Claims
- 1. A method for determining the positions of polymers which terminate with a given monomer, where said polymers are attached to a surface having a plurality of positionally distinct polymers attached thereto, said method comprising the steps of:
labeling a terminal monomer in a monomer type specific manner; and scanning said surface, thereby determining the positions of said label.
- 2. A method of claim 1, wherein said polymers are polynucleotides.
- 3. A method of claim 1, wherein the labeling of the terminal marker comprises incorporation of a labeled terminal monomer selected from the group of nucleotides consisting of adenine, cytidine, guanidine and thymidine.
- 4. A method for concurrently determining which subset of a plurality of positionally distinct polymers attached to a solid substrate at separable locations terminates with a given terminal subunit, said method comprising the steps of:
mixing said solid substrate with a solution comprising a reagent, which selectively marks positionally distinct polymers which terminate with said given terminal subunit; and determining with a detector which separable locations are marked, thereby determining which subset of said positionally distinct polymers terminated with said given terminal subunit.
- 5. A method of claim 4, wherein said solution comprises a reagent which marks said positionally distinct polymer with a fluorescent label moiety.
- 6. A method of claim 4, wherein said terminal subunit is selected from the group consisting of adenosine, cytosine, guanosine, and thymine.
- 7. A method for determining which subset of a plurality of primer polynucleotides have a predetermined oligonucleotide, wherein the polynucleotides are complementary to distinctly positioned template strands which are attached to a solid substrate, said method comprising the steps of:
selectively marking said subset of primer polynucleotides having the predetermined oligonucleotide; and detecting which polynucleotides are marked.
- 8. A method of claim 7, wherein said oligonucleotide subunit is a single nucleotide.
- 9. A method of claim 8, wherein the marking comprises elongating said primer with a labeled nucleotide which is complementary to a template.
- 10. A method of claim 7, wherein the marking step uses a polymerase and a blocked and labeled adenine.
- 11. A method for concurrently obtaining sequence information on a plurality of polynucleotides by use of a single label detector, said method comprising the steps of:
attaching a plurality of positionally distinct polynucleotides to a solid substrate at separable locations; labeling said plurality of polynucleotides with a terminal nucleotide specific reagent, said label being detectable using said label detector; determining whether said specific labeling reagent has labeled each separable location.
- 12. A method of claim 11, wherein said labeling is performed with reagents which can distinguishably label alternative possible nucleotide monomers.
- 13. A method of claim 11, wherein at least four replica substrates are produced, each of which is labeled with a specific labeling reagent for adenine, cytosine, guanine, or thymine.
- 14. A method of claim 11, wherein said labeling and determining steps are performed in succession using reagents specific for each of adenine, cytosine, guanine, and thymine monomers.
- 15. A method for concurrently obtaining sequence information on a plurality of polynucleotides, said method comprising the steps of:
attaching distinct polynucleotides to a plurality of distinct solid substrates; labeling said plurality of solid substrates with a terminal nucleotide specific labeling reagent; and determining whether said specific labeling reagent has labeled each distinct substrate.
- 16. A method of claim 15, wherein said labeling step is performed in a continuous flow of distinct solid substrates through a reaction solution.
- 17. A method for simultaneously sequencing a plurality of polymers made up of monomer units, said plurality of polymers attached to a substrate at definable positions, said method comprising the steps of:
mixing said substrate with a reagent which specifically recognizes a terminal monomer, thereby providing identification among various terminal monomer units; and scanning said substrate to distinguish signals at definable positions on said substrate; and correlating said signals at defined positions on said substrate to provide sequential series of sequence determinations.
- 18. A method of claim 17, wherein said plurality of polymers are synthesized by a plurality of separate cell colonies.
- 19. A method of claim 17, wherein said plurality of polymers are attached to said substrate is by a carbonyl linkage.
- 20. A method of claim 17, wherein said polymers are polynucleotides.
- 21. A method of claim 17, wherein said substrate comprises silicon.
- 22. A method of claim 17, wherein said scanning identifies a fluorescent label.
- 23. A method of claim 17, wherein said reagent exhibits specificity of removal of terminal monomers.
- 24. A method of claim 17, wherein said reagent exhibits specificity of labeling of terminal monomers.
- 25. A method for sequencing a plurality of distinctly positioned polynucleotides attached to a solid substrate comprising the steps of:
hybridizing complementary primers to said plurality of polynucleotides; elongating a complementary primer hybridized to a polynucleotide by adding a single nucleotide; and identifying which of said complementary primers have incorporated said nucleotide.
- 26. A method of claim 25, wherein said elongating step is performed simultaneously on said plurality of polynucleotides linked to said substrate.
- 27. A method of claim 25, wherein said substrate is a two dimensional surface and said identifying results from a positional determination of said complementary primers incorporating said single defined nucleotide.
- 28. A method of claim 25, wherein said substrate is a silicon substrate.
- 29. A method of claim 25, wherein said linking is by photocrosslinking said polynucleotide to said complementary primer, where said primer is attached to said substrate.
- 30. A method of claim 25, wherein said elongating is catalyzed by a DNA dependent polymerase.
- 31. A method of claim 25, wherein said single defined nucleotide has a removable blocking moiety to prevent further elongation.
- 32. A method of claim 31, wherein said blocking moiety is NVOC.
- 33. A method of claim 25, wherein said single nucleotide has both a blocking moiety and labeling moiety.
Parent Case Info
[0001] This is a continuation-in-part application of commonly assigned patent application by Pirrung et al., U.S. Ser. No. 07/362,901 (VLSIPS parent), filed Jun. 7, 1989; and Pirrung et al., U.S. Ser. No. 07/492,462, “Very Large Scale Immobilized Polymer Synthesis”, filed on Mar. 7, 1990, and which is incorporated herein by reference. Related cases Barrett et al., U.S. Ser. No. 07/435,316 (caged biotin parent), filed on Nov. 13, 1989, and Barrett et al, U.S. Ser. No. 07/612,671 (caged biotin CIP), filed on Nov. 13, 1990, are also incorporated herein by reference. Additional applications Fodor et al., U.S. Ser. No. ______, attorney docket number 11509-28 ______, (automated VLSIPS); and Fodor et al., U.S. Ser. No. ______, attorney docket number 11509-30 (sequencing by hybridization), are filed on the same day as this application and incorporated herein by reference.
Continuations (3)
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Number |
Date |
Country |
Parent |
08829893 |
Apr 1997 |
US |
Child |
10077070 |
Feb 2002 |
US |
Parent |
08679478 |
Jul 1996 |
US |
Child |
08829893 |
Apr 1997 |
US |
Parent |
07626730 |
Dec 1990 |
US |
Child |
08679478 |
Jul 1996 |
US |