Unimolecular segment amplification and sequencing

• US 6,329,150 B1
• Filed: 06/23/2000
• Issued: 12/11/2001
• Est. Priority Date: 11/21/1995
• Status: Expired due to Term

• Current Assignee: Yale University
• Original Assignee: Yale University
• Inventors: Caplan, Michael, Lizardi, Paul M.
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US09/602,428
• Time in Patent Office: 536 Days
• Field of Search: 435/6, 435/91.2, 536/23.1, 536/24.3, 935/76, 935/77, 935/78
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2531/143 Promoter based amplification, e.g. NASBA, 3SR, TAS
• CPC Class Codes: C12Q 2537/125 Sandwich assay format
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2539/113 Differential Display Analysis [DDA]
• 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 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels

Abstract

Disclosed are compositions and a method for amplification of and multiplex detection of molecules of interest involving rolling circle replication. The method is useful for simultaneously detecting multiple specific nucleic acids in a sample with high specificity and sensitivity. The method also has an inherently low level of background signal. A preferred form of the method consists of an association operation, an amplification operation, and a detection operation. The association operation involves association of one or more specially designed probe molecules, either wholly or partly nucleic acid, to target molecules of interest. This operation associates the probe molecules to a target molecules present in a sample. The amplification operation is rolling circle replication of circular nucleic acid molecules, termed amplification target circles, that are either a part of, or hybridized to, the probe molecules. A single round of amplification using rolling circle replication results in a large amplification of the amplification target circles. Following rolling circle replication, the amplified sequences are detected using combinatorial multicolor coding probes that allow separate, simultaneous, and quantitative detection of multiple different amplified target circles representing multiple different target molecules. Since the amplified product is directly proportional to the amount of target sequence present in a sample, quantitative measurements reliably represent the amount of a target sequence in a sample. Major advantages of this method are that a large number of distinct target molecules can be detected simultaneously, and that differences in the amounts of the various target molecules in a sample can be accurately quantified. It is also advantageous that the DNA replication step is isothermal, and that signals are strictly quantitative because the amplification reaction is linear and is catalyzed by a highly processive enzyme.

Claims

1. A method of amplifying nucleic acid sequences, the method comprising,

(a) mixing one or more rolling circle replication primers with one or more amplification target circles, to produce a primer-ATC mixture, and incubating the primer-ATC mixture under conditions that promote hybridization between the amplification target circles and the rolling circle replication primers in the primer-ATC mixture,

wherein the amplification target circles each comprise a single-stranded, circular DNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to at least one of the rolling circle replication primers, and

(b) mixing DNA polymerase with the primer-ATC mixture, to produce a polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote replication of the amplification target circles,

wherein replication of the amplification target circles results in the formation of tandem sequence DNA;

wherein the method further comprises at least one of the following;

(1) an amplification operation, (2) the use of at least one rolling circle replication primer coupled to a specific binding molecule, (3) the use of at least one amplification target circle tethered to a specific binding molecule, (4) a nucleic acid collapse operation, (5) a combinatorial multicolor coding detection operation, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing,

wherein the amplification operation (i) is performed simultaneous with, or following step (b), (ii) is selected from the group consisting of nested ligation mediated rolling circle amplification, secondary DNA strand displacement, and transcription, and (iii) results in the formation of secondary tandem sequence DNA or tandem sequence RNA.

2. The method of claim 1 wherein

at least one of the rolling circle replication primers is coupled to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule, or

at least one of the amplification target circles is tethered to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule.

3. The method of claim 2 wherein the method includes at least one of the following:

(1) the amplification operation, (2) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (3) a step of bringing the specific binding molecule into contact with the target molecule, (4) the nucleic acid collapse operation, (5) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing.

4. The method of claim 2 wherein the target molecule is a primary amplification target circle, wherein the primary amplification target circle is formed by

(i) mixing an open circle probe with a primary target sample, to produce an OCP-target sample mixture, and incubating the OCP-target sample mixture under conditions that promote hybridization between the open circle probe and a primary target sequence in the OCP-target sample mixture,

wherein the primary target sequence comprises a 5′

region and a 3′

region, and

wherein the open circle probe comprises a single-stranded, linear DNA molecule comprising, from 5′

end to 3′

end, a 5′

phosphate group, a right target probe portion, a spacer portion, a left target probe portion, and a 3′

hydroxyl group, wherein the left target probe portion is complementary to the 3′

region of the primary target sequence and the right target probe portion is complementary to the 5′

region of the primary target sequence,

(ii) mixing ligase with the OCP-target sample mixture, to produce a ligation mixture, and incubating the ligation mixture under conditions that promote ligation of the open circle probe resulting in the formation of the primary amplification target circle.

5. The method of claim 1 wherein the method includes the amplification operation and wherein the amplification operation comprises, simultaneous with, or following, step (b),

(c) mixing RNA polymerase with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote transcription of the tandem sequence DNA, wherein transcription of the tandem sequence DNA results in the formation of tandem sequence RNA, or

(c) mixing a secondary DNA strand displacement primer with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote (i) hybridization between the tandem sequence DNA and the secondary DNA strand displacement primer, and (ii) replication of the tandem sequence DNA in the polymerase-ATC mixture, wherein replication of the tandem sequence DNA results in the formation of secondary tandem sequence DNA.

6. The method of claim 5 wherein the amplification operation comprises,

(c) mixing a secondary DNA strand displacement primer with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote (i) hybridization between the tandem sequence DNA and the secondary DNA strand displacement primer, and (ii) replication of the tandem sequence DNA in the polymerase-ATC mixture, wherein replication of the tandem sequence DNA results in the formation of secondary tandem sequence DNA, and

(d) mixing RNA polymerase with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote transcription of the secondary tandem sequence DNA, wherein transcription of the secondary tandem sequence DNA results in the formation of tandem sequence RNA.

7. The method of claim 6 wherein the method includes at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

8. The method of claim 1 wherein the method includes at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

9. The method of claim 8 wherein the method includes, following the formation of tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, primer extension sequencing, wherein primer extension sequencing comprises

(i) forming an interrogation mixture, wherein one or more interrogation primers are hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA,

(ii) simultaneous with, or following, step (i), mixing at least two different tagged chain terminating nucleotides and DNA polymerase with the interrogation mixture, wherein each different tagged chain terminating nucleotide comprises a different chain terminating nucleotide triphosphate coupled to a different tag molecule,

(iii) incubating the interrogation mixture under conditions that promote template-based addition of the tagged chain terminating nucleotides to the interrogation primers, wherein addition of the tagged chain terminating nucleotides to the interrogation primers results in association of the tagged chain terminating nucleotides with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and

(iv) detecting the association of the tagged chain terminating nucleotides with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA.

10. The method of claim 9 wherein formation of the interrogation mixture comprises

(i)(a) mixing an interrogation probe and a plurality of degenerate probes with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, to produce a probe mixture, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the interrogation probe and degenerate probes, wherein each degenerate probe has a 3′

blocking group,

(i)(b) mixing ligase with the probe mixture, to produce a degenerate ligation mixture, and incubating the degenerate ligation mixture under conditions that promote ligation of the interrogation probe to one of the degenerate probes hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, wherein the degenerate probe that is ligated to the interrogation probe is a ligated degenerate probe,

(i)(c) removing the 3′

blocking group of the ligated degenerate probe,

wherein ligation of the interrogation probe to one or more degenerate probes results in the formation of the interrogation primer, wherein the formation of the interrogation primer results in formation of the interrogation mixture.

11. The method of claim 10 wherein formation of the interrogation mixture further comprises, following step (i)(c),

(i)(d) mixing the plurality of degenerate probes with the ligation mixture, to produce a secondary probe mixture, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the degenerate probes,

(i)(e) mixing ligase with the secondary probe mixture, to produce a secondary degenerate ligation mixture, and incubating the secondary degenerate ligation mixture under conditions that promote ligation of the ligated degenerate probe to one of the degenerate probes hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, wherein the degenerate probe that is ligated to the ligated degenerate probe is a secondary ligated degenerate probe,

(i)(f) removing the 3′

blocking group of the secondary degenerate probe,

wherein steps (i)(d), (i)(e), and (i)(f) are performed, in order, one or more times.

12. The method of claim 9 wherein formation of the interrogation mixture comprises mixing an interrogation primer with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the interrogation primer.

13. The method of claim 8 wherein the method includes the combinatorial multicolor coding detection operation, and wherein the combinatorial multicolor coding detection operation comprises separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA by

mixing a set of detection probes with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, under conditions that promote hybridization between (i) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (ii) the detection probes, wherein the set of detection probes is labeled using combinatorial multicolor coding.

14. A method of amplifying nucleic acid sequences, the method comprising,

(a) mixing one or more different open circle probes with a target sample comprising one or more target sequences, to produce an OCP-target sample mixture, and incubating the OCP-target sample mixture under conditions that promote hybridization between the open circle probes and the target sequences in the OCP-target sample mixture,

(b) mixing ligase with the OCP-target sample mixture, to produce a ligation mixture, and incubating the ligation mixture under conditions that promote ligation of the open circle probes to form amplification target circles,

(c) mixing a rolling circle replication primer with the ligation mixture, to produce a primer-ATC mixture, and incubating the primer-ATC mixture under conditions that promote hybridization between the amplification target circles and the rolling circle replication primer in the primer-ATC mixture, and

(d) mixing DNA polymerase with the primer-ATC mixture, to produce a polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote replication of the amplification target circles,

wherein replication of the amplification target circle results in the formation of tandem sequence DNA;

wherein the method further comprises at least one of the following;

(1) an amplification operation, (2) the use of at least one rolling circle replication primer that is coupled to a specific binding molecule, (3) the use of a reporter binding agent as at least one of the target sequences, (4) a nucleic acid collapse operation, (5) a combinatorial multicolor coding detection operation, (6) differential amplification, and (7) primer-extension sequencing, (8) the use of one or more gap oligonucleotides, (9) the use of a primary amplification target circle as at least one of the target sequences,

wherein the amplification operation (i) is performed simultaneous with, or following step (d), (ii) is selected from the group consisting of nested ligation mediated rolling circle amplification, secondary DNA strand displacement, and transcription, and (iii) results in the formation of secondary tandem sequence DNA or tandem sequence RNA, and

wherein the primary amplification target circle is formed by

(i) mixing a primary open circle probe with a primary target sample, to produce a primary OCP-target sample mixture, and incubating the primary OCP-target sample mixture under conditions that promote hybridization between the primary open circle probe and a primary target sequence in the primary OCP-target sample mixture,

wherein the primary target sequence comprises a 5′

region and a 3′

region, and

wherein the primary open circle probe comprises a single-stranded, linear DNA molecule comprising, from 5′

end to 3′

end, a 5′

phosphate group, a right target probe portion, a spacer portion, a left target probe portion, and a 3′

hydroxyl group, wherein the left target probe portion is complementary to the 3′

region of the primary target sequence and the right target probe portion is complementary to the 5′

region of the primary target sequence,

(ii) mixing ligase with the primary OCP-target sample mixture, to produce a primary ligation mixture, and incubating the primary ligation mixture under conditions that promote ligation of the primary open circle probe resulting in the formation of the primary amplification target circle.

15. The method of claim 14 wherein the target sequences each comprise a 5′

region and a 3′

region,

wherein the open circle probes each comprise a single-stranded, linear DNA molecule comprising, from 5′

end to 3′

end, a 5′

phosphate group, a right target probe portion, a spacer portion, a left target probe portion, and a 3′

hydroxyl group, wherein the spacer portion comprises a primer complement portion, and wherein the left target probe portion and the right target probe portion of the same open circle probe are each complementary to the 3′

region and the 5′

region, respectively, of the same target sequence,

wherein at least one of the target sequences further comprises a central region located between the 5′

region and the 3′

region,

wherein neither the left target probe portion of the open circle probe nor the right target probe portion of any of the open circle probes is complementary to the central region of the target sequences, and

wherein step (a) further comprises, prior to incubating, mixing one or more gap oligonucleotides with the target sample, such that the OCP-target sample mixture comprises the one or more open circle probes, the one or more gap oligonucleotides, and the target sample, wherein each gap oligonucleotide comprises a single-stranded, linear DNA molecule comprising a 5′

phosphate group and a 3′

hydroxyl group, wherein each gap oligonucleotide is complementary all or a portion of the central region of at least one of the target sequences.

16. The method of claim 15 wherein the method includes the amplification operation and wherein the amplification operation comprises, simultaneous with, or following, step (d),

(e) mixing RNA polymerase with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote transcription of the tandem sequence DNA, wherein transcription of the tandem sequence DNA results in the formation of tandem sequence RNA, or

(e) mixing a secondary DNA strand displacement primer with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote (i) hybridization between the tandem sequence DNA and the secondary DNA strand displacement primer, and (ii) replication of the tandem sequence DNA in the polymerase-ATC mixture, wherein replication of the tandem sequence DNA results in the formation of secondary tandem sequence DNA.

17. The method of claim 16 wherein the method includes at least one of the following:

(1) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (2) the nucleic acid collapse operation, (3) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (4) differential amplification of at least two of the amplification target circles, and (5) primer-extension sequencing.

18. The method of claim 15 wherein at least one of the target sequences is coupled to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule.

19. The method of claim 18 wherein the method includes at least one of the following:

(1) the amplification operation, (2) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (3) a step of bringing the specific binding molecule into contact with the target molecule, (4) the nucleic acid collapse operation, (5) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing.

20. The method of claim 15 wherein at least one of the rolling circle replication primers is coupled to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule.

21. The method of claim 20 wherein the method includes at least one of the following:

(1) the amplification operation, (2) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (3) a step of bringing the specific binding molecule into contact with the target molecule, (4) the nucleic acid collapse operation, (5) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing.

22. The method of claim 15 wherein the method further comprises at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

23. The method of claim 22 wherein the method includes the combinatorial multicolor coding detection operation, and wherein the combinatorial multicolor coding detection operation comprises separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA by

mixing a set of detection probes with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, under conditions that promote hybridization between (i) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (ii) the detection probes, wherein the set of detection probes is labeled using combinatorial multicolor coding.

24. The method of claim 15 wherein the target molecule is part of a solid-state sample.

25. The method of claim 24 wherein the method includes at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

26. The method of claim 14 wherein the method includes the amplification operation and wherein the amplification operation comprises, simultaneous with, or following, step (d),

(e) mixing RNA polymerase with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote transcription of the tandem sequence DNA, wherein transcription of the tandem sequence DNA results in the formation of tandem sequence RNA, or

(e) mixing a secondary DNA strand displacement primer with the polymerase-ATC mixture, and incubating the polymerase-ATC mixture under conditions that promote (i) hybridization between the tandem sequence DNA and the secondary DNA strand displacement primer, and (ii) replication of the tandem sequence DNA in the polymerase-ATC mixture, wherein replication of the tandem sequence DNA results in the formation of secondary tandem sequence DNA.

27. The method of claim 26 wherein the method includes at least one of the following:

(1) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (2) the nucleic acid collapse operation, (3) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (4) differential amplification of at least two of the amplification target circles, and (5) primer-extension sequencing.

28. The method of claim 14 wherein at least one of the target sequences is coupled to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule.

29. The method of claim 28 wherein the method includes at least one of the following:

(1) the amplification operation, (2) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (3) a step of bringing the specific binding molecule into contact with the target molecule, (4) the nucleic acid collapse operation, (5) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing.

30. The method of claim 14 wherein at least one of the rolling circle replication primers is coupled to a specific binding molecule, wherein the specific binding molecule interacts with a target molecule.

31. The method of claim 30 wherein the method includes at least one of the following:

(1) the amplification operation, (2) the use of a solid-state sample wherein the solid-state sample comprises the target molecule, (3) a step of bringing the specific binding molecule into contact with the target molecule, (4) the nucleic acid collapse operation, (5) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (6) differential amplification of at least two of the amplification target circles, and (7) primer-extension sequencing.

32. The method of claim 14 wherein the method includes at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

33. The method of claim 32 wherein the method includes, following the formation of tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, primer extension sequencing, wherein primer extension sequencing comprises

(i) forming an interrogation mixture, wherein one or more interrogation primers are hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA,

(ii) simultaneous with, or following, step (i), mixing at least two different tagged chain terminating nucleotides and DNA polymerase with the interrogation mixture, wherein each different tagged chain terminating nucleotide comprises a different chain terminating nucleotide triphosphate coupled to a different tag molecule,

(iii) incubating the interrogation mixture under conditions that promote template-based addition of the tagged chain terminating nucleotides to the interrogation primers, wherein addition of the tagged chain terminating nucleotides to the interrogation primers results in association of the tagged chain terminating nucleotides with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and

(iv) detecting the association of the tagged chain terminating nucleotides with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA.

34. The method of claim 33 wherein formation of the interrogation mixture comprises

(i)(a) mixing an interrogation probe and a plurality of degenerate probes with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, to produce a probe mixture, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the interrogation probe and degenerate probes, wherein each degenerate probe has a 3′

blocking group,

(i)(b) mixing ligase with the probe mixture, to produce a degenerate ligation mixture, and incubating the degenerate ligation mixture under conditions that promote ligation of the interrogation probe to one of the degenerate probes hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, wherein the degenerate probe that is ligated to the interrogation probe is a ligated degenerate probe,

(i)(c) removing the 3′

blocking group of the ligated degenerate probe,

wherein ligation of the interrogation probe to one or more degenerate probes results in the formation of the interrogation primer, wherein the formation of the interrogation primer results in formation of the interrogation mixture.

35. The method of claim 34 wherein formation of the interrogation mixture further comprises, following step (i)(c),

(i)(d) mixing the plurality of degenerate probes with the ligation mixture, to produce a secondary probe mixture, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the degenerate probes,

(i)(e) mixing ligase with the secondary probe mixture, to produce a secondary degenerate ligation mixture, and incubating the secondary degenerate ligation mixture under conditions that promote ligation of the ligated degenerate probe to one of the degenerate probes hybridized to the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, wherein the degenerate probe that is ligated to the ligated degenerate probe is a secondary ligated degenerate probe,

(i)(f) removing the 3′

blocking group of the secondary degenerate probe,

wherein steps (i)(d), (i)(e), and (i)(f) are performed, in order, one or more times.

36. The method of claim 33 wherein formation of the interrogation mixture comprises mixing an interrogation primer with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, under conditions that promote hybridization between (1) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (2) the interrogation primer.

37. The method of claim 32 wherein the method includes the combinatorial multicolor coding detection operation, and wherein the combinatorial multicolor coding detection operation comprises separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA by

mixing a set of detection probes with the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, under conditions that promote hybridization between (i) the tandem sequence DNA, secondary tandem sequence DNA, or tandem sequence RNA, and (ii) the detection probes, wherein the set of detection probes is labeled using combinatorial multicolor coding.

38. The method of claim 14 wherein the target molecule is part of a solid-state sample.

39. The method of claim 38 wherein the method further comprises at least one of the following:

(1) the nucleic acid collapse operation, (2) a multiplex detection operation comprising separately and simultaneously detecting a plurality of different sequences present in the tandem sequence DNA, (3) differential amplification of at least two of the amplification target circles, and (4) primer-extension sequencing.

40. A kit for selectively detecting one or more target molecules, the kit comprising,

(a) one or more amplification target circles,

wherein the amplification target circles each comprise a single-stranded, circular DNA molecule comprising a primer complement portion, and

(b) a rolling circle replication primer comprising a single-stranded, linear nucleic acid molecule comprising a complementary portion that is complementary to the primer complement portion of one or more of the amplification target circles,

wherein either (1) each amplification target circle is tethered to a specific binding molecule, or (2) the rolling circle replication primer is coupled to a specific binding molecule,

wherein the specific binding molecule interacts with at least one of the target molecules.

41. The kit of claim 40 further comprising a secondary DNA strand displacement primer comprising a single-stranded, linear nucleic acid molecule comprising a matching portion that matches a portion of one or more of the amplification target circles.

42. The kit of claim 40 further comprising an interrogation probe and a plurality of degenerate probes.

43. The kit of claim 40 further comprising an interrogation primer.