Universal tag assay

• US 20040086892A1
• Filed: 04/24/2003
• Published: 05/06/2004
• Est. Priority Date: 11/06/2002
• Status: Abandoned Application

• Current Assignee: Geneohm Sciences Incorporated (Becton, Dickinson & Co)
• Original Assignee: Geneohm Sciences Incorporated (Becton, Dickinson & Co)
• Inventors: Holmlin, R. Erik, Crothers, Donald M.
• Application Number:
  US10/424,542
• Publication Number:
  US 20040086892A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• 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 2521/301 Endonuclease
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2531/137 Ligase Chain Reaction [LCR]
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The present invention disclosure provides methods and compositions for a universal tag assay wherein a universal detector having detection probes is incubated with tagged molecules having identifier tags corresponding to targets, and hybridization of an identifier tag to a complementary detection probe indicates the presence of the corresponding target in the material being assayed. In particular, the invention disclosure provides methods and compositions for detecting target nucleotide sequences in a sample by target-dependent manipulations that generate tagged molecules having identifier tags corresponding to target nucleotide sequence, where incubation of tagged molecules with a universal detector having detection probes permits hybridization of identifier tags to complementary detection probes, thereby indicating the presence of the target nucleotide sequence corresponding to each identifier tag. Preferred embodiments include use of the universal tag assay for detecting variant sequences including single nucleotide polymorphisms (SNPs), allelic variants, and splice variants. Preferred embodiments further include the use of ruthenium amperometry to detect hybridization of tagged DNA or RNA molecules to detection probes immobilized on a universal detector, preferably a universal chip having gold or carbon electrodes.

Claims

1. A method for detecting a target nucleotide sequence in a sample, comprising:

a) generating at least one tagged molecule comprising at least one identifier tag selected as an identifier for said target nucleotide sequence, wherein said identifier tag is generated only when said target nucleotide sequence corresponding to said identifier tag is present in said sample;

b) incubating said at least one tagged molecule with a universal detector having at least one detection probe complementary to said identifier tag; and

c) measuring hybridization of any said identifier tag to any said detection probe complementary to said identifier tag;

wherein said hybridization of any said identifier tag to any said detection probe complementary to said identifier tag indicates said target nucleotide sequence corresponding to said identifier tag is present in said sample.

2. The method of claim 1, wherein said at least one tagged molecule further comprises a copy or complement of said target nucleotide sequence.

3. The method of claim 1, wherein said universal detector comprises detection probes coupled to a detection means for said measuring hybridization of any said identifier tag to any said detection probe complementary to said identifier tag.

4. The method of claim 3, wherein said detection means is electrochemical, fluorescent, calorimetric, radiometric or magnetic.

5. The method of claim 3, wherein said detection means is electrochemical.

6. The method of claim 3, wherein said detection probes coupled to a detection means are attached to a surface, film, or particle.

7. The method of claim 6, wherein said detection probes are attached to said surface, film, or particle by covalent bonds, ionic bonds, electrostatic interactions, or adsorption.

8. The method of claim 6, wherein said detection probes are attached to a particle such as a bead.

9. The method of claim 6, wherein said detection probes are attached to a plurality of particles.

10. The method of claim 3, wherein said universal detector comprises an array of detection probes coupled to detection means, said array comprising electrodes attached to a substrate.

11. The method of claim 10, wherein said electrodes are gold or carbon.

12. The method of claim 11, wherein said electrodes are gold.

13. The method of claim 10, further comprising measuring hybridization of any said identifier tag to any said detection probe complementary to said identifier tag by ruthenium amperometry.

14. The method of claim 10, wherein said electrodes are coated with protein which can be bound by oligonucleotides derivatized with a moiety that binds said protein that coats said electrode.

15. The method of claim 14, wherein said electrodes are coated with avidin such that said electrodes can be bound by biotin-labelled oligonucleotides.

16. A method for detecting a target nucleotide sequence in a sample, comprising:

a) obtaining template comprising said target nucleotide sequence or complement thereof;

b) amplifying said template to generate at least one tagged molecule comprising at least one identifier tag selected as an identifier for said target nucleotide sequence;

c) incubating said at least one tagged molecule with a universal detector comprising detection probes coupled to a detection means, said detection probes comprising at least one detection probe complementary to said identifier tag; and

d) detecting hybridization of any said identifier tag to any said detection probe complementary to said identifier tag;

wherein hybridization of any said identifier tag to any said complementary detection probe indicates the presence of the corresponding target nucleotide sequence in the sample being assayed.

17. The method of claim 16 for detecting a plurality of target nucleotide sequences in a sample, wherein each target nucleotide sequence in said plurality of target nucleotide sequences has a distinct identifier tag, such that hybridization of each said distinct identifier tag to a complementary detection probe indicates the presence of the corresponding target nucleotide sequence.

18. The method of claim 16, wherein said at least one tagged molecule comprises exogenous nucleotide sequence not found in said identifier tag or said target nucleotide sequence.

19. The method of claim 18, wherein said exogenous sequence is sequence involved in trimming tagged molecules and said method further comprises trimming said at least one tagged molecule to generate at least one smaller tagged molecule.

20. The method of claim 16, wherein said amplifying said template comprises rolling circle (RC) amplification comprising the steps of:

a) providing a rolling circle (RC) probe comprising sequence complementary to said template comprising target nucleotide sequence of complement thereof, and further comprising sequence complementary to said identifier tag selected as an identifier for said target nucleotide sequence;

b) incubating said RC probe with said template under conditions such that said RC probe will hybridize to complementary sequence on said template;

c) providing polymerase enzyme under conditions such that said polymerase replicates said RC probe, generating at least one amplification product comprising a tagged molecule having repeating copies of said identifier tag and said target nucleotide sequence or complement thereof;

d) incubating said amplification product with a universal detector comprising detection probes coupled to a detection means, said detection probes comprising at least one detection probe complementary to said identifier tag; and

e) detecting hybridization of any said identifier tag in said amplification product to any said detection probe complementary to said identifier tag;

wherein hybridization of any said identifier tag to any said complementary detection probe indicates the presence of the corresponding target nucleotide sequence in the sample being assayed.

21. The method of claim 20, wherein said RC probe provided in Step a) is a circular RC probe.

22. The method of claim 20, wherein said RC probe provided in Step a) is linear, such that Step b) further comprises incubating said RC probe with said template under conditions such that the 3′

end of said RC probe and the 5′

end of said RC probe will hybridize adjacently to contiguous complementary sequence on said template, and said 3′

end and said 5′

end are ligated to form a circular RC padlock probe.

23. The method of claim 20, wherein said template is DNA or RNA.

24. The method of claim 20, wherein said at least one amplification product further comprises exogenous sequence not found in said identifier tag or said template comprising target nucleotide sequence or complement thereof.

25. The method of claim 24, wherein said exogenous sequence is involved in primer binding to said amplification product, forming polymerase promoters on said amplification product, or trimming said amplification product.

26. The method of claim 25, wherein said exogenous sequence involved in trimming said amplification product comprises self-complementary sequences that form hairpin structures.

27. The method of claim 26, wherein said self-complementary sequences that form hairpin structures comprise at least one restriction enzyme recognition site for a restriction enzyme involved in said trimming.

28. The method of claim 25, wherein said at least one exogenous nucleotide sequence comprises sequences that form at least one restriction enzyme recognition site for a restriction enzyme involved in said trimming upon addition of at least one auxiliary oligonucleotide.

29. The method of claim 16, wherein said amplifying said template comprises ligation-mediated amplification comprising:

a) providing at least one pair of ligation pimers comprising a first ligation primer having a 3′

portion of sequence complementary to a portion of said template comprising said target nucleotide sequence or complement thereof, and a second ligation primer having a 5′

portion of sequence complementary to a contiguous portion of said template comprising target nucleotide sequence or complement thereof, wherein at least one ligation primer further comprises an identifier tag selected as an identifier for said target nucleotide sequence;

b) incubating said at least one pair of ligation primers with said template under conditions such that said first and second ligation primers will hybridize to said template, said 3′

end of said first ligation primer hybridizing adjacently to said 5′

end of said second ligation primer;

c) ligating said 3′

end of said first ligation primer to said 5′

end of said second ligation primer, thereby generating a ligation product comprising a tagged molecule, wherein said tagged molecule comprises a copy or complement of said target nucleotide sequence and further comprises at least one identifier tag corresponding to said target nucleotide sequence;

d) contacting said ligation product with a universal detector comprising detection probes coupled to a detection means, said detection probes comprising at least one detection probe complementary to said identifier tag; and

e) detecting hybridization of any said identifier tag in said ligation product to any said detection probe complementary to said identifier tag;

wherein hybridization of any said identifier tag to any said complementary detection probe indicates the presence of the corresponding target nucleotide sequence in the sample being assayed.

30. The method of claim 29, wherein said template comprises target nucleotide sequence, such that said first ligation primer comprises sequence complementary to a portion of said target nucleotide sequence and said second ligation primer comprises sequence complementary a contiguous portion of said target nucleotide sequence, with the result that said first ligation primer and said second ligation primer hybridize to contiguous portions of template and are ligated, generating a ligation product comprising an identifier tag and sequence complementary to said target nucleotide sequence.

31. The method of claim 29, wherein said template comprises complement of target nucleotide sequence, such that said first ligation primer comprises a portion of said target nucleotide sequence and said second ligation primer comprises a contiguous portion of said target nucleotide sequence, with the result that said first ligation primer and said second ligation primer hybridize to contiguous portions of template and are ligated, generating a ligation product comprising an identifier tag and said target nucleotide sequence.

32. The method of claim 29, wherein said ligating said 3′

end of said first ligation primer to said 5′

end of said second ligation primer is carried out by enzymatic means.

33. The method of claim 32, wherein said enzymatic means is ligase.

34. The method of claim 29, wherein said ligating said 3′

end of said first ligation primer to said 5′

end of said second ligation primer is carried out by non-enzymatic means.

35. The method of claim 29, wherein said incubating and ligating steps are repeated using temperature cycling for amplification of said target nucleotide sequence.

36. The method of claim 29 for detecting a plurality of target nucleotide sequences, comprising providing a plurality of pairs of ligation primers wherein at least one said pair of ligation primers of said plurality of pairs is complementary to each target nucleotide sequence of said plurality of target nucleotide sequences, and further wherein at least one ligation primer of each said pair comprises an identifier tag selected to serve as an identifier for said target nucleotide sequence.

37. The method of claim 29, wherein said method comprises detecting at least one variant sequence of said target nucleotide sequence.

38. The method of claim 37, wherein said at least one variant sequence is a single nucleotide polymorphism (SNP), an allelic variant, or a splice variant.

39. The method of claim 38, wherein said at least one variant sequence is a SNP.

40. A method for detecting a target nucleotide sequence in a sample, comprising:

a) obtaining template comprising said target nucleotide sequence or complement thereof;

b) providing at least one pair of ligation primers comprising a first ligation primer having a 3′

portion of sequence complementary to a portion of said template and a second ligation primer having a 5′

portion of sequence complementary to a contiguous portion of said template, wherein each ligation primer of said pair of ligation primers further comprises exogenous sequence not complementary to said template;

c) incubating said at least one pair of ligation primers with said template under conditions such that said first and second ligation primers will hybridize to said template, said 3′

end of said first ligation primer hybridizing adjacently to said 5′

end of said second ligation primer;

d) ligating said 3′

end of said first ligation primer to said 5′

end of said second ligation primer, thereby generating a ligation product comprising a copy or complement of said target nucleotide sequence and further comprising exogenous 3′ and

5′

sequence not complementary to said template;

e) providing a rolling circle (RC) probe comprising sequence complementary to said ligation product and further comprising sequence complementary to an identifier tag selected to serve as an identifier for said target nucleotide sequence, wherein said sequence complementary to said ligation product comprises sequence complementary to said target nucleotide sequence or complement thereof, flanked by sequence complementary to said exogenous sequence of said ligation product;

f) incubating said RC probe with said ligation product under conditions such that said RC probe will hybridize to said ligation product;

g) providing polymerase enzyme under conditions such that said polymerase replicates said RC probe, generating at least one amplification product comprising a tagged molecule, wherein said tagged molecule comprises repeating copies of said identifier tag and repeating copies of said target nucleotide sequence or complement thereof;

h) incubating each said amplification product with a universal detector comprising detection probes coupled to a detection means, said detection probes comprising at least one detection probe complementary to said identifier tag; and

i) detecting hybridization of any said identifier tag in said amplification product to any said detection probe complementary to said identifier tag;

wherein hybridization of any said identifier tag to any said complementary detection probe indicates the presence of the corresponding target nucleotide sequence in the sample being assayed.

41. The method of claim 40, wherein said RC probe provided in Step e) is a circular RC probe.

42. The method of claim 40, wherein said RC probe provided in Step e) is linear, such that Step f) further comprises incubating said RC probe with said ligation product comprising said target nucleotide sequence or complement thereof, under conditions such that the 3′

end of said RC probe and the 5′

end of said RC probe will hybridize to adjacently to contiguous complementary sequence on said template, such that said 3′

end and said 5′

end of said linear RC probe are ligated to form a circular RC padlock probe.

43. The method of claim 40, wherein said at least one amplification product further comprises exogenous sequence not found in said ligation product.

44. The method of claim 43, wherein said exogenous sequence is involved in primer binding to said amplification product, forming polymerase promoters on said amplification product, or trimming said amplification product.

45. The method of claim 44, wherein said exogenous sequence involved in trimming said amplification products comprises self-complementary sequences that form hairpin structures.

46. The method of claim 45, wherein said self-complementary sequences that form hairpin structures comprise at least one restriction enzyme recognition site for a restriction enzyme involved in said trimming step.

47. The method of claim 44, wherein said at least one exogenous nucleotide sequence comprises sequences that form at least one restriction enzyme recognition site for a restriction enzyme involved in said trimming step upon addition of at least one auxiliary oligonucleotide.

48. A universal tag assay comprising:

a) a set of minimally cross-hybridizing tags and probes selected such that at least one tag will serve as an identifier tag for a target in a sample being assayed and each said identifier tag has at least one complementary detection probe in said set;

b) at least one tagged molecule comprising at least one said identifier tag, wherein said identifier tag is generated only when said target corresponding to said identifier tag is present in said sample being assayed; and

c) a universal detector comprising at least one said detection probe coupled to a detection means such that hybridization of said any identifier tag to any said complementary detection probe can be measured;

wherein measuring hybridization of any said identifier tag to any said complementary detection probe indicates that said target corresponding to said identifier tag is present in said sample being assayed.

49. The universal tag assay of claim 48, wherein said at least one tagged molecule comprises the identifier tag for a target and further comprises a copy or complement of said target.

50. The universal tag assay of claim 48, wherein said at least one tagged molecule comprises the identifier tag molecule for a target and does not contain a copy or complement of said target.

51. A set of complementary tags and probes suitable for use with the universal tag assay of claim 48, wherein said set comprises minimally cross-hybridizing oligonucleotides wherein all duplexes formed by said complementary tags and probes have approximately the same melting temperature and stacking energy.