Compositions, methods, and kits for fabricating coded molecular tags

• US 20050069895A1
• Filed: 08/29/2003
• Published: 03/31/2005
• Est. Priority Date: 08/29/2003
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hyldig-Nielsen, Jens J., Woudenberg, Timothy M., Schroeder, Benjamin, Sharaf, Muhammad A., Bahatt, Dar, Liu, Timothy Z., Ermakov, Serguei, Vatta, Paolo, Connell, Charles R.
• Application Number:
  US10/651,561
• Publication Number:
  US 20050069895A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 33/532 Production of labelled immunochemicals
• CPC Class Codes: G01N 33/533 with fluorescent label

Abstract

The teachings herein generally relates to probes comprising fabricated coded molecular tags for detecting analytes. The teachings also relate to compositions, methods, and kits for fabricating coded molecular tags comprising a multiplicity or reporter groups in an ordered pattern.

Claims

1. A coded molecular tag comprising an ordered pattern of reporter group species.

2. The coded molecular tag of claim 1, further comprising at least one adapter.

3. The coded molecular tag of claim 1, further comprising at least one capture ligand.

4. The coded molecular tag of claim 1, comprising a multiplicity of fluorescent reporter group species, and further comprising at least one capture ligand, and at least one crosslinker.

5. The coded molecular tag of claim 4, wherein the at least one crosslinker is cleavable.

6. A coded molecular tag comprising, two complementary strands, wherein both of the complementary strands comprise at least one reporter group species.

7. A coded molecular tag comprising, two complementary strands, wherein one of the complementary strands comprises at least one reporter group species.

8. A method for fabricating at least one coded molecular tag comprising,

combining at least two coded molecular tag subunits, each comprising at least one reporter group species;

and

fabricating at least one coded molecular tag.

9. The method of claim 8, wherein the at least one coded molecular tag comprises at least one fluorescent reporter group species.

10. The method of claim 8, wherein at least one of the at least two coded molecular tag subunits comprises at least one reporter group species that is different from at least one reporter group species present in at least one other coded molecular tag subunit.

11. The method of claim 8, wherein at least one of the subunits is synthetic.

12. The method of claim 8, wherein at least one of the subunits is semi-synthetic.

13. The method of claim 8, wherein at least one on the subunits is enzymatically labeled with reporter groups.

14. The method of claim 8, wherein at least one subunit is chemically labeled with at least one reporter group species.

15. The method of claim 8, wherein the at least one of the reporter group species comprises at least one fluorescent reporter group.

16. The method of claim 8, wherein the at least one subunit comprises at least one intercalating reporter group species.

17. A method for fabricating at least one coded molecular tag comprising,

combining at least one oligonucleotide comprising at least one reporter group species with at least one template;

and

fabricating the at least one coded molecular tag.

18. The method of claim 17, wherein the combining comprises a multiplicity oligonucleotides, wherein at least one first oligonucleotide comprises at least one first reporter group species and at least one second oligonucleotide comprises at least one second reporter group species, wherein the first reporter group species and the second reporter group species are different.

19. The method of claim 18, further comprising ligating at least one coded molecular tag.

20. The method of claim 17, further comprising ligating at least one coded molecular tag.

21. The method of claim 17, wherein the at least one oligonucleotide is synthetic.

22. The method of claim 17, wherein the at least one oligonucleotide is chemically labeled.

23. The method of claim 17, wherein the at least one oligonucleotide is enzymatically labeled.

24. A method for fabricating at least one coded molecular tag comprising,

combining at least one template with at least one peptide nucleic acid (PNA) comprising at least one reporter group species, at least one pseudocomplementary PNA (pcPNA) comprising at least one reporter group species, or at least one PNA comprising at least one reporter group species and at least one pcPNA comprising at least one reporter group species;

and

fabricating at least one coded molecular tag.

25. The method of claim 24, wherein the at least one coded molecular tag comprises at least one PNA comprising at least one first reporter group species and at least one pcPNA comprising at least one second reporter group species, wherein the first reporter group species and the second reporter group species are the same of different.

26. A kit for fabricating at least one coded molecular tag comprising, at least one PNA comprising at least one first reporter group, at least one pcPNA comprising at least one second reporter group species, at least one antibody comprising at least one third reporter group, or combinations thereof;

wherein the first reporter group species, the second reporter group species, and the third reporter group species are the same;

or at least two of the first reporter group species, the second reporter group species, and the third reporter group species are different.

27. The kit of claim 26, further comprising at least one nucleic acid template.

28. The kit of claim 27, wherein the at least one nucleic acid template comprises at least one double-stranded sequence, at least one single-stranded sequence, or at least one double-stranded sequence and at least one single-stranded sequence.

29. A kit for fabricating at least one coded molecular tag comprising, at least one nucleic acid template and at least one oligonucleotide comprising at least one reporter group species.

30. The kit of claim 29, further comprising at least one polymerase, at least one ligation agent, or at least one polymerase and at least one ligation agent.