U.S. patent application number 10/836514 was filed with the patent office on 2004-10-14 for tiling process for constructing a chemical array.
Invention is credited to Schembri, Carol T..
Application Number | 20040203049 10/836514 |
Document ID | / |
Family ID | 24972095 |
Filed Date | 2004-10-14 |
United States Patent
Application |
20040203049 |
Kind Code |
A1 |
Schembri, Carol T. |
October 14, 2004 |
Tiling process for constructing a chemical array
Abstract
A process of constructing an array of chemical moieties having
the following steps: forming multiple discrete physical entities
(tiles) from a substantially planar material having one or more
species of chemical moiety attached thereto; and picking and
placing the entities (tiles) stably on a support at spatially
distinct ascertainable locations to form an array of chemical
moieties. The formed array includes at least two species of
chemical moiety and preferably from about 50 to about 1000 species.
The claimed invention includes an array formed by this process.
Inventors: |
Schembri, Carol T.; (San
Mateo, CA) |
Correspondence
Address: |
AGILENT TECHNOLOGIES, INC.
INTELLECTUAL PROPERTY ADMINISTRATION, LEGAL DEPT.
P.O. BOX 7599
M/S DL429
LOVELAND
CO
80537-0599
US
|
Family ID: |
24972095 |
Appl. No.: |
10/836514 |
Filed: |
April 30, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10836514 |
Apr 30, 2004 |
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08739396 |
Oct 31, 1996 |
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Current U.S.
Class: |
435/6.11 ;
702/20 |
Current CPC
Class: |
B01J 2219/00563
20130101; B01J 2219/00659 20130101; B01J 2219/0063 20130101; B01J
2219/00565 20130101; B01J 2219/00585 20130101; B01J 2219/0061
20130101; B01J 2219/00626 20130101; B01J 2219/00637 20130101; C40B
40/06 20130101; B01J 2219/00596 20130101; B01J 2219/00527 20130101;
B01J 2219/00605 20130101; B01J 2219/00725 20130101; B01J 2219/0054
20130101; B01J 2219/00722 20130101; C40B 40/10 20130101; B01J
2219/00662 20130101; B01J 2219/00538 20130101; B01J 2219/00547
20130101; C07B 2200/11 20130101; B01J 2219/00617 20130101; C07K
1/045 20130101; C40B 70/00 20130101; C07K 1/047 20130101; B01J
19/0046 20130101 |
Class at
Publication: |
435/006 ;
702/020 |
International
Class: |
C12Q 001/68; G06F
019/00; G01N 033/48; G01N 033/50 |
Claims
What is claimed is:
1. A method comprising linking a tagged file of information with an
array of chemical moieties wherein said tagged file of information
is linked with said array by either physically encoding said tagged
file on said array or its housing or using information identifying
the array to said tagged file, which identifying information is
included on the array or its housing.
2. The method according to claim 1, wherein said tagged file of
information is linked with said array by physically encoding said
tagged file on said array or its housing.
3. The method according to claim 2, wherein said tagged file is
present in the form of a silicon chip.
4. The method according to claim 2, wherein said tagged file is
present in the form of a magnetic strip.
5. The method according to claim 2, wherein said tagged file is
present in the form of a barcode.
6. The method according to claim 1, wherein said tagged file is
linked with said array by using information identifying the array
to said tagged file, which identifying information is included on
the array or its housing.
7. The method according to claim 6, wherein said tagged file is
stored on a computer.
8. The method according to claim 6, wherein said tagged file is
stored in a data analysis device.
9. The method according to claim 6, wherein said tagged file is
stored in a computer in communication with a data analysis
device.
10. The method according to claim 6, wherein said identifying
information is present in the form of a barcode.
11. The method according to claim 6, wherein said identifying
information is present in the form of a silicon chip.
12. The method according to claim 6, wherein said identifying
information is present in the form of a magnetic strip.
13. The method according to claim 1., wherein said method is a
method of using said array in a molecular recognition-based
assay.
14. A method of using an array of chemical moieties comprising
linking a tagged file with the array using information identifying
the array to said tagged file, which identifying information is
included on the array or its housing.
15. The method according to claim 14, wherein said tagged file is
stored on a computer.
16. The method according to claim 14, wherein said tagged file is
stored in a data analysis device.
17. The method according to claim 14, wherein said tagged file is
stored in a computer in communication with a data analysis
device.
18. The method according to claim 14, wherein said method is a
method of using said array in a molecular recognition-based
assay.
19. A method of using an array of chemical moieties comprising
linking a tagged file with the array using information identifying
the array to said tagged file, which identifying information is in
the form of a barcode and included on the array or its housing.
20. The method according to claim 19, wherein said tagged file is
stored on a computer.
21. The method according to claim 19, wherein said tagged file is
stored in a data analysis device.
22. The method according to claim 19, wherein said tagged file is
stored in a computer in communication with a data analysis
device.
23. A method of linking an array of chemical moieties with a file
containing the identity and position of chemical moieties in the
array, comprising physically encoding the file on the array or its
housing, or including information identifying the array with the
file on the array or its housing.
Description
TECHNICAL FIELD
[0001] This invention relates generally to a process of forming an
array of bioorganic molecular probes on a support, and to an array
formed by this process.
BACKGROUND
[0002] Arrays of immobilized probes are currently being developed
for use in assays to detect and identify components in biological
samples and for screening molecular libraries. The ability to
screen for multiple species of molecules in a single assay test is
particularly valuable for purposes of drug discovery and clinical
genetics. Accordingly, array manufacturing technologies have been
developed to permit a large number of different probes to be
incorporated into an array at separate and known locations (see,
e.g., Fodor et al., Science 251, 767-773 (1991); Southern et al.,
Nucleic Acids Research 22: 1368-1373 (1994); U.S. Pat. No.
5,510,270; U.S. Pat. No. 5,474,796; U.S. Pat. No. 5,429,807; and
U.S. Pat. No. 5,472,672). In these prior art methods, the probe
molecules are synthesized in situ on a solid support surface at
predetermined locations.
[0003] There are disadvantages to forming an array in this manner
when the array is comprised of biopolymers such as
oligonucleotides. The in situ method currently used for the
commercial manufacture of oligonucleotide arrays is not well suited
for the efficient production of arrays of long chain polymer probes
because of the number of cycles of elongation required and the
variable efficiency of each attachment step. For example, in order
to synthesize n species of oligonucleotide having m variable
positions, n.times.m elongation cycles are required. Although
solutions have been devised to shorten the time of the overall
process by segregating groups of sites for the simultaneous
addition of a given nucleotide (see, e.g., Frank et al., Nucleic
Acids Res. 11, 4365-4377 (1983); U.S. Pat. No. 5,510,270),
manufacturing an array in this way is inefficient, particularly
when the desired array is intended to include hundreds of different
probe sequences and probe lengths in excess of 30 nucleotides. Each
attachment step requires a finite time for covalent bond formation,
and each is associated with a failure rate of between 2% and 15%.
The problems with probe fidelity necessitate a high level of probe
redundancy, and it is only after the entire array is formed that
defects are discoverable.
[0004] Additionally, if reagents are dispensed as microdroplets,
precautions must be taken to avoid intermixing of chemical moieties
in neighboring droplets either by precisely depositing the droplet
at its designated attachment site or by forming a pattern of
differential polarities on the attachment surface to constrain the
droplets to their designated attachment regions by means of surface
tension.
[0005] What is needed is a process for forming an array with probes
of known high fidelity in which the chemistry of attachment can be
independently optimized for each different probe in the array, the
density of each type of attached probe can be quantitatively
assessed prior to array formation and probes not meeting
specifications can be corrected or discarded prior to array
assembly. The number of overall steps required to form the array is
reduced in this process compared to prior art methods, and the
total number of tests required to ensure the quality of
manufactured arrays is equal to the number of probes in the array,
not the number of arrays produced.
SUMMARY OF THE INVENTION
[0006] To address the above-mentioned need in the art, the
invention disclosed and claimed herein provides a process for
constructing an array of chemical moieties by forming multiple
tiles comprised of a substantially planar material, each tile
having attached to it at least one species of chemical moiety, and
picking and placing each tile stably on a support at a separate and
distinct spatial location to form an array of chemical moieties.
The array formed by this process includes at least two species of
chemical moiety and preferably from about 50 to about 1000 species
of chemical moiety. The chemical moieties are preferably bioorganic
molecular probes, most preferably nucleic acids, proteins,
polysaccharides, and lipids.
[0007] An objective of this invention is to increase the speed and
reproducibility of the array manufacturing process by attaching
presynthesized probes to discrete physical entities which can be
moved robotically to separate predetermined locations on a support
to create the array. The attachment step is preferably carried out
in a batchwise manner to optimize the linker chemistry and
attachment density of each type of probe in the array independently
of the assembly of the array.
[0008] A related objective is to provide means for optimizing the
linker chemistry and attachment density of each type of probe in
the array independently of the assembly of the array.
[0009] Yet another objective of this invention is to streamline the
quality control procedure and lower the cost of producing an array
with a high degree of chemical complexity. The fidelity of
synthesis of each probe type in the array and its density of
attachment can be verified prior to tiling the array. The entire
surface of a discrete physical entity can be tested prior to
subdividing it into hundreds of thousands of tiles for placement
into hundreds of thousands of arrays, thereby permitting the early
detection and correction of manufacturing problems.
BRIEF DESCRIPTION OF THE FIGURES
[0010] FIG. 1 illustrates schematically the steps involved in the
process of forming an array of this invention.
[0011] FIG. 2 illustrates an embodiment of the array in which the
tiles are cylindrically arranged on a support surface.
DETAILED DESCRIPTION OF THE INVENTION
[0012] Before the invention is described in detail, it is to be
understood that this invention is not limited to the particular
component parts or process steps of the methods described, as such
parts and methods may vary. It is also to be understood that the
terminology used herein is for purposes of describing particular
embodiments only, and is not intended to be limiting. As used in
the specification and the appended claims, the singular forms "a",
"an", and "the" include plural referents unless the context clearly
indicates otherwise.
[0013] In this specification and in the claims which follow,
reference will be made to a number of terms which are used as
defined below.
[0014] An "array" is an arrangement of objects in space in which
each object occupies a separate predetermined spatial position.
Each of the objects in the array of this invention comprise one or
more species of chemical moiety attached to a "discrete physical
entity", such that the physical location of each species is known
or ascertainable. A "discrete physical entity" is a unit of
substantially planar material (e.g., a solid material, a membrane,
a gel or a combination of materials) that can be handled and still
maintain its identity, and can be subdivided into "tiles" for
recombining in various ways to form a physical array. Preferably,
the tiles will have regular geometric shapes, e.g., a sector of a
circle, a rectangle, and the like, with radial or linear dimensions
of about 100 .mu.m to about 10 mm, most preferably about 250 .mu.m
to about 1000 .mu.m. The subdivision of the entity into tiles can
be made either before or after attachment of the chemical moiety,
and by any suitable method for cutting the entity, e.g., with a
dicing saw. These methods are well-known in the art of
semiconductor chip manufacture and can be optimized by one skilled
in the art for the particular material selected for use in this
invention.
[0015] A "support" is a surface or structure for the attachment of
tiles. The "support" may be of any desired shape and size and can
be fabricated from a variety of materials. The support material can
be treated for biocompatibility (i.e., to protect biological
samples and probes from undesired structure or activity changes
upon contact with the support surface) and to reduce non-specific
binding of biological materials to the support. These procedures
are well-known in the art (see, e.g., Schoneich et al, Anal. Chem.
65: 67-84R (1993)). The tiles can be attached to the support by
means of an adhesive, by insertion into a pocket or channel formed
in the support, or by any other means that will provide a stable
and secure spatial arrangement.
[0016] "Tiling" is the process of forming an array by picking and
placing individual tiles comprising single or multiple species of
chemical moieties on a support in a fixed spatial pattern.
[0017] A "chemical moiety" is an organic or inorganic molecule that
is preformed at the time of attachment to a discrete physical
moiety, in distinction to an organic molecule that is synthesized
in situ on an array surface. The preferred mode of attachment is by
covalent bonding, although noncovalent means of attachment or
immobilization might be appropriate depending on the particular
type of chemical moiety that is used. If desired, a "chemical
moiety" can be covalently modified by the addition or removal of
groups after the moiety is attached to a physically distinct
entity.
[0018] The chemical moieties of this invention are preferably
"bioorganic molecules" of natural or synthetic origin, are capable
of synthesis or replication by chemical, biochemical or molecular
biological methods, and are capable of interacting with biological
systems, e.g., cell receptors, immune system components, growth
factors, components of the extracellular matrix, DNA and RNA, and
the like. The preferred bioorganic molecules for use in the arrays
of this invention are "molecular probes" selected from nucleic
acids (or portions thereof), proteins (or portions thereof),
polysaccharides (or portions thereof), and lipids (or portions
thereof), for example, oligonucleotides, peptides, oligosaccharides
or lipid groups that are capable of use in molecular recognition
and affinity-based binding assays (e.g., antigen-antibody,
receptor-ligand, nucleic acid-protein, nucleic acid-nucleic acid,
and the like). An array may contain different families of
bioorganic molecule, e.g., proteins and nucleic acids, but
typically will contain two or more species of the same family of
molecule, e.g., two or more sequences of oligonucleotide, two or
more protein antigens, two or more chemically distinct small
organic molecules, and the like. An array can be formed from two
species of molecule, although it is preferred that the array
contain several tens to thousands of species of molecule,
preferably from about 50 to about 1000 species. Each species of
course can be present in multiple copies if desired.
[0019] An "analyte" is a molecule whose detection is desired and
which selectively or specifically binds to a molecular probe. An
analyte can be the same or different type of molecule as the
molecular probe to which it binds.
[0020] The steps involved in constructing an array by the process
of this invention are diagrammed in FIG. 1.
[0021] A substantially planar "discrete physical entity" (step a,
1) is derivatized with chemically reactive groups (step b, 3).
These groups are covalently attached to linker molecules (step c,
5). Of course, either or both of these steps can be bypassed if
suitable functional groupings and/or linkers are inherent in the
material selected for use. The linkers serve as attachment sites
for chemical moieties. The linkers are contacted with a solution or
droplets of chemical moieties. After binding has taken place
between the linkers and chemical moieties, unreacted moieties are
removed by washing. Unreacted linkers are treated so as to render
them chemically inert in successive array manufacturing steps and
minimize their ability to interact with analytes during subsequent
assay procedures. This treatment is generically referred to herein
as "capping". Thus, e.g., a reactive aldehyde or isothiocyanate
group can be capped with an amine or ammonia, a reactive epoxy
group can be converted with an acidic solution into a diol, and so
on. In step (d), all of the linkers are shown attached to the same
species of chemical moiety (7). It should be understood however
that more than one species of chemical moiety may be linked to a
particular entity as a matter of choice. The material is subdivided
into individual tiles (step (e), 9). The subdivision can take place
prior to or after step (b). In step (f), tiles comprising the same
or different species of chemical moiety (shown generally at 11) are
arranged on a support (13) to form an array. In an embodiment of
the invention shown in FIG. 2, the tiles (20) are cylindrically
arranged on a support (22). The support can be a solid rod having
tiles disposed on the periphery as shown here, or the support can
be a tubular structure wherein the tiles are disposed on the
exterior or interior surface of the tube, or between exterior and
interior surfaces, if these are spaced apart. Other variations of
this shape are intended to be within the scope of this
invention.
[0022] Any material can be used as a discrete physical entity,
provided it is capable of subdivision into tiles, is compatible
with the chemistry selected for attachment of chemical moieties to
the surface, and compatible optically with detection method of the
assay in which the array is to be used. Examples of suitable
materials include, without limitation, glass, silicon, and
plastic.
[0023] A routine method for derivatizing a glass or silicon surface
for attachment of linkers is by formation of siloxane bonds, using
organosilanes such as such as 3-glycidoxypropyl-trimethoxysilane
("GOPS"), 3-aminopropyltriethoxysilane (APS), and the like, which
have well-understood chemistries. The linker molecule may be a
bifunctional reagent that covalently binds the surface to one group
and the chemical moiety to the other. Alternatively, the linker may
be a reagent that is bound to the surface covalently (e.g.,
streptavidin) and to the molecule of interest by a high affinity
noncovalent interaction (e.g., biotin). Methods for covalently
linking chemical moieties to various materials for use in affinity
purification procedures are well-known. See, generally, Affinity
Techniques. Enzyme Purification: Part B. Methods in Enzymology,
Vol. 34, ed. W. B. Jakoby, M. Wilchek, Acad. Press, NY (1974) and
Immobilized Biochemicals and Affinity Chromatography, Advances in
Experimental Medicine and Biology, Vol. 42, ed. R. Dunlap, Plenum
Press, NY (1974). The covalent attachment of oligonucleotides to
solid supports for use in hybridization assays is described in
Ghosh & Musso, Nuc. Acids Res. 15: 5353-5372 (1987) and Eggers
et al, Bio Techniques 17: 516-524 (1994). Of course, the attached
chemical moieties must able to interact freely with analytes in
binding assays (e.g., an attached oligonucleotide must be free to
hybridize to a complementary nucleic acid or to bind a
sequence-specific protein, an antigen must be capable of
interacting with an antibody, and so on).
[0024] The chemical moieties intended for use in the arrays of this
invention are bioorganic molecules as defined above, having
molecular weights in the range of about several hundreds of daltons
to about several hundreds of kilodaltons. The density of molecules
attached to a single physically discrete entity is intended to be
in the range of about 1000 to about 100,000 molecules per square
micron of surface. Various methods can be used to measure the
density of molecules on monolayer surfaces. For example, the
chemical moiety can be provided with a hydrolyzable group that is
cleaved and measured after the moiety has attached to surface, or
the chemical moiety may include labels that are directly measurable
by spectrometric or microscopic techniques. These techniques and
measurements are within the knowledge of one skilled in the
art.
[0025] The chemical moieties are contained in a solution that can
be delivered to the attachment surface of the entity in the form of
droplets (see, e.g., EP 0268237 for an example of an apparatus
suitable for dispensing and printing reagents) or, preferably, the
solution can be held in contact with the surface. It is intended
that some of the arrays formed by the process of this invention
will comprise multiple arrays of chemical moieties, which can be
formed in various ways. For example, an array can be printed onto a
tile for placement into a tiled array. Alternatively, multiple
stripes of chemical moieties, each stripe containing a unique
species of chemical moiety, can be deposited on a discrete physical
entity and the entity divided into multiple tiles that include each
of the species at a known position on the tiles.
[0026] As noted above, the tiles can be formed in any manner
appropriate to subdividing the material. Typically, the material is
diced with a commercial dicing saw in the following manner. The
material is placed on a thin film adhesive backing for mounting on
a vacuum chuck. The dicing instrument is programmed with
information about the shape of the material to be cut, the desired
depth of cutting, and speed of travel of the chuck towards the
blade (assuming the position of the blade is fixed). The material
is cut in a first direction with a metal or diamond-impregnated
blade rotating at a speed of about 20,000 rpm. Debris generated by
cutting can be directed away from the cut surface with a jet of
air, gas or liquid. The material is then rotated through a desired
angle and cutting is continued in a second direction until the
formation of tiles is completed.
[0027] The array is formed by transferring the tiles from the thin
film adhesive backing (see above) to a support in a stable
predetermined spatial arrangement. The transfer (herein referred to
as "picking and placing") can be performed with procedures that are
known in the manufacture of integrated circuits and LEDs (see,
e.g., U.S. Pat. No. 5,256,792). The following automated procedure
is an example of a robotics procedure that has been used to pick
and place tiles comprising oligonucleotides and proteins one at a
time on a support in a stable spatial arrangement. An individual
tile resting on an adhesive carrier within an x-y grid was located
with the aid of a camera. The tile was ejected from the underside
of its adhesive backing with a needle, picked up with a vacuum
probe, re-inspected with a camera, moved with an x-y planar motor
to a predetermined position on a support, and inserted into a
holder in the support. Preferably, the tiles are arranged in a
circular pattern and held in place by grooved channels formed
within the support, rather than by an adhesive. The techniques for
forming microstructures such as pockets, grooves or channels
capable of attaching tiles in a support are well-known in the art
of microfabrication.
[0028] The arrays formed by the above-described process are
intended for use in a molecular recognition-based assay, in which a
sample containing an analyte whose detection is desired is brought
into contact with an array of molecules of known, structure or
activity located at predetermined spatial positions on a support;
the analyte is recognized by and selectively binds to an array
molecule; and the binding is of sufficiently high affinity to
permit the analyte to be retained by the array molecule until
detection of the analyte has been accomplished. The selective
recognition might be based on a distinguishing physicochemical
characteristic of the analyte (e.g., a domain having a particular
charge distribution or polarity that is capable of recognition by
an array molecule), or a specific chemical feature of the analyte
(e.g., a specific primary sequence in a nucleic acid, protein or
polysaccharide, a secondary or higher order conformational
structure, or a specific chemical group or combination of groups to
form an active site). It is contemplated that the arrays formed by
the process of this invention will be useful for screening chemical
and molecular biological libraries for new therapeutic agents, for
identifying ligands for known biological receptors and new
receptors for known ligands, for identifying expressed genes,
characterizing genetic polymorphisms, genotyping human populations
for diagnostic and therapeutic purposes, and many other uses.
[0029] In using an array formed according to the process of this
invention, the identity of a chemical moiety bound to an analyte at
any particular location in the array can be determined by detecting
the location of the analyte and linking this with the array's
tagged file. The tagged file is a file of information wherein the
identity and position of each chemical moiety in the array
pertaining to the file is stored. There are various methods of
linking this tagged file with the physical array. For example, the
tagged file can be physically encoded on the array or its housing
by means of a silicon chip, magnetic strip or bar code.
Alternatively, the information identifying the array to a
particular tagged file might be included on an array or its
housing, with the actual file stored in the data analysis device or
in a computer in communication with the device. The linking of the
tagged file with the physical array would take place at the time of
data analysis. Yet another way of doing this would be to store the
tagged file in a device such as a disc or card that could be
inserted into the data analysis device by the array user at the
time the array was used in the assay.
[0030] It should be understood that the above description and
examples are intended to illustrate the invention and to provide
those of ordinary skill in the art with a complete disclosure and
description of how to use the method of the invention, and is not
intended to limit the scope of what the inventors regard as their
invention. The process of forming the array can be varied in
numerous insubstantial ways including changing the order in which
the steps are carried out, the selection of materials used, the
geometry of the array, the size and shape of the tiles, the methods
of forming discrete physical entities comprising chemical moieties
and subdividing these into tiles, and the method of picking,
placing and immobilizing tiles on a supporting surface. Other
aspects, advantages and modifications within the scope of the
invention will be apparent to those skilled in the art to which the
invention pertains. All of the above-mentioned patents and
publications are incorporated by reference herein.
* * * * *