High throughput assay system for monitoring ESTs

• US 6,458,533 B1
• Filed: 12/22/1998
• Issued: 10/01/2002
• Est. Priority Date: 12/19/1997
• Status: Expired due to Fees

• Current Assignee: High Throughput Genomics, Inc.
• Original Assignee: High Throughput Genomics, Inc.
• Inventors: Seligmann, Bruce, Felder, Stephen, Kris, Richard M.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/218,089
• Time in Patent Office: 1,379 Days
• Field of Search: 435/6, 435/91.2, 536/23.3, 536/24.3
• US Class Current: 435/6.16
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In one embodiment of the invention, the test regions (which can be wells) are further subdivided into smaller subregions (indentations, or dimples).

In one embodiment of the invention, ESTs are mapped. In another embodiment, the presence of a target nucleic acid is detected by protecting the target against nuclease digestion with a polynucleotide fragment, and analyzing the protected polynucleotide by mass spectrometry.

Claims

1. A method of determining which of a plurality of ESTs are complementary to a given nucleic acid, comprising,

a) incubating an immobilized array of oligonucleotide probes, wherein at least one of said probes is complementary to a portion of a first strand of each of said plurality of ESTs, and wherein the second strands of at least two of said ESTs are complementary to different or overlapping portions of said given nucleic acid, with a test sample which may contain said given nucleic acid, to obtain, if said test sample contains said given nucleic acid, hybridization products between said oligonucleotide probes and said given nucleic acid,

b) incubating the hybridization products in said array with a detector oligonucleotide, wherein, for each hybridization product, said detector oligonucleotide is complementary to a portion of a first strand of an EST to which the oligonucleotide probe in said hybridization product is complementary, but which is complementary to a different portion of that EST strand than is said oligonucleotide probe, and

c) detecting which oligonucleotide probes of said array are labeled by said detector oligonucleotide, thereby determining which of said plurality of ESTs are complementary to said given nucleic acid,

wherein said array of oligonucleotide probes is immobilized on a region of a combination, wherein said combination comprises

i) a surface comprising a number of spatially discrete, substantially identical, regions equal to the number of ESTs to be studied, each region comprising

ii) a number of different anchors equal to the number of ESTs to be studied, each anchor in association with

iii) a bifunctional linker which has a first portion that is specific for the anchor, and a second portion that comprises an oligonucleotide probe which is specific for at least one of said ESTs.

2. The method of claim 1, further comprising, after a) and/or b), removing unbound portions of said sample.

3. The method of claim 1, which is a method of determining which of at least eight ESTs are complementary to a given nucleic acid.

4. The method of claim 3, comprising

a) contacting each of a number of samples corresponding to the number of ESTs to be studied, wherein each of said samples may comprise molecules of said given nucleic acids, with a different region of a combination, wherein each said region comprises an array of oligonucleotide probes, at least one of which is complementary to a portion of a first strand of each of said ESTs,

b) incubating said samples with said regions, thereby permitting molecules of said nucleic acid to bind to said oligonucleotide probes, thereby forming hybridization products, and

c) incubating each of said regions comprising said hybridization products with a different detector oligonucleotide, wherein each of said detector oligonucleotide is complementary to a portion of a first strand of an EST to which a given one of the oligonucleotide probes of said array corresponds, but which is complementary to a different portion of the EST strand than is said given oligonucleotide probe, thereby binding detector oligonucleotides to nucleic acid molecules which have bound to said given oligonucleotide probe or to other oligonucleotide probes which are complementary to said nucleic acid.

5. A method of determining which of a plurality of ESTs are complmentary to a given nucleic acid, comprising,

a) incubating a collection of bifunctional oligonucleotide linker molecules, each of which comprises a first portion which is an oligonucleotide probe that is complementary to a portion of a first strand of at least one of said plurality of ESTs, and a second portion which is specific for an anchor oligonucleotide, with a test sample which may contain said given nucleic acid, to obtain, if said test sample contains said given nucleic acid, a first set of hybridization products between said oligonucleotide probes and said given nucleic acid, wherein the second strand of at least two of said ESTs are complementary to different or overlapping portions of said given nucleic acid,

b) incubating said first hybridization products with an immobilized array of anchor oligonucleotides, wherein each anchor oligonucleotide is complementary to the anchor-specific portion of at least one of said linker molecules, to form a second set of hybridization products comprising said anchors, said linker molecules and said given nucleic acid, and

c) incubating either said first or said second hybridization product with a detector oligonucleotide, wherein, for each hybridization product, said detector oligonucleotide is complementary to a portion of a first strand of an EST to which the oligonucleotide probe in said hybridization product is complementary, but which is complementary to a different portion of that EST strand than is said oligonucleotide probe, and

d) detecting which oligonucleotide probes of said array are labeled by said detector oligonucleotide,

wherein said array of anchor oligonucleotide is immobilized on a region of a combination, wherein said combination comprises

i) a surface comprising a number of spatially discrete, substantially identical, regions equal to the number of ESTs to be studied, each region comprising

ii) a number of different anchors equal to the number of ESTs to be studied.

6. The method of claim 5, further comprising, after a), b) and/or c), removing unbound portions of said sample.

7. The method of claim 5, which is a method of determining which of at least eight ESTs are complementary to a given nucleic acid.

8. A method of determining which of a plurality of polynucleotides are complementary to a given nucleic acid, comprising,

a) incubating an immobilized array of oligonucleotide probes, wherein at least one of said probe is complementary to a portion of a first strand of each of said plurality of polynucleotides, and wherein the second strands of at least two of said polynucleotides are complementary to different or overlapping portions of said given nucleic acid, with a test sample which may contain said given nucleic acid, to obtain, if said test sample contains said given nucleic acid, hybridization products between said oligonucleotide probes and said given nucleic acid,

b) incubating the hybridization prodcts in said array with a detector oligonucleotide, wherein, for each hybridization product, said detector oligononucleotide is complementary to a portion of a first strand of a polynucleotide to which the oligonucleotide probe in said hybridization product is complementary, but which is complementary to a different portion of that polynucleotide strand than is said oligonucleotide probe, and

c) detecting which oligonucleotide probes of said array are labeled by said detector oligonucleotide, thereby determining which of said plurality of polynucleotides are complementary to said given nucleic acid,

wherein said array of oligonucleotide probes is immobilized on a region of a combination, wherein said combination comprises

i) a surface comprising a number of spatially discrete, identical, regions equal to the number of polynucleotides to be studies, each region comprising

ii) a number of different anchors equal to the number of polynucleotides to be studied, each anchor in association with

iii) a bifunctional linker which has a first portion that specific for the anchor, and a second portion that comprises an oligonucleotide probe which is specific for at least one of said polynucleotide.

9. The method of claim 8, further comprising, after a), b) and/or c), removing unbound portions of said sample.

10. The method of claim 8, which is a method of determining which of at least eight polynucleotides are complementary to a given nucleic acid.

11. The method of claim 10, comprising

a) contacting each of a number of samples corresponding to the number of polynucleotides to be studied, wherein each of said samples may comprise molecules of said given nucleic acid, with a different region of a combination, wherein each said region comprises an array of oligonucleotide probes, at least one of which is complementary to a portion of a first strand of each of said polynucleotides,

b) incubating said samples with said regions, thereby permitting molecules of said nucleic acid to bind to said oligonucleotide probes, thereby forming hybridization products, and

c) incubating each of said regions comprising said hybridization products with a different detector oligonucleotide, wherein each of said detector oligonucleotides is complementary to a portion of a first strand of an polynucleotide to which a given one of the oligonucleotide probes of said array corresponds, but which is complementary to a different portion of the polynucleotide strand than is said given oligonucleotide probe, therby binding detector oligonucleotides to nucleic acid molecules which have bound to said given oligonucleotide probe or to other oligonucleotide probes which are complementary to said nucleic acid.

12. A method of determining which of a plurality of ESTs are complementary to a given nucleic acid, comprising;

a) incubating an immobilized array of oligonucleotide probes, wherein at least one of said probes is complementary to a portion of a first strand of each of said plurality of ESTs, and wherein the second strands of at least two of said ESTs are complementary to different or overlapping portions of said given nucleic acid, with a test sample which may contain said given nucleic acid, to obtain, if said test sample contains said given nucleic acid, hybridization products between said oligonucleotide probes and said given nucleic acid,

b) incubating the hybridization products in said array with a detector oligonucleotide, wherein, for each hybridization product, said detector oligonucleotide is complementary to a portion of a first strand of an EST to which the oligonucleotide probe in said hybridization product is complementary, but which is complementary to a different portion of that EST strand than is said oligonucleotide probe, and

c) detecting which oligonucleotide probes of said array are labeled by said detector oligonucleotide, thereby determining which of said plurality of ESTs are complementary to said given nucleic acid.