Replica amplification of nucleic acid arrays

• US 6,432,360 B1
• Filed: 08/28/1998
• Issued: 08/13/2002
• Est. Priority Date: 10/10/1997
• Status: Expired due to Term

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Church, George M.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US09/143,014
• Time in Patent Office: 1,446 Days
• Field of Search: 435/6, 435/810, 422/50, 422/68.1, 536/23.1, 536/24.1, 536/24-- 2, 536/25.3, 935/77.78
• US Class Current: 422/68.1
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2531/113 PCR

Abstract

A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

Claims

1. A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of,

a) providing a first nucleic acid array comprising a pool of nucleic acid molecules immobilized to a support with the nucleic acid molecules being randomly patterned, and amplifying in situ the nucleic acid molecules,

b) transferring at least a subset of nucleic acid molecules produced by said amplifying is to a second support, and

c) immobilizing said subset to said second support to form a second nucleic acid array, wherein the nucleic acid molecules of said second array occupy positions that correspond to those of said nucleic acid molecules from which they were amplified on said first array to produce said plurality.

2. The method according to claim 1, further comprising the step after step b) of repeating steps b) and c).

3. The method according to claim 2, further comprising the step, after step b) or a repetition thereof, of repeating step a).

4. The method according to claim 1, further comprising after step b) the step of transferring and immediately at least a subset of the molecules transferred to said second support to a third support.

5. The method according to claim 1, further comprising the step of amplifying said nucleic acid molecules of said second array.

6. The method according to claim 1, wherein said pool of nucleic acid molecules is prepared from RNA or DNA.

7. The method according to claim 6, wherein said pool of nucleic acid molecules comprises cDNA or genomic DNA.

8. The method according to claim 1, wherein said pool of said nucleic acid molecules is a library.

9. The method according to claim 1, wherein said pool of nucleic acid molecules is prepared by

a) cloning genomic DNA or cDNA into a cloning site on a nucleic acid vector and

b) subsequently cleaving said nucleic acid molecules from said vector, wherein said cloning site is flanked on either side by oligonucleotide sequences that will remain linked to said nucleic acid molecules after said cleaving of step b).

10. The method of claim 9, wherein said oligonucleotide sequences comprise recognition sites for a restriction enzyme(s).

11. The method according to claim 10, wherein subsequent cleavage of the nucleic acid molecules of said library to which said sites are linked with said enzyme(s) results in the release of pairs of oligonucleotide primers that comprise sequences unique to either end of each member of said library.

12. The method according to claim 10, wherein said recognition sites are those of type IIS restriction enzymes.

13. The method according to claim 1, wherein said support is semi-solid.

14. The method according to claim 13, wherein said semi-solid support is selected from the group that includes polyacrylamide, cellulose, polyamide (nylon) and cross-linked agarose, -dextran and -polyethylene glycol.

15. The method according to claim 1, wherein said amplifying of nucleic acid molecules of step a) is performed by polymerase chain reaction (PCR).

16. The method according to claim 1, wherein said immediately is performed using a covalent linker that is selected from the group that includes oxidized 3-methyl uridine, an acrylyl group and hexaethylene glycol.

17. The method according to claim 1, wherein said step of immobilizing includes hybridization of members of said pool to nucleic acid molecules that are covalently bound to said support.

18. The method according to claim 9, wherein said nucleic acid molecules bound to said support are synthetic oligonucleotides.

19. The method according to claim 1, wherein said transferring of step b) comprises contacting said first array with a support, such that at least a subset of said nucleic acid molecules produced by said amplifying of step a) are transferred to said support.

20. The method according to claim 1, wherein said transferring of step b) comprises the steps of

i) contacting said first array with a carrier selected from the group that includes a cylindrical roller, a stamping device, a membrane and a support, such that at least a subset of said nucleic acid molecules produced by said amplifying of step a) are transferred to said carrier, and

ii) subsequently contacting said carrier with a support.

38. The method of claim 1, wherein said method further comprises the step, after step c), of identifying a feature of a said first or second array.

39. The method of claim 38, wherein said identifying is performed using sequencing by hybridization (SBH), quantitative incremental fluorescent nucleotide addition sequencing (QIFNAS) or stepwise ligation and cleavage.

21. A plurality of a nucleic acid array, wherein said plurality comprises

a) a first template randomly-patterned, covalently immobilized nucleic acid array comprising a pool of nucleic acid molecules randomly immobilized on a support, and

b) a second randomly-patterned, covalently immobilized nucleic acid array, wherein the nucleic acid molecules of said second array are nucleic acid amplification products of said pool and wherein said nucleic acid molecules of said second array occupy positions on said second array that correspond to those of said nucleic acid molecules from which they were amplified on said first array.

22. A method for determining the sequential order of genetic elements of a chromosome, comprising providing an immobilized nucleic acid array, comprising the steps of

a) providing an immobilized chromosome,

b) amplifying the nucleic acid sequences of said chromosome,

c) contacting said amplified sequences with a support, such that a subset of nucleic acid molecules produced by said amplifying are retained by said support,

d) immobilizing said nucleic acid molecules so retained to said support to form a first immobilized nucleic acid array, wherein the positions of the members of said array correspond to the positions of the DNA sequences from which they were amplified on said chromosome, and

e) determining the order of genetic elements on said chromosome, wherein said ordering comprises identifying the features of said array and wherein the position of a first feature relative that of a second feature on said array corresponds to the position of a first genetic element relative to that of a second genetic element on said chromosome.

23. The method according to claim 22, wherein said amplifying is performed by PCR.

24. The method according to claim 22, wherein said identifying is performed using sequencing by hybridization (SBH), quantitative incremental fluorescent nucleotide addition sequencing (QIFNAS) or stepwise ligation and cleavage.

29. The method according to claims 22 or 25, further comprising the steps after step c) of

i) amplifying the molecules of said first array by PCR and

ii) contacting said first array with a second support, such that at least a subset of said amplified nucleic acid molecules are transferred to said support, and

iii) immobilizing said nucleic acid molecules to said second support to form a second immobilized nucleic acid array, wherein the positions of the members of said second array correspond to the positions of said molecules from which they were amplified on said first array.

25. A method for localizing RNA molecules within a cell or a tissue section comprising providing an immobilized nucleic acid array, comprising the steps of

a) providing an immobilized cell or a tissue section,

b) reverse transcribing RNA molecules of said cell or said tissue section to produce an array of features comprising reverse transcripts,

c) contacting said array with a support, such that at least a subset of said reverse transcripts are retained by said support, and

d) immobilizing said reverse transcripts to said support to form an immobilized nucleic acid array, and

e) localizing said RNA molecules, comprising identifying said features of said array, wherein the positions of said features on said array correspond to the positions of said RNA molecules in said cell or said tissue section.

26. The method according to claim 25 further comprising the step after step b) of amplifying said reverse transcripts.

27. The method according to claim 26, wherein said amplifying is performed by PCR.

28. The method according to claim 25, wherein said identifying is performed using sequencing by hybridization (SBH), quantitative incremental fluorescent nucleotide addition a sequencing (QIFNAS) or stepwise ligation and cleavage.

30. A method of obtaining a plurality of immobilized nucleic acid arrays, wherein the arrays of the plurality are derived from different nucleic acid pools, comprising the steps of

a) providing a first immobilized nucleic array acid comprising a first pool of nucleic acid molecules that have linked to both ends oligonucleotide sequences each comprising a restriction enzyme(s) recognition site, such that cleavage of the nucleic acid molecules of said pool with said enzyme(s) results in the release of pairs of oligonucleotide primers that comprise sequences unique to either end of each member of said pool,

b) amplifying by PCR the nucleic acid molecules of said array,

c) contacting said first immobilized nucleic acid array with a support such that at least a subset of nucleic acid molecules produced by said amplifying are transferred to said support,

d) immobilizing said nucleic acid molecules to said support to form a replica of said first immobilized nucleic acid array, wherein the positions of said nucleic acid molecules on said replica correspond to the positions of said nucleic acid molecules of said first array from which they were amplified,

e) cleaving said nucleic acid molecules of said replica with said restriction enzyme(s), thereby forming an array of immobilized oligonucleotide primers that comprise sequences unique to either end of each feature of said first nucleic acid array,

f) washing from said oligonucleotide primers the nucleic acid fragments released from them by said cleaving,

g) contacting said primers with a second pool of nucleic acid molecules under conditions that permit hybridization of the nucleic acid molecules that are complementary, such that hybridization occurs between said oligonucleotide primers and the nucleic acid molecules of said second nucleic acid pool,

h) amplifying the nucleic acid molecules of said second pool so hybridized to said primers, wherein said immobilized oligonucleotide primers to which they are hybridized serve to prime said amplifying, thereby forming an immobilized array of nucleic acid molecules of said second pool.

31. The method according to claim 30, wherein said amplifying is performed by PCR.

32. The method according to claim 30, wherein cycles of said steps c) through h) are repeated.

33. The method according to claim 30, further comprising the steps between steps d) and e) of

i) amplifying in situ the nucleic acid molecules of said replica, and

ii) contacting said replica with a second support, such that at least a subset of the nucleic acid molecules produced by said amplifying are transferred to said second support,

iii) immobilizing the termini of said nucleic acid molecules to said second support to form a second replica of said first immobilized nucleic acid array, wherein the positions of nucleic acid molecules on said second replica correspond to the positions of the nucleic acid molecules of said replica from which they were amplified..

34. The method according to claim 30, wherein said different nucleic acid pools are obtained from different tissues of an individual organism.

35. The method according to claim 30, wherein said different nucleic acid pools are obtained from different individual organisms of a single species.

36. The method according to claim 30, wherein said different nucleic acid pools are obtained from organisms of different species.

37. The method according to claim 30, wherein said first and second pools of nucleic acid molecules are libraries.