Adapter directed expression analysis

• US 6,232,067 B1
• Filed: 08/17/1998
• Issued: 05/15/2001
• Est. Priority Date: 08/17/1998
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Perkinelmer Incorporated
• Inventors: Richards, John H., Hunkapiller, Michael W.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): Taylor, Janell E.
• Application Number:
  US09/135,381
• Time in Patent Office: 1,002 Days
• Field of Search: 435/6, 435/5, 435/7, 435/91, 435/91.1, 435/91.2, 436/501, 536/26, 536/27, 536/28, 935/77, 935/78
• US Class Current: 506/4
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• 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 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides

Abstract

The present invention relate to methods and compositions for simultaneously analyzing multiple different polynucleotides of a polynucleotide composition comprising multiple diverse polynucleotide sequences. The subject methods and compositions may also be applied to analyze or identify single polynucleotides; however, the subject methods and compositions are particularly useful for analyzing large diverse populations of polynucleotides, e.g., cDNA libraries. Most embodiments of the invention involve hybridizing terminus probes (of known base sequence) and internal fragment probes (of known base sequence) at adjacent positions on an adapter-modified restriction fragment generated from polynucleotide for analysis, and subsequently joining the terminus probes and internal fragment probes to each other. The terminus probe hybridizes to bases of restriction endonuclease recognition site present at the terminus of a restriction fragment generated from the polynucleotide for analysis. Internal fragment probes hybridizes to the same strand of the restriction fragment that the terminus probe hybridizes to and hybridizes to the restriction fragment portion of adapter-modified representative restriction fragments. The terminus probes and internal fragment probes may be marked so as to facilitate the simultaneous testing of multiple polynucleotides for the presence of many possible nucleotide base sequences. The identity or expression of a particular polynucleotide of interest may be ascertained (or at least partially determined) by producing a short identifier sequence derived from the nucleotide base sequence information obtained from (1) the hybridization of a terminus probe and an internal fragment probe, each of known base sequence, at adjacent positions on a polynucleotide of interest, and (2) the recognition site of a restriction endonuclease used to generate the polynucleotide molecule of interest. Multiple identification sequences may be obtained in parallel, thereby permitting the rapid characterization of a large number of diverse polynucleotides. Parallel processing may be achieved by differentially marking terminus probes or internal fragment probes. Parallel processing may be achieved by using ordered arrays of oligonucleotides that are terminus probes.

Claims

1. A method of analyzing a polynucleotide, said method comprising:

forming a representative restriction fragment corresponding to the polynucleotide, wherein the representative restriction fragment has a first and second terminus and at least one of the termini is generated by a restriction endonuclease, hybridizing a terminus probe to a single strand of the restriction fragment at a position on the restriction fragment including the terminus generated by the restriction endonuclease, hybridizing an internal fragment probe to the single strand of restriction fragment at a position adjacent to the terminus probe, and joining the terminus probe to the internal fragment probe.

2. The method according to claim 1, said method further comprising the step of,

combining (i) the nucleotide sequence information from the terminus probe with (ii) the nucleotide sequence information from the internal fragment probe and (iii) the nucleotide sequence of the recognition site of the restriction endonuclease used to produce the terminus, so as to produce an identifier sequence.

3. The method according to claim 1 wherein the polynucleotide is a cDNA.

4. The method according to claim 2 further comprising the step of comparing the identifier sequence with a DNA sequence database.

5. The method of claim 2 further comprising the steps of preparing a oligonucleotide hybridization probe comprising a base sequence encoding the identifier sequence.

6. A method according to claim 1, wherein the terminus probe is a feature of an oligonucleotide array.

7. A method according to claim 1 further comprising:

of joining first and second adapters to the first and second termini of the representative restriction fragment, respectively, whereby an adapter-modified representative restriction fragment is formed, wherein the joining of the adapters to the termini occurs before the hybridizing of the terminus probe and the internal probe.

8. A method according to claim 7, further comprising the step of amplifying the adapter-modified representative restriction fragment, whereby amplification products of the adapter-modified representative restriction fragments are formed.

9. A method according to claim 8, wherein the step of hybridizing the terminus probe comprises

contacting the amplification products with an oligonucleotide array under nucleic acid hybridization conditions, wherein the array comprises features that are terminus probes, said terminus probes having constant and variable regions, whereby a strand of the amplification product is hybridized to a terminus probe.

10. A method according to claim 9, wherein the step of hybridizing the internal fragment probe comprises,

contacting the amplification product strand hybridized to a terminus probe with a solution comprising an internal fragment probe, wherein the contact occurs under nucleic acid hybridization conditions.

11. The method according to claim 10, wherein the solution comprises a plurality of internal fragment probes.

12. The method of claim 11, wherein each of the internal fragment probes is labeled with a different fluorescent label.

13. A method according to claim 12, further comprising the step of of contacting the hybridized amplification products with a second solution comprising at least one internal fragment probe that has a different nucleotide sequence than an internal fragment probe in the first solution.

14. A method according to claim 13, wherein the second solution comprises a plurality of different terminus probes, wherein each terminus probe in the second solution is labeled with a distinctive label.

15. A method according to claim 11, wherein the array comprises at least one subarray of 1024 distinct features, the variable region of each feature is five nucleotides in length, and each of the variable regions of the subarray has a different nucleotide sequence from the other variable regions of the terminus probes in the same subarray.

16. A method according to claim 12, wherein the constant region of the feature are at least 4 nucleotides in length.

17. A method according to claim 12, wherein the constant regions of the features are identical to each other.

18. A method according to claim 12, wherein the array comprises a plurality of subarrays wherein at least two of the subarrays comprise the same set of features.

19. A method according to claim 18, wherein the oligonucleotide probe solution comprises a plurality of internal probes and each different probe is labeled with a distinct identification label.

20. A method according to claim 19, wherein the oligonucleotide probes are labeled with different fluorescent labels.

21. A method according to claim 19, further comprising the step of of contacting the hybridized amplification products with a second solution comprising at least one internal fragment probe that has a different nucleotide sequence than an internal fragment probe in the first solution.

22. A method according to claim 21, wherein the second solution comprises a plurality of different terminus probes, wherein each terminus probe in the second solution is labeled with a distinctive label.

23. A method according to claim 7, wherein the internal fragment probe or the terminus probe comprises an array sorting signal.

24. A method according to claim 23, comprising the step of contacting the adapter-modified representative restriction fragment with an array comprising a plurality sorting signal receptors at a predetermined locations on the array.

25. A method according to claim 1, wherein the representative restriction fragment is generated by a method comprising the steps,

immobilizing the polynucleotide on a solid support,

contacting the polynucleotide with a first restriction endonuclease, whereby an immobilized restriction fragment is produced, and

purifying the immobilized restriction fragment.

26. The method of claim 25, further comprising the steps of

contacting the immobilized restriction fragment with a second restriction endonuclease, whereby the representative restriction fragment is produced, and

purifying the representative restriction fragment.

27. The method according to claim 2, further comprising:

joining a linker to the terminus produced by the first restriction enzyme on the immobilized restriction fragment, whereby an adapter-modified immobilized restriction fragment was produced, and contacting the adapter-modified immobilized restriction fragment with a second restriction endonuclease, whereby the representative restriction fragment is produced.

28. The method of claim 27, wherein the adapter comprises a type IIS restriction site and the second restriction endonuclease is a type IIS restriction endonuclease recognizes the type IIS restriction site in the adapter and cleaves within the immobilized restriction fragment.

35. A method according to claim 23, wherein the array sorting signal and the sorting signal receptors are polynucleotides.

29. A polynucleotide population analysis kit, said kit comprising,

an oligonucleotide array comprising a plurality of terminus probes, and a a plurality of internal probes.

30. The kit according to claim 29, wherein the internal probes are in a first solution.

31. The kit according to claim 29, said kit further comprising a second solution, wherein the second solution comprises a plurality of internal probes, each of the internal probes in the second solution is labeled with a distinctive label, and at least one of the internal probes in the second solution has a different nucleotide base sequence than the internal probes in the first solution.

32. The kit according to claim 29, wherein the array comprises a plurality of subarrays.

33. A polynucleotide population analysis kit, said kit comprising:

a sorting array comprising,

a plurality of sorting signal receptors,

a plurality of terminus probes marked with a sorting signal, wherein the sorting signals are specific for the sorting signal receptors on the sorting array, and a

a plurality of internal fragment probes label with a detectable labeled, wherein at least two of the internal fragment probes are labeled with different detectable labels.

34. A polynucleotide population analysis kit, said kit comprising:

a sorting array comprising a plurality of sorting signal receptors,

a plurality of internal fragment probes marked with a sorting signal, wherein the sorting signal are specific for the sorting signal receptors on the sorting array, and a a plurality of terminus probes labeled with a detectable label, wherein at least two of the internal fragment probes are labeled with different detectable labels.