 4a). The 20 amino
acid solutions are then flowed along 20 new predefined stripes
(each perpendicular to the original set of stripes). In each of
these two process steps, the 20 predefined regions (the stripes
along the flow channels) are first activated and then contacted
with the individual monomers so that all 20 stripes are reacted
before the next activation step is necessary. In other words, 20
coupling steps are conducted in parallel, greatly reducing the
number of necessary activation steps.
[0089] The four remaining coupling steps employ the second and
third templates. In the third and fourth process steps (FIG. 4b),
20 channels are devoted to each monomer, and in the fifth and sixth
process steps (FIG. 4c), 400 channels are devoted to each monomer.
As with the first two steps, the entire substrate undergoes
reaction during a single process step. Thus, only six process steps
(requiring a total of about 24 hours) are required to produce the
entire library of 64,000,000 peptide hexamers. In a different
embodiment, a single template having 8000 channels to control
delivery (e.g. 400 channels for each of the 20 amino acids in the
first round) can produce the full library of hexamers with only a
single rotation step. Thus, the present invention offers extremely
rapid methods of preparing diverse polymer arrays.
[0090] FIGS. 5a and 5b illustrate details of a first embodiment of
a device used for performing the synthesis steps described above.
In particular, FIG. 5a illustrates the device in top view, while
FIG. 5b illustrates the device in cross-sectional side view. In the
particular embodiment shown in FIG. 5, the device is used to
synthesize polymer sequences on substrate 401. Substrate 401 is
coupled to a rotating stage 403 and removably held by clamp 405 to
channel block 407. Channel block 407 has etched therein a plurality
of channels 409 in the form of stripes therein. Each channel is
provided with a flow inlet 411 and an outlet 413. A vacuum source
415 is applied to one or more of the outlets 413, while a pipettor
417 is slidably mounted on arm 419 to deliver selected reagents
from reservoir(s) 421 to selected flow inlets 411.
[0091] The details of a second preferred embodiment are shown in
FIGS. 6-11. FIG. 6 displays an apparatus for holding a substrate
111 in place against a channel block 109 by evenly distributing
pressure over the substrate in a pressure chamber 101. Pressurized
gas is admitted through gas pressure inlet 103 to provide clamping
pressure to immobilize the substrate while fluids are flowed from
fluid flow inlet 115, through channel 123, and out fluid outlet
117. The upper and lower portions of the pressure chamber housing
105 and 125 are held together by nuts 121 and bolts 104. Of course,
other means such as clamps can be used to hold the pressure chamber
housing portions together.
[0092] FIG. 7 illustrates preferred flow path configurations in
channel blocks of the present invention. As shown in FIG. 7a, fluid
delivery sites 127, 129, 131, 133, 135, and 137 are connected to
channels leading to reaction region 141. A similar arrangement is
shown for comparision in FIG. 7b where the orientation of the flow
channels in the reaction regions is shifted by 90 degrees on a
rectangular channel block. Vacuum ports 145 and 146 to an external
vacuum line are provided so that substrate position is maintained
during fluid flow.
[0093] The channels shown in FIGS. 7a and 7b form a "fanned channel
array" on channel block 139 in a manner analogous to that of the
lead pattern employed in integrated circuits. This provides
significantly increased separation of fluid delivery points in
comparison to the high density of channels in the reaction region.
In a 2 inch by 3 inch substrate, at least about a 4:1 increase in
spatial separation typically can be attained by the fanned
arrangement. Thus, if the channels in the reaction regions are
separated by 200 microns, the delivery ports can be separated by
0.8 mm.
[0094] The spatial separation can be further increased by
staggering the delivery ports as shown for ports 127, 129, and 131.
This can provide an additional channel separation of at least about
3:1. Thus, for the channels separated by 200 microns, a staggered
fanned array provides 2.4 mm separation between the delivery ports.
Thus, fluid can be delivered to a high-density array of of channels
in the reaction region from standard 1.6 mm Teflon.TM. tubing. If
additional spacing is necessary, the substrate size can be
increased, while preserving the reaction region size.
[0095] As shown in FIG. 8, the fluid delivery ports are accessed
from holes in the back surface of a stabilizing plate 108 on the
channel block. The stabilizing plate, which is preferably made from
fused pyrex, provides structural integrity to the channel block
during clamping in the pressure chamber. It may also provide a
means to access the channel block ports and reduce leakage between
ports or channels. In preferred embodiments, the channels 123 of
the channel block are formed on a wafer 106 which generally may be
any machinable or cast material, and preferably may be etched
silicon or a micromachined ceramic. In other embodiments, the
channel block is pressure-formed or injection-molded from a
suitable polymer material. The entire channel block arrangement is
mounted on a rigid channel block sub-plate 110 including a vacuum
line 112, ports for fluid delivery lines 115, ports for fluid
outlet lines 117, and recessed regions for plug ends 151 and 153.
With this arrangement, the substrate can be clamped against the top
surface of the channel block (by vacuum or pressurized gas as shown
in the embodiment of FIG. 6) while fluid enters and exits from
below. Preferably, the subplate will be made from a rigid material
such as stainless steel or anodized aluminum.
[0096] Individual micro tubing connections can be made for each
channel as shown in FIG. 9. Plug ends 151 are provided with a
conical upper surface that mates with a conical recess 118 in pyrex
stabilizing plate 108. Plug ends 151 also have a cylindrical lower
surface that mates with cylindrical recess 116 in sub-plate 110.
The subplate and stabilizing plate are held together by bolt 114
and threaded insert 112 or other suitable engagement means.
[0097] FIG. 10 shows a fluid flow diagram of a preferred system of
the present invention. The pressure is controlled at point 25 (P1)
and point 21 (P2) so that a pressure drop (P1-P2) is maintained
across the system. Coupling compounds such as activated monomers
are supplied from reservoirs 31, 32, and 33. Additional reagents
are supplied from reservoirs 15, 17, and 19. Of course, the monomer
and coupling reagent reservoirs shown in FIG. 10 are representative
of a potentially much larger series of reservoirs. The reagents and
coupling compounds are combined at nodes 27, 28, and 29 before
being directed to channel block 139. Mixing of the appropriate
reagents and coupling compounds is controlled by valves at the
nodes which are in turn controlled by electronic control 23. Waste
fluids that have been directed across the substrate are removed
through line 35.
[0098] The system displayed in FIG. 10 allows control of all
channels in parallel by regulating only a few variables. For
example, a constant pressure gradient is maintained across all
channels simultaneously by fixing P1 and P2. Thus, the flow rate in
each channel is dependent upon the cross-sectional area of the flow
channel and the rheological properties of the fluids. Because the
channels have a uniform cross-section and because the coupling
compounds are typically provided as dilute solutions of a single
solvent, a uniform flow rate is created across all channels. With
this system the coupling time in all channels can be varied
simultaneously by simply adjusting the pressure gradient across the
system. The valves of the system are preferably controlled by a
single electronic output from control 23.
[0099] The fanned channel array design shown in FIG. 7 provides for
two separate channel blocks to be used in successive process steps
during a chemical synthesis. One block forms a horizontal array on
the solid substrate, while the other block forms a vertical array.
To create a matrix of intersecting rows and columns of chemical
compounds, the solid substrate is transferred from one block to the
other during successive process steps. While many experiments
require only a single transfer from one block to the other during a
series of process steps, the fanned channel array transfer block 75
illustrated in FIGS. 11a and 11b provides one device for
maintaining accurate registration of the solid substrate 71
relative to the channel blocks 79 during repeated transfers. In
some embodiments, a single channel block can be used for horizontal
and vertical arrays by simply rotating it by 90 degrees as
necessary.
[0100] The transfer block is positioned with respect to the channel
block so that the dimensional characteristics of the solid
substrate are not used in the alignment. The transfer block 75 is
aligned to the channel block by kinematic mount 81 while vacuum is
switched from vacuum line 83 on the channel block to vacuum line 77
on the transfer block (during normal operation, a vacuum holds the
substrate against the channel block). The substrate and transfer
block are then moved and repositioned relative to the second
channel bock. Vacuum is then switched to the second channel block,
retaining the substrate in proper alignment. This way, accurate
registration can be assured between process steps regardless of
variation in the dimensions of individual substrates. The transfer
block system also maintains alignment of the matrix area during
transfers to and from the flow cell during experiments utilizing
both mechanical and light directed process steps.
[0101] In some embodiments the channel block need not be utilized.
Instead, in some embodiments, small "strips" of reagent are applied
to the substrate by, for example, striping the substrate or
channels therein with a pipettor. Such embodiments bear some
resemblance to the spotting embodiments of this invention.
According to other embodiments the channels will be formed by
depositing a photoresist such as those used extensively in the
semiconductor industry. Such materials include polymethyl
methacrylate (PMMA) and its derivatives, and electron beam resists
such am poly(olefin sulfones) and the like (more fully described in
Ghandi, "VLSI Fabrication Principle," Wiley (1983) Chapter 10,
incorporated herein by reference in its entirety for all purposes).
According to these embodiments, a resist is deposited, selectively
exposed, and etched, leaving a portion of the substrate exposed for
coupling. Theme steps of depositing resist, selectively removing
resist and monomer coupling are repeated to form polymers of
desired sequence at desired locations.
[0102] In some embodiments, a resist can be used to activate
certain regions of the substrate. Certain resist materials such as
acid-generating polymers, for example, will release protons upon
irradiation. According to these embodiments, a substrate covered
with such material is irradiated through a mask or otherwise
selectively irradiated so that the irradiated regions of the
substrate are exposed to acidic conditions. Acid-labile protecting
group on the substrate or oligomers on the substrate are removed,
leaving an activated region. At this point, all or part of the
resist may be removed. In preferred embodiments, the resist will be
removed only in the activated regions, so that the channels are
formed at the activated regions. Alternatively, the resist can be
removed from the entire substrate. In this case, a separate channel
block can then be contacted with the substrate to define flow
channels, or a conventional VLSIPS.TM. procedure can be
employed.
[0103] In preferred embodiments, the substrate is conventional
glass, pyrex, quartz, any one of a variety of polymeric materials,
or the like. Of course, the substrate may be made from any one of a
variety of materials such as silicon, polystyrene, polycarbonate,
or the like. In preferred embodiments the channel block is made of
silicon or polychlorotrifluorethylene, such as material known under
the trade name KelF.TM. 80 made by 3H, although a wide variety of
materials such as polystyrene, polycarbonate, glass, elastomers
such as Kalrez made by DuPont, various ceramics, stainless steel,
or the like may be utilized.
[0104] The channels in the channel block are preferably made by
machining, compression molding, injection molding lithography,
laser cutting, or the like depending upon the material of interest.
In some embodiments employing larger channel blocks, the raised
portions of the channels in the channel block are treated by
lapping with lapping film (0.3 .mu.m grit). Such smooth surfaces
provide good seals to the substrate without the use of a sealant
and, therefore, without the possibility of leaving sealant material
on the substrate when rotating the channel block. Preferably, all
operations are conducted at substantially ambient temperatures and
pressures.
[0105] A particularly preferred channel block is prepared by
chemical etching of polished silicon wafers. Chemical etching is a
widely used technique in integrated circuit fabrications. It can
easily provide 60 or more100 micron channels on a 12.8 mm region of
a polished silicon wafer. Even after etching, the top (unetched)
surface regions of the wafer retains the very flat profile of the
unetched wafer. Thus, close contact with the substrate is ensured
during flow cell operation.
[0106] In operation, the surface of the substrate is appropriately
treated by cleaning with, for example, organic solvents, methylene
chloride, DMF, ethyl alcohol, or the like. Optionally, the
substrate may be provided with appropriate linker molecules on the
surface thereof. The linker molecules may be, for example, aryl
acetylene, ethylene glycol oligomers containing from 2-10 monomers
or more, diamines, diacids, amino acids, or combinations thereof.
Thereafter, the surface is provided with protected surface active
groups such as TBOC or FMOC protected amino acids. Such techniques
are well known to those of skill in the art.
[0107] Thereafter, the channel block and the substrate are brought
into contact forming fluid-tight channels bounded by the grooves in
the channel block and the substrate. When the channel block and the
substrate are in contact, a protecting group removal agent is,
thereafter, directed through a first selected channel or group of
channels by placing the pipettor on the flow inlet of the selected
channel and, optionally, the vacuum source on the outlet of the
channel. In the case of, for example, TBOC protected amino acids,
this protecting group removal agent may be, for example,
trifluoroacetic acid (TFA). This step is optionally followed by
steps of washing to remove excess TFA with, for example,
dichloromethane (DCH).
[0108] Thereafter, a first amino acid or other monomer A is
directed through the first selected flow channel. Preferably this
first amino acid is also provided with an appropriate protecting
group such as TBOC, FMOC, NVOC, or the like. This step is also
followed by appropriate washing steps. The of deprotection/coupling
steps employed in the first group of channels are concurrently with
or thereafter repeated in additional groups of channels. In
preferred embodiments, monomer A will be directed through the first
group of channels, monomer B will be directed through a second
group of flow channels, etc., so that a variety of different
monomers are coupled on parallel channels of the substrate.
[0109] Thereafter, the substrate and the channel block are
separated and, optionally, the entire substrate is washed with an
appropriate material to remove any unwanted materials from the
points where the channels contact the substrate.
[0110] The substrate and/or block is then, optionally, washed and
translated and/or rotated with the stage. In preferred embodiments,
the substrate is rotated 90 degrees from its original position,
although some embodiments may provide for greater or less rotation,
such as from 0 to 180 degrees. In other embodiments, such as those
discussed in connection with the device shown in FIG. 7, two or
more different channel blocks are employed to produce different
flow patterns across the substrate. When the channel block Lo
rotated, it may simultaneously be translated with respect to the
substrate. "Translated" means any relative motion of the substrate
and/or channel block, while "rotation" is intended to refer to
rotation of the substrate and/or channel block about an axis
perpendicular to the substrate and/or channel block. According to
some embodiments the relative rotation is at different angles for
different stages of the synthesis.
[0111] The steps of deprotection, and coupling of amino acids or
other monomers is then repeated, resulting in the formation of an
array of polymers on the surface of the substrate. For example, a
monomer B may be directed through selected flow channels, providing
the polymer AB at intersections of the channels formed by the
channel block in the first position with the channels formed by the
channel block after 90-degree rotation.
[0112] While rotation of the channel block is provided according to
preferred embodiments of the invention, such rotation is not
required. For example, by simply flowing different reagents through
the channels, polymers having different monomer sequences may be
formed. Merely by way of a specific example, a portion of the
channels may be filled with monomer "A," and a portion filled with
monomer "B" in a first coupling step. All or a portion of the first
channels are then filled with a monomer "C," and all or a portion
of the second channels are filled with a monomer "D," forming the
sequences AB and CD. Such steps could be used to form 100 sequences
using a basis set of 10 monomers with a 100-groove channel
block.
[0113] In another embodiment, the invention provides a multichannel
solid-phase synthesizer as shown in FIG. 12. In this embodiment, a
collection of delivery lines such as a manifold or collection of
tubes 1000 delivers activated reagents to a synthesis support
matrix 1002. The collection of tubes 1000 may take the form of a
rigid synthesis block manifold which can be precisely aligned with
the synthesis support matrix 1002. The support matrix contains a
plurality of reaction regions 1004 in which compounds may be
immobilized or synthesized. In preferred embodiments, the reaction
regions include synthesis frits, pads, resins, or the like.
[0114] The solutions delivered to the individual reactant regions
of the support matrix flow through the reaction regions to waste
disposal regions, recycling tank(s), separators, etc. In some
embodiments, the reaction solutions simply pass through the
reaction regions under the influence of gravity, while in other
embodiments, the solutions are pulled or pushed through the
reaction regions by vacuum or pressure.
[0115] The individual reaction regions 1004 of the support matrix
are separated from one another by walls or gaskets 1006. Theme
prevent the reactant solution in one reaction region from moving to
and contaminating adjacent reaction regions. In one embodiment, the
reaction regions are defined by tubes which may be filled with
resin or reaction mixture. The gasketing allows close contact
between the support matrix 1002 and a "mask" (not shown). The mask
serves to control delivery of a first group reactant solutions
through predetermined lines (tubes) to a first set of reaction
regions. By ensuring close contact between the delivery tubes 1000,
the mask, and the support matrix 1002, the probability that
reaction solutions will be accidently added to the wrong reaction
site is reduced.
[0116] After each process step, the mask can be changed go that a
new group reactants is delivered to a new set of reaction regions.
In this manner, a combinatorial strategy can be employed to prepare
a large array of polymers or other compounds. In other embodiments,
mechanisms other than masks can be employed to block the individual
delivery tubes. For example, an array of control valves within the
tubes may be suitable for some embodiments.
[0117] By adjusting the thickness of the synthesis support matrix,
the quantity of immobilized material in the reaction regions can be
controlled. For example, relatively thin support synthesis matrices
can be used to produce small amounts of surface bound. oligomers
for analysis, while thicker support matrices can be used to
synthesize relatively large quantities of oligomers which can be
cleaved from the support for further use. In the latter embodiment,
a collector having dimensions matching the individual synthesis
supports can be employed to collect oligomers that are ultimately,
freed from the reaction matrix.
[0118] To illustrate the ability of this system to synthesize
numerous polymers, a square synthesis matrix measuring 10 cm along
each side and having 5 mm reaction regions separated by 5 mm wide
gaskets provides 100 individual syntheses sites (reaction regions).
By reducing the size of the reaction regions to 2.5 mm on each
side, 400 reactions regions become available.
[0119] While linear grooves are shown herein in the preferred
aspects of the invention, other embodiments of the invention will
provide for circular rings or other shapes such as circular rings
with radial grooves running between selected rings. According to
some embodiments, channel blocks with different geometric
configurations will be used from one step to the next, such as
circular rings in one step and linear stripes in the next. FIG. 13a
illustrates one of the possible arrangements in which the channels
409 are arranged in a serpentine arrangement in the channel block
407. Through appropriate translation and/or rotation of the channel
block, polymers of desired monomer sequence are formed at the
intersection of the channels during successive polymer additions,
such as at location 501, where the intersection of a previous or
subsequent set of channels, is shown in dashed lines. FIG. 13b
illustrates another arrangement in which channels (in this case
without flow paths 413) are provided in a linear arrangement, with
groups 503 and 505 located in adjacent regions of the substrate and
extending only a portion of the substrate length.
[0120] In some embodiments of the invention, the various reagents,
such as those containing the various monomers, are not pumped
through the apertures 413. Instead, the reagent is placed in one of
the grooves, such as the grooves 409 shown in FIG. 13b, filling the
groove. The substrate is then placed on top of the channel block,
and the exposed portions of the substrate are permitted to react
with the materials in the grooves. In preferred embodiments, the
channels are of the same width as the raised regions between the
channels. According to these embodiments, the substrate may then be
moved laterally by one channel width or an integer multiple of a
channel width, permitting reaction with and placement of monomers
on the regions between the channels in a previous coupling step.
Thereafter, the substrate or channel block will be rotated for the
next series of coupling steps.
[0121] In preferred embodiments, the process is repeated to provide
more than 10 different polymer sequences on the surface of the
substrate. In more preferred embodiments, the process is repeated
to provide more than 10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5,
10.sup.6, or more polymer sequences on a single substrate. In some
embodiments the process is repeated to provide polymers with as few
as two monomers, although the process may be readily adapted to
form polymers having 3, 4, 5, 6, 10, 15, 20, 30, 40, 50, 75, 100 or
more monomers therein.
[0122] According to preferred embodiments, the array of polymer
sequences is utilized in one or more of a variety of screening
processes, one of which is described in copending application U.S.
Ser. No. 796,947, filed on Nov. 22, 1991 and incorporated herein by
reference for all purposes. For example, according to one
embodiment, the substrate is then exposed to a receptor of interest
such as an enzyme or antibody. According to preferred embodiments,
the receptor is labelled with fluorescein, or otherwise labelled,
so as to provide for easy detection of the location at which the
receptor binds. According to some embodiments, the channel block is
used to direct solutions containing a receptor over a synthesized
array of polymers. For example, according to some embodiments the
channel block is used to direct receptor solutions having different
receptor concentrations over regions of the substrate.
[0123] According to most preferred embodiments, amplification of
the signal provided by way of fluorescein labelling is provided by
exposing the substrate to the antibody of interest, and then
exposing the substrate to a labelled material which is
complementary to the antibody of interest and which preferably
binds at multiple locations of the antibody of interest. For
example, in one specific embodiment, if a mouse antibody is to be
studied, a labelled second antibody may be exposed to the substrate
which is, for example, goat antimouse. Such techniques are
described in PCT Publication No. WO92/10092, previously
incorporated herein by reference.
V. SPOTTING EMBODIMENTS
[0124] According to some embodiments monomers (or other reactants)
are deposited from a dispenser in droplets that fill predefined
regions. For example, in a single coupling step, the dispenser
deposits a first monomer in a series of predefined regions by
moving over a first region, dispensing a droplet, moving to a
second region, dispensing a droplet, and so on until the each of
the selected regions has received the monomer. Next the dispenser
deposits a second monomer in a second series of predefined regions
in much the same manner. In some embodiments, more than one
dispenser may be used so that more than one monomer are
simultaneously deposited. The monomers may react immediately on
contact with the reaction regions or may require a further
activation step, such as the addition of catalyst. After some
number of monomers have been deposited and reacted in predefined
regions throughout the substrate, the unreacted monomer solution is
removed from the substrate. This completes a first process
step.
[0125] For purposes of this embodiment, the spacing between the
individual reaction regions of the substrate preferably will be
less than about 3 mm, and more preferably between about 5 and 100
.mu.m. Further, the angular relation between the regions is
preferably consistent to within 1 degree and more preferably to
within 0.1 degree. Preferably, the substrate will include at least
about 100 reaction regions, more preferably at least about 1000
reaction regions, and most preferably at least about 10,000
reaction regions. Of course, the density of reaction regions on the
substrate will vary. In preferred embodiments, there are at least
about 1000 reaction regions per cm.sup.2 of substrate, and more
preferably at least about 10,000 regions per cm.sup.2.
[0126] To deposit reactant droplets consistently at precisely
specified regions, a frame of reference common to the delivery
instrument and the substrate is required. In other words, the
reference coordinates of the instrument must be accurately mapped
onto the reference coordinates of the substrate. Ideally, only two
reference points on the substrate are necessary to map the array of
polymer regions completely. The dispenser instrument locates these
reference points and then adjusts its internal reference
coordinates to provide the necessary mapping. After this, the
dispenser can move a particular distance in a particular direction
and be positioned directly over a known region. Of course, the
dispenser instrument must provide precisely repeatable movements.
Further, the individual regions of the array must not move with
respect to the reference marks on the substrate after the reference
marks have been formed. Unfortunately, pressing or other mechanical
operations commonly encountered during fabrication and use of a
substrate can warp the substrate such that the correspondence
between the reference marks and the reaction regions is
altered.
[0127] Thus, in preferred embodiments, a substrate containing both
"global" and "local" reference marks is employed. In preferred
embodiments, two global reference marks are conveniently located on
the substrate to define the initial frame of reference. When these
points are located, the dispenser instrument has an approximate map
of the substrate and the predefined regions therein. To assist in
locating the exact position of the regions, the substrate is
further subdivided into local frames of reference. Thus, in an
initial, "course" adjustment, the dispenser is positioned within
one of the local frames of reference. Once in the local region, the
dispensing instrument looks for local reference marks to define
further a local frame of reference. From these, the dispenser moves
exactly to the reaction region where the monomer is deposited. In
this manner, the effects of warpage or other deformation can be
minimized. The number of local reference marks is determined by the
amount of deformation expected in the substrate. If the substrate
is sufficiently rigid so that little or no deformation will occur,
very few local reference marks are required. If substantial
deformation is expected, however, more local reference marks are
required.
[0128] In order to locate the appropriate reference point initially
and align the dispenser with respect to it, a vision or blind
system may be employed. In a vision system, a camera is rigidly
mounted to the dispenser nozzle. When the camera locates the
reference point(s), the dispenser is known to be a fined distance
and direction away from the point, and a frame of reference is
established. Blind systems of the present invention locate the
reference point(s) by capacitive, resistive, or optical techniques,
for example. In one example of an optical technique, a laser beam
is transmitted through or reflected from the substrate. When the
beam encounters a reference mark, a change in light intensity is
detected by a sensor. Capacitive and resistive techniques are
similarly applied. A sensor registers a change in capacitance or
resistivity when a reference point is encountered.
[0129] Starting at a single reference point, the dispenser is
translated from one reaction region to other regions of the
substrate by a correct distance in the correct direction (this is
the "dead reckoning" navigational technique). At each stop, the
dispenser deposits correctly metered amounts of monomer. Analogous
systems widely used in the microelectronic device fabrication and
testing arts can move at rates of up to 3-10 stops per second. The
translational (X-Y) accuracy of such systems is well within 1
.mu.m.
[0130] Translational mechanisms for moving the dispenser are
preferably equipped with closed loop position feedback mechanisms
(encoders) and have insignificant backlash and hysteresis. In
preferred embodiments, the translation mechanism has a high
resolution, i.e. better than one motor tick per encoder count.
Further, the electromechanical mechanism preferably has a high
repeatability relative to the reaction region diameter travel
distance (typically.+-.1 .mu.m or better).
[0131] To deposit a drop of monomer solution on the substrate
accurately, the dispenser nozzle must be placed a correct distance
above the surface. In one embodiment, the dispenser tip preferably
will be located about 5-50 .mu.m above the substrate surface when a
five nanoliter drop is released. More preferably, the drop will be
about 10 .mu.m above the substrate surface when the drop is
released. The degree of control necessary to achieve such accuracy
is attained with a repeatable high-resolution translation mechanism
of the type described above. In one embodiment, the height above
the substrate is determined by moving the dispenser toward the
substrate in small increments, until the dispenser tip touches the
substrate. At this point, the dispenser is moved away from the
surface a fixed number of increments which corresponds to a
specific distance. From there the drop is released to the cell
below. Preferably, the increments in which the dispenser moves less
than about 5 .mu.m and more preferably less than about 2 .mu.m.
[0132] In an alternative embodiment, the dispenser nozzle is
encircled by a sheath that rigidly extends a fixed distance beyond
the dispenser tip. Preferably, this distance corresponds to the
distance the solution drop will fall when delivered to the selected
reaction region. Thus, when the sheath contacts the substrate
surface, the movement of the dispenser is halted and the drop is
released. It is not necessary in this embodiment to move the
dispenser back, away from the substrate, after contact is made. The
point of contact with the surface can be determined by a variety of
techniques such as by monitoring the capacitance or resistance
between the tip of the dispenser (or sheath) and the substrate
below. A rapid change in either of these properties is observed
upon contact with the surface.
[0133] To this point, the spotting system has been described only
in terms of translational movements. However, other systems may
also be employed. In one embodiment, the dispenser is aligned with
respect to the region of interest by a system analogous to that
employed in magnetic and optical storage media fields. For example,
the region in which monomer is to be deposited is identified by a
track and sector location on the disk. The dispenser is then moved
to the appropriate track while the disk substrate rotates. When the
appropriate cell is positioned below the dispenser (as referenced
by the appropriate sector on the track), a droplet of monomer
solution is released.
[0134] Control of the droplet size may be accomplished by various
techniques. For example, in one embodiment, a conventional
micropipetting instrument is adapted to dispense droplets of five
nanoliters or smaller from a capillary. Such droplets fit within
regions having diameters of 300 .mu.m or leas when a non-wetting
mask of the invention is employed.
[0135] In another embodiment, the dispenser is a piezoelectric pump
that generates charged droplets and guides them to the reaction
region by an electric field in a manner analogous to conventional
ink-jet printers. In fact, some ink-jet printers can be used with
minor modification by simply substituting a monomer containing
solution for ink. For example, Wong et al., European Patent
Application 260 965, incorporated herein by reference for all
purposes, describes the use of a commercial printer to apply an
antibody to a solid matrix. In the process, a solution containing
the antibody is forced through a small bore nozzle that is
vibrating in a manner that fragments the solution into discrete
droplets. The droplets are subsequently charged by passing through
an electric field and then deflected onto the matrix material.
[0136] A conventional ink drop printer includes a reservoir in
which ink is held under pressure. The ink reservoir feeds a pipe
which is connected to a nozzle. An electromechanical transducer is
employed to vibrate the nozzle at some suitable high frequency. The
actual structure of the nozzle may have a number of different
constructions, including a drawn glass tube which is vibrated by an
external transducer, or a metal tube vibrated by an external
transducer (e.g. a piezoelectric crystal) or a magnetostrictive
metal tube which is magnetostrictively vibrated. The ink
accordingly is ejected from the nozzle in a Stream which shortly
thereafter breaks into individual drops. An electrode may be
present near the nozzle to impart a charge to the droplets.
Conventional ink drop dispensers are described in U.S. Pat. Nos.
3,281,860 and 4,121,222, which are incorporated by reference herein
for all purposes.
[0137] In a different preferred embodiment, the reactant solutions
are delivered from a reservoir to the substrate by an
electrophoretic pump. In this device, a thin capillary connects a
reservoir of the reactant with the nozzle of the dispenser. At both
ends of the capillary, electrodes are present to provide a
potential difference. As is known in the art, the speed at which a
chemical species travels in a potential gradient of an
electrophoretic medium is governed by a variety of physical
properties, including the charge density, size, and shape of the
species being transported, as well as the physical and chemical
properties of the transport medium itself. Under the proper
conditions of potential gradient, capillary dimensions, and
transport medium rheology, a hydrodynamic flow will be set up
within the capillary. Thus, in an electrophoretic pump of the
present invention, bulk fluid containing the reactant of interest
is pumped from a reservoir to the substrate. By adjusting the
appropriate position of the substrate with respect to the
electrophoretic pump nozzle, the reactant solution is precisely
delivered to predefined reaction regions.
[0138] In one particularly useful application, the electrophoretic
pump is used to produce an array containing various fractions of an
unknown reactant solution. For example, an extract from a
biological material such as leaf or a cell culture might contain
various unknown materials, including receptors, ligands, alkaloids,
nucleic acids, and even biological cells, some of which may have a
desired activity. If a reservoir of such extract is
electrophoretically pumped, the various species contained therein
will move through the capillary at different rates. Of course, the
various components being pumped should have some charge so that
they can be separated. If the substrate is moved with respect to
the dispenser while the extract components are being separated
electrophoretically, an array containing various independent
species in produced. This array is then tested for activity in a
binding assay or other appropriate test. Those elements of the
array that show promising activity are correlated with a fraction
of the extract which is subsequently isolated from another source
for further study. In some embodiments, the components in the
extract solution are tagged with, for example, a fluorescent label.
Then, during the process of delivering the solution with the
electrophoretic pump, a fluorescence detector determines when
labeled species are being, deposited on the substrate. In some
embodiments, the tag selectively binds to certain types of
compounds within the extract, and imparts a charge to those
compounds.
[0139] Other suitable delivery means include osmotic pumps and cell
(biological) sorters. An osmotic pump delivers a steady flow of
solution for a relatively long period. The construction of such
pumps is well-known in the art, generally incorporating a solution
of the extract of interest within a solvent permeable bag. Osmotic
pressure is applied to the extract solution by solvent molecules
diffusing across the bag to equalize a concentration difference.
The extract is thus forced out of a nozzle in the bag at a constant
rate. Cell sorters are also well-known in the art, and can be used
in applications where it is desirable to apply single biological
cells to distinct locations on the substrate.
[0140] Although the above embodiments have been directed to systems
employing liquid droplets, minuscule aliquots of each test
substance can also be delivered to the cell as miniature pellets.
Such pellets can be formed from the compound of interest (e.g.
ligands for use in an affinity assay) and one or more kinds of
inert binding material. The composition of such binders and methods
for the preparation of the pellets will be apparent to those of
skill in the art. Such "mini-pellets" will be compatible with a
wide variety of test substances, stable for long periods of time,
suitable for easy withdrawal from the storage vessel and dispensing
(i.e., non-tacky, preferably suspendable in a liquid such as
physiological buffer), and inert with respect to the binding
activity of receptors.
[0141] In preferred embodiments, the reactant solutions in each
predefined region are prevented from moving to adjacent regions by
appropriate barriers or constraining regions. For example to
confine aqueous monomer solutions, a hydrophilic material is used
to coat the reaction regions, while a hydrophobic material is used
in preferred embodiments to coat the region surrounding the
individual reaction regions. Of course, when non-aqueous or
nonpolar solvents are employed, different surface coatings are
generally preferred. By choosing appropriate materials (substrates,
hydrophobic coatings, and, reactant solvents), the contact angle
between the droplet and the substrate is advantageously controlled.
Large contact angles between the reactant droplets and the
substrate are desired because the solution then wets a relatively
small reaction region with shallow contact angles, on the other
hand, the droplet wets a larger area In extreme cases, the droplet
will spread to cover the entire surface.
[0142] The contact angle is determined by the following expression,
known as Young's equation:
cos .theta.=(.sigma..sub..infin.-.sigma..sub.d)/.sigma..sub.b
[0143] where .theta. is the wetting angle, .sigma..sub..infin. is
the solid-air tension, .sigma..sub.d is the solid-liquid tension,
and .sigma..sub.b is the liquid-air surface tension. The values of
these surface tensions are governed by thermodynamic considerations
including the chemical constituents of the liquid and the solid
substrate. The liquid-air surface tension for various chemicals is
easily measured by a variety of techniques such as those described
in Adamson, Physical Chemistry of Surfaces, John Wiley and Sons,
5th Ed. (1990) which is incorporated herein by reference for all
purposes. The difference of the solid-liquid and solid-air tensions
can, for a given system, be determined empirically from a Zisman
plot. In this approach, the contact angles are measured for a
homologous series of liquids on a given solid surface. For some
liquid in the series, a "critical contact angle" is observed,
beyond which lower surface tension liquids wet the surface. The
liquid-air surface tension of the liquid at this critical contact
angle is assumed to be the surface tension of the solid. This
approach has been found to provide quite reasonable results for low
energy solids such as Teflon, polyethylene, hydrocarbons, etc. The
information gained from such studies is used to optimize substrate
compositions to increase wetting angles for given reactant
solutions in the array.
[0144] Methods for controlling chemical composition and therefore
the local surface free energy of a substrate surface include a
variety of techniques apparent to those skilled in the art.
Chemical vapor deposition and other techniques applied in the
fabrication of integrated circuits can be applied to deposit highly
uniform layers on selected regions of a surface. As a specific
example, the wettability of a silicon wafer surface has been
manipulated on the micrometer scale through a combination of
self-assembled monolayer depositions and micromachining. See Abbott
et al., "Manipulation of the Wettability of Surfaces on the 0.1 to
1 Micrometer Scale Through Micromachining and Molecular
Self-Assembly" Science, 257, (Sep. 4, 1992) which is incorporated
herein by reference for all purposes.
[0145] In a preferred embodiment, the perimeters of the individual
regions are formed on a hydrophilic substrate defined by
selectively removing hydrophobic protecting groups from the
substrate surface. For example, a mono-layer of hydrophobic
photoprotecting groups can be coupled to, for example, linker
molecules attached to the substrate surface. The surface then is
selectively irradiated (or otherwise activated by, for example,
acid) through a mask to expose those areas where the reaction
regions are to be located. This cleaves the protecting groups from
the substrate surface causing the reaction regions to be less
hydrophobic than the surrounding area. This process produces a high
density of reaction regions on the substrate surface. Because
hydrophobic materials have lower surface free energies (surface
tensions) than water, the solution droplet in the cell beads rather
than spreads.
[0146] In some preferred embodiments, the substrate is prepared by
first covalently attaching a monolayer of the desired reactive
functional group (e.g. amine, hydroxyl, carboxyl, thio, etc.),
which is protected by a hydrophobic photolabile protecting moiety.
If the substrate provides a glass surface, the monolayer may be
deposited by a silanation reaction as shown below 1
[0147] In the above structures, Y is a spacer group such as a
polymethylene chain, X is a reactive protected group such as NH,
C(O)O, O, S, etc., and Pr is a hydrophobic photolabile protecting
group.
[0148] In an alternative preferred embodiment shown below, the
substrate surface is first derivatized by, for example, a
silanation reaction with appropriates to provide an amine layer. A
molecule including a spacer, a reactive group, and a photolabile
group is then coupled to the surface. 2
[0149] The photolabile protecting group should be sufficiently
hydrophobic as to render the substrate surface substantially
non-wettable. Removal of the protecting group in specific areas by
exposure to light through a suitable mask, liberates the reactive
functional groups. Because these groups are hydrophilic in
character, they will render the substrate wettable in the exposed
regions.
[0150] The class of nitrobenzyl protecting groups, which is
exemplified by the nitroveratryl group, imparts significant
hydrophobicity to glass surfaces to which a member of the class is
attached. The hydrophobicity of the basic nitrobenzyl protecting
group is enhanced by appending group chain hydrocarbon substituent.
Exemplary hydrophobic chains include C.sub.12H.sub.25 (lauryl) or
C.sub.18H.sub.37 (stearyl) substituents. The syntheses of suitably
activated forms (bromide, chloromethyl ether, and oxycarbonyl
chloride) of a typical protecting group is schematically outlined
in FIG. 14.
[0151] The spacer group ("Y") contributes to the net hydrophobic or
hydrophilic nature of the surface. For example, those spacers
consisting primarily of hydrocarbon chains, such as
--(CH.sub.2).sub.n--, tend to decrease wettability. Spacers
including polyoxyethylene (--(CH.sub.2CH.sub.2O).sub.n-), or
polyamide (--(CH.sub.2CONH).sub.n-) chains tend to make the surface
more hydrophilic. An even greater effect is achieved by using
spacer groups which possess, in addition to the protected
functional group, several "masked" hydrophilic moieties. This is
illustrated below. 3
[0152] In preferred embodiments, the hydrophilic reaction regions
is a two-dimensional circle or other shape having an aspect ratio
near one (i.e. the length is not substantially larger or smaller
than the width). However, in other embodiments, the hydrophilic
region may take the form of a long channel which is used to direct
flowing reactants in the manner described above.
[0153] In still other embodiments, the reaction regions are
three-dimensional areas defined by, for example, gaskets or dimples
on the substrate surface. The dimples or gaskets may also act as
identification marks directing the dispenser to the region of
interest.
[0154] If the solvent (or other liquid used to deliver the
reactant) has a sufficiently high vapor pressure, evaporation can
cause the reactant concentration to increase. If left unchecked,
this process ultimately causes the solute to precipitate from
solution. The effects of evaporation can be minimized by sealing
selected regions of the substrate when they need not be accessible.
Alternatively, the partial pressure of volatile reagents can be
adjusted so that the liquid and vapor phase fugacities are
equalized and the thermodynamic force driving evaporation is
reduced. The partial pressure of the reagents may be increased by
providing a relatively large reservoir of volatile reagents in a
sealed chamber. For example, solvents having a low vapor pressure
under the conditions of interest can be used. In some cases,
evaporation can be further controlled by application of a film or
coverplate having a reverse array pattern. Other methods of
preventing evaporation are well-known in the physical chemical arts
and may be used in the present invention.
[0155] In some preferred embodiments, evaporation is advantageously
employed to accelerate hybridization of target oligonucleotides
with immobilized oligonucleotides in the reaction regions. In one
specific embodiment, fluorescently tagged or otherwise labelled
target oligonucleotides in solution (e.g. a solution containing a
salt such as ammonium acetate or magnesium chloride) are delivered
to reaction regions containing immobilized probe oligonucleotides.
As the volatile salt solution evaporates from the reactant droplet
(in the same manner as solvent evaporates from an ink droplet
deposited by an ink jet printer), a locally high concentration
ratio of target to probe oligonucleotide results, accelerating
hybridization. If hybridization is carried out at room temperature,
ten minutes to a few hours are typically required to complete the
reaction. After sufficient time, the unhybridized DNA is washed or
otherwise removed from the substrate. Finally, the substrate is
imaged to detect regions in which the probe and target DNA have
hybridized. Of course, evaporation can be advantageously employed
to increase the local concentration of non-DNA solutes in a variety
of reactions besides hybridization. For example in some
embodiments, receptor solutions are sufficiently volatile that the
local receptor concentration increases in the reaction regions
containing peptides, for example, to be screened.
[0156] The arrays produced according to the above spotting
embodiments are generally used in much the same manner as the
arrays produced by the flow channel embodiments described above.
For example, the arrays can be used in screening with fluorescein
labelled receptors as described in PCT Publication No. WO92/10092,
previously incorporated by reference.
VI. ALTERNATIVE EMBODIMENTS
[0157] According to some embodiments of the invention, microvalve
structures are used to form channels along selected flow paths on
the substrate. According to these embodiments, an array of
microvalves is formed and operated by an overlying or underlying
array of electrodes that is used to energize selected valves to
open and close such valves.
[0158] FIG. 15 illustrates such a structure, FIG. 15a illustrating
the system in end view cross-section and FIG. 15b illustrating the
system in top view. The structure shown therein provides for only
two synthesis chambers for the purpose of clarity, but in most
embodiments a far greater number of chambers will be provided.
Microvalves are discussed in detail in, for example, Zdeblick, U.S.
Pat. No. 4,966,646, and Knutti, Advanced Silicon Microstructures,"
ASICT Conference (1989), both incorporated herein by reference for
all purposes.
[0159] As shown therein, a substrate 602 is provided with a
plurality of channels 604 formed using photolithographic, or other
related techniques. The channels lead up to a synthesis chamber
606. At the end of each channel is valve structure 608. As shown in
FIG. 15, the channels lead up to the chambers, but maybe isolated
from the chambers by the valves. Multiple valves may be provided
for each chamber. In the particular structure shown in FIG. 15, the
right valve on the left chamber and the left valve on the right
chamber are open while the remaining valves are closed.
Accordingly, if reagent is delivered to the top of the substrate,
it will flow through the open channel to and through the chamber on
the left, but not the one on the right. Accordingly, coupling steps
may be conducted on the chamber with selected reagents directed to
selected chambers, using the techniques discussed above.
[0160] According to some embodiments, a valve is supplied on one
side of the chamber 606, but the valve on the opposite side is
replaced by a semi-permeable membrane. According to these
embodiments, it becomes possible to flow a selected reagent into
the chamber 606 and, thereafter, flow another selected reagent
through the flow channel adjacent the semi-permeable membrane. The
semi-permeable membrane will permit a portion of the material on
one side or the other to pass through the membrane. Such
embodiments will be useful in, for example, cell studies.
[0161] Screening will be performed by, for example, separating or
cutting two halves of the device, enabling screening by, for
example, contacting with a fluorescein labelled antibody, or the
like followed by photodetection.
[0162] FIGS. 16a and 16b illustrate another alternative embodiment
of the invention which combines the mechanical polymer synthesis
techniques disclosed herein with light-directed synthesis
techniques. According to these embodiments, a substrate 401 is
irradiated in selected regions, shown as the stripes in FIG. 16a.
The surface of the substrate is provided with photoremovable groups
in accordance with PCT Publication No. WO92/10092 (previously
incorporated by reference) on, for example, amine groups in the
specific case of peptide synthesis. During this step regions 701,
702, and 703 of the substrate, among others, are deprotected,
leaving remaining regions of the substrate protected by
photoremovable groups such as nitroveratryl oxycarbonyl ("NVOC").
According to a specific embodiment of the invention the widths of
the irradiated regions equal the widths of the protected regions of
the substrate.
[0163] Thereafter, as shown in FIG. 16b the substrate is contacted
with a channel block 407. In the particular embodiment shown in
FIG. 16b, the channels 704, 705, and 707 are aligned with the
regions 701, 702, and 703, respectively, on the substrate 401. As
will be apparent, specific embodiments of the invention provide for
irradiated regions and channels in the form of stripes, which are
aligned during this step. Other embodiments, however, will provide
for other shapes of irradiated regions and channels, and other
relative orientations of the irradiated regions and channels. The
channel block and substrate will be aligned with, for example, an
alignment mark placed on both the substrate and the channel block.
The substrate may be placed on the channel block with, for example,
a vacuum tip.
[0164] Thereafter, a selected reagent is flowed through or placed
in the channels in the channel block for coupling to the regions
which have previously been exposed to light. As with the flow
channel embodiments described above, the substrate may be placed in
contact with a prefilled channel block in some embodiments to avoid
compression of the channel block to the substrate and dead spots
during pumping. According to preferred aspects of the invention, a
different reagent flows through each of the channels 701, 702, and
703 such as, for example, a reagent containing monomers A, B, and
C. The process may then, optionally, involve a second coupling step
in which the substrate is translated by, e.g., one channel width,
to provide coupling of a monomer in the regions between the
original channels.
[0165] Thereafter, the process of directed irradiation by light,
followed by coupling with the channel block is repeated at the
previously unexposed regions. The process is then preferably
repeated again, with the stripes of the mask and the channel block
rotated at, for example, 90 degrees. The coupling steps will
provide for the formation of polymers having diverse monomer
sequences at selected regions of the substrate through appropriate
translation of the mask and substrate, and through appropriate mask
selection. Through a combination of the light-directed techniques
and the mechanical flow channel techniques disclosed herein,
greater efficiency in forming diverse sequences is achieved,
because multiple monomers are coupled in a single
irradiation/coupling step.
[0166] In light-directed methods, the light shown through the mask
is diffracted to varying degrees around the edges of the dark
regions of the mask. Thus, some undesired removal of photosensitive
protecting groups at the edges of "dark" regions occurs. This
effect is exacerbated by the repeated mask translations and
subsequent exposures, ultimately leading to inhomogeneous synthesis
sites at the edges of the predefined regions. The effect is, of
course, dependent upon the thickness of the glass substrate and the
angle at which the light is diffracted. If the mask is positioned
on the "backside" of the substrate, a diffraction angle of
2.5.degree. and a substrate thickness of 0.7 mm creates a 60 .mu.m
strip of light (of variable intensity) flanking each edge. For a
0.1 mm thick substrate, the strip is approximately 5 .mu.m
wide.
[0167] To reduce these "bleed-over" effects of diffraction, a
pinhole mask may be employed to activate and/or define reaction
regions of the substrate. Thus, for example, light shown through
the pinhole mask is directed onto a substrate containing
photoremovable hydrophobic groups. The groups in the illuminated
regions are then removed to define hydrophilic reaction regions. In
one specific embodiment, the pinhole mask contains a series of
circular holes of defined diameter and separation, e.g., 20 .mu.m
diameter holes spaced 50 .mu.m apart. In some preferred
embodiments, a stationary pinhole mask is sandwiched between the
substrate and a translational mask of the type described in PCT
Publication No. WO92/10092. In this manner selected regions of the
substrate can be activated for polymer synthesis without
bleed-over. The translational mask is used to illuminate selected
holes of the stationary pinhole mask, and is aligned such that its
edges dissect the distance separating the holes of the stationary
mask thereby eliminating diffractive removal of photoprotecting
groups at neighboring sites. Because there is negligible bleed-over
incident light, inhomogeneous synthesis at sites juxtaposed along
the edge is eliminated. The resulting circular sites do, of course,
contain variable sequence density due to diffraction at the edges
of the pinhole mask, but the sequences at each predefined region
are homogeneous. In addition, each synthesis region is surrounded
by a "dark" region when the substrate is probed with a labeled
target. Thus, no bleed-over fluorescence signal is introduced by
binding at neighboring sites.
[0168] A pinhole mask containing 20 .mu.m circular holes separated
by 50 .mu.m requires a total synthesis area for the complete set of
octanucleotides of only 1.78 cm.sup.2. For a given pinhole mask,
thinner substrates allow for smaller-reaction sites separated by
larger distances. However, the area from which reliable data can be
obtained is also reduced when smaller sites are used. The density
of reaction sites is ultimately determined by the diffraction angle
and the distance between the pinhole mask and the reaction regions
(typically the substrate thickness).
[0169] Although the discussion so far has focused upon circular
pinholes, other shapes such as slots, squares, crescents, etc. may
be employed as is appropriate for the selected delivery method.
Thus, for some flow channel embodiments, linear or serpentine slots
may be desired.
[0170] In alternative preferred embodiments, the pinhole mask takes
the form of a layer coated on the substrate. This avoids the need
for a separate stationary mask to generate the dot pattern. In
addition, the surface layer provides well defined synthesis regions
in which to deposit reactants according to the spotting embodiments
described above. Further, the surface pinhole mask is conveniently
embossed with local reference coordinates for use in navigational
systems used to deliver monomer solutions to proper regions as
described above. Preferred pinhole masks are made from opaque or
reflective materials such as chrome.
VI. EXAMPLES
[0171] A. Leak Testing
[0172] An initial experiment was conducted using a flow channel
device to ensure that solutions could be delivered to selected
locations of a substrate and be prevented from contacting other
areas. Additionally, the experiment was used to demonstrate that
reagents could be delivered in a uniform manner.
[0173] Accordingly, a flat piece of conventional glass having
dimensions of about 42 mm.times.42 mm was derivatized with
aminopropyltriethoxysilan- e. The entire slide was deprotected and
washed using conventional techniques. A fluorescein marker of FITC
was then injected into flow channels formed when a block of
KelF.TM. 81 with 10 channels of 1 mm depth and 1 mm width were
brought into contact with the substrate. The fluorescein marker was
in a solution of DMF and flowed through the channels by injecting
the material into the groove with a manual pipet.
[0174] Fluorescein dye was similarly injected into every other
channel in the block, the block was rotated, and the process was
repeated. The expected resulting plot of fluorescent intensity
versus location is schematically illustrated in FIG. 17. Dark
regions are shown at the intersections of the vertical and
horizontal stripes, while lighter grey at non-intersecting regions
of the stripes. The dark grey regions indicate expected regions of
high dye concentration, while the light regions indicate regions of
expected lower dye concentration.
[0175] FIG. 18 is a mapping of fluorescence intensity of a portion
of an actual slide, with intensity data gathered according to the
methods of PCT Publication No. WO92/10092, previously incorporated
by reference. The results agree closely with the expected results,
exhibiting high fluorescence intensity at the intersection of the
channels (about 50% higher than non-intersecting regions of the
stripes), and lower fluorescence intensity at other regions of the
channels. Regions which were not exposed to fluorescence dye show
little activity, indicating a good signal-to-noise ratio.
Intersections have fluorescence intensity about 9.times. as high as
background. Also, regions within the channels show low variation in
fluorescence intensity, indicating that the regions are being
evenly treated within the channels.
[0176] B. Formation of YGGFL
[0177] The system was used to synthesize four distinct peptides:
YGGFL (SEQ. ID NO:1), YpGFL (SEQ. ID NO:2), pGGFL (SEQ. ID NO:3),
and ppGFL (the abbreviations are included in Stryer, Biochemistry,
Third Ed. (1988), previously incorporated herein by reference,
lower case letters indicate D-optical isomers and upper case
letters indicate L-optical isomers). An entire glass substrate was
derivatized with TBOC-protected aminopropyltriethoxysilane,
deprotected with TFA, coated with FMOC-protected caproic acid (a
linker), deprotected with piperidine, and coated with
FMOC-protected Glycine-Phenylalanine-Leucine (GFL).
[0178] This FMOC-GFL-coated slide was sealed to the channel block,
and all 10 grooves were deprotected with piperidine in DMF. After
washing the grooves, FMOC Glycine (G) was injected in the odd
grooves, and FMOC d-Proline (p) was injected in the even grooves.
After a two-hour coupling time, using standard coupling chemistry,
all grooves were washed with DMF. The grooves were vacuum dried,
the block removed and rotated 90 degrees. After resealing, all
grooves were deprotected with piperidine in DMF and washed. FMOC
Tyrosine (Y) was injected in the odd grooves, and FMOC p in the
even grooves. After coupling the grooves were washed and vacuum
dried. Accordingly, 25 regions of each of the compounds YGGFL,
YpGFL, pGGFL, and ppGFL were synthesized on the substrate. The
substrate was removed and stained with FITC-labelled antibodies
(Herz antibody 3E7).
[0179] A section of the resulting slide illustrating fluorescence
intensity is shown in FIG. 19. White squares are in locations of
YGGFL. The darkest regions are pGGFL and ppGFL. The. YGGFL sites
were the most intense, followed by the YpGFL sites. The pGGFL and
ppGFL intensities were near background levels, consistent with
expected results with the Herz antibody.
[0180] Quantitative analysis of the results show overall intensity
ratios for YGGFL:YpGFL:pGGFL:ppGFL as 1.7:1.5:1.1:1.0. However,
since there is a large standard deviation on the YGGFL and YpGFL,
comparing all the sites with each other may not accurately
represent the actual contrasts. Comparing the intensities of sites
within the same "stripe" gives larger contrasts, although they
remain on the order of 2:1.
[0181] C. 100 Micron Channel Block
[0182] A grid pattern of fluorescein isothiocyanate coupled to a
substrate was made by using a flow cell of this invention. A two by
three inch NVOC-derivatized substrate was photolyzed through a mask
to produce 400 micron activated bands on one axis. An etched
silicon channel block, having 64 parallel 100 micron channels
separated by 100 micron walls was then clamped to the substrate on
the other axis (i.e., perpendicular to the axis of 400 micron
activated bands). The clamping assembly consisting of aluminum top
and bottom clamp plates was used. Pressure was applied by
tightening two bolts with a torque wrench to 400 psi. A 7 mM
fluorescein isothiocyanate solution was flowed through the channels
by pipetting directly to exposed channel ends.
[0183] An image of the substrate (FIG. 20) showed regions of high
fluorescence indicating that the fluorescein had bound to the
substrate. White squares indicating fluorescein binding were
present as 400 micron horizontal stripes on the photolyzed regions
within the 100 micron vertical flow paths. Contrast ratios of 8:1
were observed between the channels and the channel spacings. This
demonstrates the nearly complete physical isolation of fluid
passing through 100 micron channels under 400 psi of clamping
pressure.
[0184] D. Channel Matrix Hybridization Assay
[0185] A center region of a two by three inch slide was derivatized
with bis(2-Hydroxyethyl)aminopropyltriethoxy silane. Six
nucleosides were then coupled to the entire reaction region using a
synthesis process consisting of deprotection, coupling, and
oxidation steps for each monomer applied. These first six
nucleosides were coupled in a reaction region defined by a 0.84
inch diameter circular well in an aluminum template clamped to the
two by three inch slide.
[0186] The seventh and eighth monomers were applied to the
substrate by flowing monomer solutions through 100 micron channels
in an etched silicon channel block (employed in Example C above).
The seventh base was coupled along the long axis (vertical) of the
two-inch by three-inch slide, and the eighth base perpendicular to
the seventh, along the short axis (horizontal) of the slide. This
defined an active matrix region of 1.28 by 1.28 cm having a density
of 2,500 reaction regions per square centimeter.
[0187] The channel block was centered over the reaction region and
clamped to the substrate using a clamping assembly consisting of
machined aluminum plates. This aligned the two inch by three inch
substrate relative to the channel block in the desired orientation.
Rotation of the top clamp plate and channel block relative to the
bottom clamp plate and substrate between the seventh and eighth
coupling steps provided for the matrix of intersecting rows and
columns.
[0188] In the top clamp plate, fluid delivery wells were connected
to laser-drilled holes which entered individual channels from the
back surface of the channel block. These delivery wells were used
to pipette coupling reagents into channels while the channel block
was clamped to the substrate. Corresponding fluid-retrieval wells
were connected to vacuum at the downstream of the channel block,
drawing fluid through the channels and out to a waste container.
Thus continuous fluid flow over the substrate in the channel region
during coupling steps was achieved.
[0189] The complete octamer synthesized at the channel
intersections formed by the seventh and eighth coupling steps had
the following sequence:
[0190] Substrate--(3')CGCAGCCG(5') (SEQ. ID NO:4).
[0191] After completion of the synthesis process, cleavage of
exocyclic amines was performed by immersion of the reaction region
in concentrated ammonium hydroxide. The reaction region was then
incubated at 15.degree. C. for one hour in a 10 nM solution of the
complementary base sequence 5' GCGTCGGC--F (SEQ. ID NO:5), where
"F" is a fluorescein molecule coupled to the 3' end of the
oligonucleotide. The target chain solution was then flushed from
the reaction region and replaced with neat 6.times. SSPE buffer,
also at 15.degree. C. Finally, the reaction region was then scanned
using a laser fluorescence detection system while immersed in the
buffer.
[0192] The brightest regions in the resulting image (FIG. 21)
correspond to channel intersections where a full octamer was
synthesized on the substrate surface. Vertical columns on the image
displayed the channel regions where the seventh base was coupled,
while horizontal rows display the channel regions where the eighth
base was coupled. Brightness in the channel intersection regions
indicated hybridization between the fluoresceinated target chain
and the complementary chain synthesized and bound to the substrate
in these regions. The vertical stripes of the image showed a
consistent brightness with regions of significantly greater
brightness at the intersection regions. The horizontal stripes did
not contain the consistent brightness of the vertical stripes, but
did have regions of brightness at the intersections with the
vertical stripes.
[0193] The consistent brightness along the seventh monomer axis
(vertical) indicated partial hybridization of the target chain in
areas where seven of the eight complementary bases were coupled to
the substrate surface. The lack of brightness along the eighth
monomer axis (horizontal) is consistent with the expectation that a
chain of six matching bases bound to the substrate surface will not
hybridize effectively to an octamer in solution (heptamers with six
matching bases followed by a mismatch at the seventh position). The
darker background consists of hexamers consisting of the first six
monomers coupled to the entire reaction region.
[0194] FIG. 22 is a magnified view of the image in FIG. 21. FIG. 22
demonstrates that the separate reaction regions are well
resolved.
VII. CONCLUSION
[0195] The above description is illustrative and not restrictive.
Many variations of the invention will become apparent to those of
skill in the art upon review of this disclosure. Merely by way of
example a variety of substrates, receptors, ligands, and other
materials may be used without departing from the scope of the
invention. The scope of the invention should, therefore, be
determined not with reference to the above description, but instead
should be determined with reference to the appended claims along
with their full scope of equivalents.
Sequence CWU 1
1
6 1 5 PRT Artificial Sequence peptide made by combinatorial
synthesis 1 Tyr Gly Gly Phe Leu 1 5 2 5 PRT Artificial Sequence
peptide made by combinatorial synthesis 2 Tyr Xaa Gly Phe Leu 1 5 3
5 PRT Artificial Sequence peptide made by combinatorial synthesis 3
Xaa Gly Gly Phe Leu 1 5 4 8 DNA Artificial Sequence primer 4
gccgacgc 8 5 8 DNA Artificial Sequence primer 5 gcgtcggc 8 6 5 PRT
Artificial Sequence peptide made by combinatorial synthesis 6 Xaa
Xaa Gly Phe Leu 1 5
* * * * *