Universal reagents for rolling circle amplification and methods of use

• US 8,043,834 B2
• Filed: 03/31/2003
• Issued: 10/25/2011
• Est. Priority Date: 03/31/2003
• Status: Active Grant

• Current Assignee: Qiagen GmbH (Qiagen NV), Agilix Corp. (Revvity, Inc.)
• Original Assignee: Qiagen GmbH (Qiagen NV)
• Inventors: Abarzúa, Patricio, Sparkowski, Jason, Smelkova, Natalia
• Primary Examiner(s): Benzion; Gary
• Assistant Examiner(s): Wilder; Cynthia B
• Application Number:
  US10/405,822
• Publication Number:
  US 20040191784A1
• Time in Patent Office: 3,130 Days
• Field of Search: 435/6
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2525/125 incorporating agents resulting in resistance to degradation
• CPC Class Codes: C12Q 2525/143 incorporating a promoter sequence
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2563/107 fluorescence

Abstract

Disclosed are compositions and methods useful for labeling and detection of analytes. The compositions generally are associations of three components: reporter binding agents, amplification target circles, and DNA polymerase. The compositions are assembled prior to their use in a rolling circle amplification reaction and can be stored and transported prior to use without substantial loss of activity. The reporter binding agents generally are composed of a specific binding molecule and a rolling circle replication primer. The specific binding molecule can be specific for a target molecule. The rolling circle replication primer has sequence complementary to the amplification target circle. The DNA polymerase can interact with the rolling circle replication primer and amplification target circle. For use as a general reagent, the specific binding molecule is not bound to the target molecule until the composition is used in an assay.

Claims

1. A composition comprising a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each other and form a complex, and wherein the composition is not in an assay or reaction.

2. The composition of claim 1 wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are associated via non-covalent interactions.

3. The composition of claim 1 wherein the specific binding molecule comprises an antibody.

4. The composition of claim 3 wherein the antibody comprises a whole antibody or an antibody fragment.

5. The composition of claim 1 wherein the reporter binding agent comprises a plurality of rolling circle replication primers.

6. The composition of claim 5 wherein the reporter binding agent does not comprise a plurality of specific binding molecules.

7. The composition of claim 5 wherein the amplification target circles are associated with a plurality of the rolling circle replication primers.

8. The composition of claim 7 wherein the rolling circle replication primers are the same.

9. The composition of claim 5 wherein the rolling circle replication primers are the same.

10. The composition of claim 5 wherein the rolling circle replication primers are different.

11. The composition of claim 10 wherein the amplification target circles are associated with a plurality of the rolling circle replication primers, wherein the amplification target circles are different.

12. The composition of claim 10 wherein an amplification target circle is associated with each of the rolling circle replication primers, wherein a different amplification target circle is associated with each different rolling circle replication primer.

13. The composition of claim 5 wherein the reporter binding agent comprises three or more rolling circle replication primers.

14. The composition of claim 5 wherein the reporter binding agent comprises two or three rolling circle replication primers.

15. The composition of claim 1 wherein the composition is stored at or below about 25°

C.

16. The composition of claim 15 wherein the composition is stored at or below about 4°

C.

17. The composition of claim 16 wherein the composition is stored at or below about −

20°

C.

18. The composition of claim 17 wherein the composition is stored at or below about −

70°

C.

19. The composition of claim 1 wherein the composition is stored at or below room temperature.

20. The composition of claim 1 wherein the DNA polymerase is φ

29 DNA polymerase.

21. The composition of claim 1 further comprising glycerol.

22. The composition of claim 1 further comprising from about 20% glycerol to about 50% glycerol.

23. The composition of claim 1 wherein the amplification target circle comprises a single-stranded, circular DNA molecule comprising a primer complement portion, wherein the primer complement portion is complementary to the rolling circle replication primer.

32. The composition of claim 1, wherein the composition is stored prior to use of the composition in an assay or reaction.

33. The composition of claim 32, wherein the composition is stored 1 day or longer prior to use of the composition in an assay or reaction.

34. The composition of claim 33, wherein the composition is stored 5 days or longer prior to use of the composition in an assay or reaction.

35. The composition of claim 34, wherein the composition is stored 10 days or longer prior to use of the composition in an assay or reaction.

36. The composition of claim 35, wherein the composition is stored 1 month or longer prior to use of the composition in an assay or reaction.

37. The composition of claim 1, wherein the composition is stored prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

38. The composition of claim 37, wherein the composition is stored 1 day or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

39. The composition of claim 38, wherein the composition is stored 5 days or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

40. The composition of claim 39, wherein the composition is stored 10 days or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

41. The composition of claim 40, wherein the composition is stored 1 month or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

42. The composition of claim 1, wherein the composition is stored prior to use of the composition in an amplification assay or amplification reaction.

43. The composition of claim 1, wherein the composition has not been brought into contact with an analyte sample.

44. The composition of claim 1, wherein the composition does not include any nucleotides needed for replication.

45. The composition of claim 1 further comprising from about 10% glycerol to about 60% glycerol.

46. The composition of claim 1 further comprising from about 10% glycerol to about 50% glycerol.

24. A kit comprising a composition and a buffer for rolling circle amplification,

wherein the composition comprises a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase directly associated with each other and form a complex, wherein the composition is not in an assay or reaction.

25. The kit of claim 24 further comprising nucleotide triphosphates.

26. The kit of claim 24 further comprising a solid support, wherein the solid support comprises one or more second specific binding molecules, wherein each second specific binding molecule is specific for a molecule of interest.

27. The kit of claim 26 further comprising one or more third specific binding molecules, wherein each third specific binding molecule is specific for one of the molecules of interest, wherein the third specific binding molecule is the target molecule, wherein the third specific binding molecule is an animal immunoglobulin, wherein the specific binding molecule of the reporter binding agent comprises an antibody specific for immunoglobulins from the same type of animal of which the third specific binding molecule is an immunoglobulin.

28. The kit of claim 26 wherein the target molecule is one of the molecules of interest.

29. The kit of claim 24 further comprising a solid support, wherein the solid support comprises a second specific binding molecule, wherein the second specific binding molecule is specific for a molecule of interest.

30. The kit of claim 29 further comprising a third specific binding molecule, wherein the third specific binding molecule is specific for the molecule of interest, wherein the third specific binding molecule comprises the target molecule, wherein the third specific binding molecule is an animal immunoglobulin, wherein the specific binding molecule of the reporter binding agent comprises an antibody specific for immunoglobulins from the same type of animal of which the third specific binding molecule is an immunoglobulin.

31. The kit of claim 29 wherein the target molecule comprises the molecule of interest.

47. The kit of claim 24, wherein the composition is stored prior to use of the composition in an assay or reaction.

48. The kit of claim 47, wherein the composition is stored 1 day or longer prior to use of the composition in an assay or reaction.

49. The kit of claim 48, wherein the composition is stored 5 days or longer prior to use of the composition in an assay or reaction.

50. The kit of claim 49, wherein the composition is stored 10 days or longer prior to use of the composition in an assay or reaction.

51. The kit of claim 50, wherein the composition is stored 1 month or longer prior to use of the composition in an assay or reaction.

52. The kit of claim 24, wherein the composition is stored prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

53. The kit of claim 52, wherein the composition is stored 1 day or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

54. The kit of claim 53, wherein the composition is stored 5 days or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

55. The kit of claim 54, wherein the composition is stored 10 days or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

56. The kit of claim 55, wherein the composition is stored 1 month or longer prior to use of the composition to bind a target molecule and before the amplification target circle is amplified to produce tandem sequence DNA.

57. The kit of claim 24, wherein the composition is stored prior to use of the composition in an amplification assay or amplification reaction.

58. The kit of claim 24, wherein the composition has not been brought into contact with an analyte sample.

59. The kit of claim 24, wherein the composition does not include any nucleotides needed for replication.

60. The kit of claim 24 further comprising from about 10% glycerol to about 60% glycerol.

61. The kit of claim 24 further comprising from about 10% glycerol to about 50% glycerol.

62. A composition comprising a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each other and form a complex, wherein the composition is stored at or below about 25°

C. for 1 day or longer prior to use of the composition in an assay or reaction.

63. A composition comprising a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each other and form a complex, wherein the composition is stored at or below about 4°

C. for 10 days or longer prior to use of the composition in an assay or reaction.

64. A composition comprising a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each other and form a complex, wherein the composition is stored at or below about −

20°

C. for 1 month or longer prior to use of the composition in an assay or reaction.

65. A kit comprising a composition and a buffer for rolling circle amplification,

wherein the composition comprises a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each other and form a complex, wherein the composition is stored at or below about 25°

C. for 1 day or longer prior to use of the composition in an assay or reaction.

66. A kit comprising a composition and a buffer for rolling circle amplification,

wherein the composition comprises a reporter binding agent, an amplification target circle, and DNA polymerase,

wherein the reporter binding agent comprises a specific binding molecule and a rolling circle replication primer,

wherein the specific binding molecule is specific for a target molecule, wherein the specific binding molecule is not bound to the target molecule, wherein the composition does not comprise tandem sequence DNA, wherein the reporter binding agent, the amplification target circle, and the DNA polymerase are directly associated with each and form a complex, wherein the composition is stored at or below about 4°

C. for 10 days or longer prior to use of the composition in an assay or reaction.