Rolling circle amplification method

• US 10,227,632 B2
• Filed: 11/28/2014
• Issued: 03/12/2019
• Est. Priority Date: 11/29/2013
• Status: Active Grant

• Current Assignee: Q-linea AB
• Original Assignee: Q-linea AB
• Inventors: Jarvius, Jonas
• Primary Examiner(s): Thomas, David C
• Application Number:
  US15/037,022
• Publication Number:
  US 20160257991A1
• Time in Patent Office: 1,565 Days
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• 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 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2531/125 Rolling circle

Abstract

A method for performing a rolling circle amplification (RCA) reaction includes at least two rounds of RCA. The method includes providing a concatemeric first RCA product having a multiplicity of monomer repeats, each repeat representing a complementary copy of a first RCA template, wherein the nucleic acid molecule to be detected and/or analyzed, or its compliment, is contained in the first RCA template. The first RCA product is cleaved into monomer units which are reduced in size compared to the monomer repeat of the first RCA template. Monomer units resulting from the cleavage are circularized to form second RCA templates, which are smaller than the first RCA template. A second RCA reaction is performed on the second RCA template and a primer for the second RCA to form a second RCA product. The second RCA product, or a monomer unit derived from it, is detected or analyzed.

Claims

1. A method of detecting and/or analyzing a nucleic acid molecule, said method comprising:

performing a rolling circle amplification (RCA) reaction comprising at least two rounds of RCA, wherein said reaction comprises;

(a) providing a concatemeric first RCA product comprising a multiplicity of monomer repeats, each repeat representing a complementary copy of a first RCA template, wherein said nucleic acid molecule to be detected and/or analyzed, or its complement, is contained in said first RCA template;

(b) cleaving the first RCA product into monomer units, wherein the monomer unit is reduced in size as compared to the monomer repeat of the first RCA product;

(c) circularizing monomer units resulting from said cleavage to form second RCA templates wherein the second RCA template is smaller than the first RCA template; and

(d) performing a second RCA reaction using said second RCA template of (c) and a primer for said second RCA, to form a second RCA product;

wherein any one or more of steps (a) to (d) may be performed sequentially or in combination; and

detecting and/or analyzing said second RCA product and/or a monomer unit derived therefrom.

2. The method of claim 1, wherein steps (b) to (d) are repeated one or more times.

3. The method of claim 1, wherein steps (b) and (c) are performed in combination.

4. The method of claim 1, wherein step (a) comprises the step of generating a first RCA product from a first RCA template.

5. The method of claim 1, wherein cleavage of the first RCA product results directly in the generation of a monomer unit having a reduced size.

6. The method of claim 1, wherein said method comprises a separate step of reducing the size of a monomer unit created by the cleavage of the first RCA product.

7. The method of claim 1, wherein said cleavage is performed using a cleavage enzyme.

8. The method of claim 1, wherein each monomer repeat of the first RCA product comprises one or more cleavage recognition sites.

9. The method of claim 8, wherein a double-stranded cleavage recognition site is provided by intramolecular hybridization of two self-complementary regions of the first RCA product, said intramolecular hybridization creating a stem-like structure, and/or by intermolecular hybridization to a complementary cleavage oligonucleotide.

10. The method of claim 1, wherein each monomer repeat comprises a single cleavage recognition site.

11. The method of claim 1, wherein each monomer repeat contains two or more cleavage recognition sites.

12. The method of claim 1, wherein the cleavage enzyme is a restriction enzyme.

13. The method of claim 1, wherein the monomer units of step (c) are circularized by ligation using a separately provided ligation template oligonucleotide.

14. The method of claim 13, wherein the ligation template oligonucleotide serves as a primer for the second RCA reaction.

15. The method of claim 1, wherein a primer for the second RCA reaction is separately provided.

16. The method of claim 1, wherein the monomer units of step (c) are able to hybridize into an ‘

open circle’

structure capable of self-templated ligation.

17. The method of claim 1, wherein the cleavage recognition site is contained in the stem of a stem-loop structure, and the cleavage releases the loop part of the structure and a residual reduced monomer unit, wherein the loop part is optionally retained as a separate monomer unit.

18. The method of claim 1, wherein each monomer repeat contains two or more cleavage sites and cleavage releases the reduced monomer units from between the cleavage sites.

19. The method of claim 18, wherein the cleavage site is formed by hybridization of a cleavage oligonucleotide, and optionally the same oligonucleotide is used as ligation template for circularization of the monomer units.

20. The method of claim 1, wherein each monomer repeat contains a single cleavage recognition site for a type lls restriction enzyme, wherein cleavage occurs externally to the cleavage recognition site.

21. The method of claim 1, wherein each monomer repeat comprises two or more deoxyribozyme sequences, wherein upon activation the deoxyribozymes act to cleave the first RCA product.

22. The method of claim 1, wherein each monomer repeat of the first RCA product comprises one or more stem-like structures comprising a nicking site for cleavage by a nickase enzyme to release monomer units.

23. The method of claim 1, wherein each monomer repeat of the first RCA product comprises one or more stem-like structures comprising a restriction site for cleavage by a restriction enzyme to release monomer units, wherein the monomer units are able to form self-hybridized open-circle structures capable of self-templated ligation to form second RCA templates.

24. The method of claim 23, wherein each monomer repeat comprises two or more stem-like structures and/or wherein a loop part of the stem-like structure is removed.

25. The method of claim 1, wherein a monomer unit released by cleavage of the first RCA product is hybridized to a ligation template to create a structure having a protruding end which is removed by cleavage to form a reduced monomer unit.

26. The method of claim 1, wherein cleavage of the first RCA product results in the generation of different monomer units and it is selected which monomer units are circularized, and optionally wherein said selection is by using ligation templates which hybridize selectively to a selected monomer unit.

27. The method of claim 1, wherein all monomer units are circularized.

28. The method of claim 1, wherein the monomer unit which is circularized comprises a reporter domain.

29. The method of claim 1, wherein the monomer unit which is circularized comprises a target nucleic acid molecule for detection and/or analysis.

30. The method of claim 1, wherein the first RCA template is a reporter molecule, a circularized probe, or a circularized molecule comprising captured target nucleic acid molecule.

31. The method of claim 1, wherein one or more steps of the method are carried out using a solid phase.

32. The method of claim 1, wherein the analysis is sequencing.

33. The method of claim 1, wherein the nucleic acid molecule is a target analyte for detection, or is indicative of the presence of a target analyte in a sample, and wherein the first circular RCA template comprises or is generated from a nucleic acid analyte or is used or generated as a marker for said analyte, and a first RCA reaction is performed using said first RCA template to generate a first RCA product, wherein the target analyte is detected by detecting and/or analyzing said second RCA product and/or a monomer unit derived therefrom.

34. The method of claim 1, wherein said first circular RCA template includes a tag sequence or captured sequence, wherein the complement thereof is retained in the reduced monomer unit and which, or its complement, is detected in the second or subsequent RCA product and/or monomer unit derived therefrom.