ID-tag complexes, arrays, and methods of use thereof

• US 20060292586A1
• Filed: 11/30/2005
• Published: 12/28/2006
• Est. Priority Date: 12/17/2004
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Schroth, Gary P., Straus, Neil A., Lao, Kai Qin
• Application Number:
  US11/291,444
• Publication Number:
  US 20060292586A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6823 Release of bound markers
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2537/125 Sandwich assay format
• CPC Class Codes: C12Q 2537/1373 Displacement by a nucleic acid
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide

Abstract

The present invention relates to the detection of target sequences. Detection can be achieved through the use of ID-tag complexes. These ID-tag complexes are relatively stable in the absence of a target sequence. In the presence of a target sequence, the complexes dissociate and form new complexes or duplexes, which can be purified or eliminated and detected on an ID-tag system.

Claims

1. An ID-tag complex comprising:

a probe section comprising a probe sequence, an ID-tag sequence, and a detectable marker, wherein the probe sequence is connected to the ID-tag sequence and the detectable marker; and

a probe complement section comprising a probe complement sequence connected to a first coupling molecule, wherein at least a portion of said probe sequence and said probe complement sequence are configured to hybridize to one another, and wherein the length of the probe sequence is at least 1 nucleotide greater than the length of the probe complement sequence.

2. The ID-tag complex of claim 1, wherein the detectable marker is connected to an end of the probe sequence and the ID-tag sequence is connected an opposite end of the probe sequence

3. The ID-tag complex of claim 1, wherein the probe section comprises an analog probe sequence.

4. The ID-tag complex of claim 3, wherein the analog probe sequence comprises L-DNA.

5. The ID-tag complex of claim 3, wherein the analog probe sequence comprises PNA.

6. The ID-tag complex of claim 1, wherein the probe sequence can bind to RNA.

7. The ID-tag complex of claim 6, wherein the probe sequence can bind to a RNA target sequence.

8. The ID-tag complex of claim 1, wherein the probe sequence can bind to miRNA.

9. The ID-tag complex of claim 8, wherein the probe sequence is complementary to a miRNA target sequence.

10. The ID-tag complex of claim 1, wherein the probe sequence is 5-10 bases longer than the probe complement sequence.

11. The ID-tag complex of claim 1, wherein the extra length of the probe sequence compared to the probe complement sequence is as an overhang on one end of the probe sequence.

12. The ID-tag complex of claim 11, wherein the probe sequence has an overhang of 6 or 7 bases over the probe complement sequence.

13. The ID-tag complex of claim 1, wherein the probe sequence comprises 2′

O-methyl RNA.

14. The ID-tag complex of claim 1, wherein the first coupling molecule comprises biotin.

15. The ID-tag complex of claim 1, wherein the detectable marker comprises DIG.

16. The ID-tag complex of claim 1, wherein the ID-tag sequence comprises an analog nucleotide.

17. The ID-tag complex of claim 16, wherein the ID-tag sequence comprises L-DNA.

18. The ID-tag complex of claim 1, further comprising a linker between the probe sequence and the ID-tag sequence.

19. An ID-tag detection complex comprising:

a probe section, said probe section comprising a first ID-tag sequence connected to a probe sequence, wherein said probe sequence is also connected to a detectable marker;

a target section comprising a target sequence, wherein said target sequence is hybridized to the probe sequence; and

an ID-tag detection section comprising a second ID-tag sequence that is hybridized to said first ID-tag sequence

20. The ID-tag detection complex of claim 19, wherein said ID-tag detection section is located at a first location in an array system.

21. A method of detecting a target segment in a sample, said method comprising:

contacting an ID-tag complex with a sample such that the probe sequence hybridizes to a target sequence in the sample, wherein said ID-tag complex comprises

     1) a probe section comprising a probe sequence, an ID-tag sequence, and a detectable marker, wherein the probe sequence is connected to the ID-tag sequence and is further connected to the detectable marker, and the ID-tag complex further comprises

     2) a probe complement section comprising a probe complement sequence connected to a first coupling molecule, wherein at least a portion of said probe sequence and said probe complement sequence are configured to hybridize to one another, and wherein the length of the probe sequence is at least 1 nucleotide greater than the length of the probe complement sequence;

contacting a second coupling molecule to the sample so that the second coupling molecule can bind to substantially all of the first coupling molecule;

removing substantially all of the second coupling molecule; and

detecting the detectable marker in the sample, thereby detecting a target segment in the sample.

22. The method of claim 21, further comprising the steps of:

adding the sample to an array, said array comprising an ID-tag detection sequence that is complementary to the ID-tag sequence of the ID-tag complex at a first position; and

detecting the presence of the detectable marker at the first position, thereby detecting the presence the target segment in the sample.

23. The method of claim 22, wherein the target is RNA.

24. The method of claim 23, wherein the target is miRNA.

25. The method of claim 22, wherein the first coupling molecule is biotin.

26. The method of claim 22, wherein the second coupling molecule is streptavidin.

27. The method of claim 22, wherein the array comprises more than one ID-tag detection sequence.

28. The method of claim 27, wherein the array comprises an ID-tag detection sequence that is specific for the same ID-tag sequence.

29. The method of claim 27, wherein the array comprises ID-tag detection sequences that are specific for different ID-tag target sequences.

30. The method of claim 22, wherein 1) the array comprises at least two different ID-tag detection sequences and 2) there are at least parts of two different ID-tag probe complexes that are added to a sample, wherein at least one of the ID-tag probe complexes has a probe sequence that is different from probe sequence in a different ID-tag probe complex.

31. The method of claim 22, wherein at least three different ID-tag sequences comprising three different ID-tag probes are used.

32. An ID-tag complex kit comprising:

an ID-tag complex comprising

     1) a probe section comprising a detectable marker, an ID-tag sequence, and a probe sequence; and

     2) a probe complement section comprising a first coupling molecule attached to a probe complement sequence, wherein at least a portion of said probe complement sequence and said probe sequence are capable of hybridizing.

33. The kit of claim 32, further comprising a second coupling molecule;

34. The kit of claim 33, further comprising an array, said array comprising an ID-tag detection sequence, wherein said ID-tag detection sequence can hybridize to said first ID-tag sequence.

35. The kit of claim 32, further comprising an RNase inhibitor.

36. The kit of claim 32, further comprising a means for isolating miRNA.