Process for labeling a nucleic acid

• US 6,902,891 B2
• Filed: 12/15/2000
• Issued: 06/07/2005
• Est. Priority Date: 12/17/1999
• Status: Expired due to Term

• Current Assignee: Bio Merieux, Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Bio Merieux, Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Menou, Lionel, Tora, Christelle, Friedenberg, Matthew C., Banerjee, Aloke R., Hajjar, Fred F., Browne, Kenneth A., Becker, Michael M., Laayoun, Ali
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US09/736,151
• Publication Number:
  US 20020081586A1
• Time in Patent Office: 1,635 Days
• Field of Search: 435/6, 435/91.2, 536/25.3, 536/25.31, 540/465, 540/474, 556/1, 556/6
• US Class Current: 435/6.15
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents

Abstract

A process of fragmenting and labeling a synthetic or natural nucleic acid, comprising the steps of providing a mixture containing a nucleic acid, a labeling agent containing a detectable label, and at least one multivalent metal cation in a substantially aqueous solution; chemically fragmenting the nucleic acid in the mixture to produce a multiplicity of nucleic acid fragments; and attaching at least one label to at least one of the nucleic acid fragments to produce a detectably labeled nucleic acid fragment.

Claims

1. A process for fragmenting and labeling at least one synthetic or natural DNA, RNA or chimeric DNA-RNA polymer, comprising the steps of:

obtaining a mixture in which the at least one DNA, RNA or chimeric DNA-RNA polymer has been subject to an in vitro nucleic acid amplification reaction;

chemically fragmenting the at least one DNA, RNA or chimeric DNA RNA polymer in the mixture in the presence of at least one multivalent metal cation in an aqueous solution, to produce a plurality of DNA or RNA fragments having freed terminal phosphates for further reaction; and

attaching a labeling agent on a plurality of said fragments at freed terminal phosphates located at the 3′

end and/or 5′

end of said fragments, wherein the fragmenting and attaching steps take place in an in vitro nucleic acid amplification mixture.

3. The process according to claim 1, further comprising a treating step that physically separates labeled nucleic acid fragments from unattached labeling agent after the fragmenting and attaching steps.

4. The process according to claim 3, wherein the treating step uses an organic solvent to separate the labeled nucleic acid fragment from the unattached labeling agent.

5. The process according to claim 3, wherein the treating step separates a labeled nucleic acid fragment from unattached labeling agent by using solid phase extraction of the labeled nucleic acid fragment on a solid support.

6. The process according to claim 3, wherein the treating step precipitates a labeled nucleic acid fragment at ambient temperature from the mixture that further contains betaine, dodecyl trimethylammonium bromide (DTAB) and unlabeled nucleic acid.

7. The process according to claim 1, wherein the fragmenting and attaching steps are effected in separate steps.

8. The process according to claim 1, wherein the DNA, RNA, or chimeric DNA-RNA polymer comprises at least one thiophosphate nucleotide.

9. The process according to claim 8, wherein the fragmenting step for RNA or chimeric DNA-RNA polymer comprising at least one thiophosphate nucleotide is performed in the presence of at least one multivalent metal cation selected from the group consisting of Sr²⁺, Ba²⁺, Pb²⁺, Cd²⁺, Fe²⁺, Ni²⁺, Ru³⁺, Ce³⁺, Eu³⁺, Tb³⁺, Tm³⁺, Yb³⁺, and Lu³⁺ and a chemical catalyst.

10. The process according to claim 8, wherein the fragmenting step for RNA or chimeric DNA-RNA polymer comprising at least one thiophosphate nucleotide is performed in the presence of at least one multivalent metal cation selected from the group consisting of Cr³⁺, Ce³⁺, Yb³⁺, Tb³⁺, Eu²⁺and Pb²⁺.

11. The process according to claim 8, wherein the fragmenting step for RNA or chimeric DNA-RNA polymer comprising at least one thiophosphate nucleotide is performed in the presence of at least one multivalent metal cation selected from the group consisting of Be²⁺, Cr³⁺, Pb²⁺, In³⁺, Tb³⁺, Ce³⁺, Yb³⁺and Ni²⁺.

12. The process according to claim 1, wherein the attaching step attaches a label to an internal or terminal thiophosphate nucleotide.

13. The process according to claim 1, wherein the fragmenting step further includes use of a chemical catalyst.

14. The process according to claim 13, wherein the chemical catalyst is selected from the group consisting of imidazole, a substituted analogue of imidazole and a compound that includes an imidazole ring or a substituted analogue of an imidazole ring.

15. The process according to claim 13, wherein the chemical catalyst is selected from the group consisting of N-methylimidazole, 3-(N-morpholino) propane sulfonic acid (MOPS), N′

-2-hydroxyethylpiperazine-N′

-2-ethanesulfonic acid (HEPES), piperazine-N,N′

-bis(2-ethane sulfonic acid) (PIPES) and bioorganic polyamines.

16. The process according to claim 1, wherein the fragmenting step for RNA or chimeric DNA-RNA polymer is performed in the presence of at least one multivalent metal cation selected from the group consisting of Sr²⁺, Ba²⁺, Pb²⁺, Cd²⁺, Fe²⁺, Ni²⁺, Ru³⁺, Ce³⁺, Eu³⁺, Tb³⁺, Tm³⁺, Yb³⁺ and Lu³⁺ and a chemical catalyst.

18. The process according to claim 1, wherein the fragmenting step for DNA or chimeric DNA-RNA polymer is performed in the presence of Tb³⁺ and a chemical catalyst.

19. The process according to claim 1, wherein the fragmenting step for DNA or chimeric DNA-RNA polymer is performed in the presence of at least one multivalent metal cation selected from the group consisting of Be²⁺, Cr³⁺, Pb²⁺, In³⁺, Ce³⁺, Yb³⁺ and Ni²⁺.

20. The process according to claim 1, wherein the multivalent metal cation is selected from the group consisting of Tb³⁺ and Ce³⁺.

21. The process according to claim 1, wherein the mixture contains the labeling agent in a concentration of from 0.1 mM to 4 mM.

22. The process according to claim 21, wherein the mixture contains the labeling agent in a concentration of from 0.1 mM to 1 mM.

23. The process according to claim 21, wherein the mixture contains the labeling agent in a concentration of from 0.3 mM to 0.55 mM.

24. The process according to claim 1, wherein the labeling agent contains alkyl halide or haloacetamide reactive functions.

25. The process according to claim 1, wherein the labeling agent is selected from the group consisting of 5-(bromomethyl)fluoroscein, 6-(bromomethyl)fluorescein, 6-iodoacetamidofluorescein and 5-iodoacetamidofluorescein.

2. A process for fragmenting and labeling a synthetic or natural DNA or RNA nucleic acid, comprising the steps of:

obtaining a mixture in which the DNA or RNA nucleic acid has been subject to an in vitro nucleic acid amplification reaction;

chemically fragmenting said nucleic acid in the mixture in the presence of at least one multivalent metal cation in an aqueous solution, to produce a plurality of DNA or RNA fragments having freed terminal phosphates for further reaction;

attaching a labeling agent on a plurality of said fragments at freed terminal phosphates located at the 3′

end and/or 5′

end of said fragments; and

treating said mixture to decrease or eliminate unattached labeling agent, wherein the treating step physically separates the labeled nucleic acid fragment from unattached labeling agent in the mixture after the fragmenting and attaching steps, and wherein the treating step dilutes the mixture.

26. The process according to claim 2, wherein the treating step further includes adding an acid to the aqueous solution after the fragmenting and attaching steps.

27. The process according to claim 2, wherein the treating step uses an organic solvent to separate the labeled nucleic acid fragment from the unattached labeling agent.

28. The process according to claim 27, wherein the organic solvent is selected from the group consisting of 1-butanol, 2-butanol, isopentyl alcohol, 1-pentanol and cyclohexanol.

29. The process according to claim 2, wherein the treating step separates a labeled nucleic acid fragment from unattached labeling agent by using solid phase extraction of the labeled nucleic acid fragment on a solid support.

30. The process according to claim 29, wherein said solid support is selected from the group consisting of beads, gels, ion exchange resin, reverse phase resin, silica matrix and a membrane.

31. The process according to claim 29, wherein the labeled nucleic acid fragment is eluted from the solid support by using a buffer containing betaine.

32. The process according to claim 2, wherein the treating step precipitates the labeled nucleic acid fragment at ambient temperature from the aqueous solution that further contains betaine, dodecyl trimethylammonium bromide (DTAB) and unlabeled nucleic acid.

33. The process according to claim 2, wherein the treating step comprises adding a quencher to the aqueous solution after the fragmenting and attaching steps.

34. The process according to claim 33, wherein the quencher is selected from the group consisting of pyrophosphate, thiol derivative, chelating agent, phosphate anion and carbonate anion.

35. The process according to claim 2, wherein the fragmenting and attaching steps are effected in separate steps.

36. The process according to claim 2, wherein the DNA or RNA nucleic acid comprises at least one thiophosphate nucleotide.

37. The process according to claim 36, wherein the RNA nucleic acid comprising at least one thiophosphate nucleotide is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Sr²⁺, Ba²⁺, Pb²⁺, Cd²⁺, Fe²⁺, Ni²⁺, Ru³⁺, Ce³⁺, Eu³⁺, Tb³⁺, Tm³⁺, Yb³⁺ and Lu³⁺ and a chemical catalyst.

38. The process according to claim 36, wherein the RNA nucleic acid comprising at least one thiophosphate nucleotide is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Cr³⁺, Ce³⁺, Yb³⁺, Tb³⁺, Eu²⁺ and Pb²⁺.

39. The process according to claim 36, wherein the DNA nucleic acid comprising at least one thiophosphate nucleotide is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Be²⁺, Cr³⁺, Pb²⁺, In³⁺, Tb³⁺, Yb³⁺ Ni²⁺.

40. The process according to claim 2, wherein the RNA nucleic acid is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Sr²⁺, Ba²⁺, Pb²⁺, Cd²⁺, Fe²⁺, Ni²⁺, Ru³⁺, Ce³⁺, Eu³⁺, Tb³⁺, Tm³⁺, Yb³⁺ and Lu³⁺ and a chemical catalyst.

41. The process according to claim 2, wherein the RNA nucleic acid is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Cr³⁺, Ce³⁺, Yb³⁺, Tb³⁺, Eu²⁺ and Pb²⁺.

42. The process according to claim 2, wherein the DNA nucleic acid is chemically fragmented in the presence of Tb³⁺ and a chemical catalyst.

43. The process according to claim 2, wherein the DNA nucleic acid is chemically fragmented in the presence of at least one multivalent metal cation selected from the group consisting of Be²⁺, Cr³⁺, Pb²⁺, In³⁺, Tb³⁺, Ce³⁺, Yb³⁺ and Ni²⁺.

44. The process according to claim 2, wherein the multivalent metal cation is selected from the group consisting of Tb³⁺ and Ce³⁺.

45. The process according to claim 2, wherein the aqueous solution contains the labeling agent in a concentration of from 0.1 mM to 4 mM.

46. The process according to claim 45, wherein the aqueous solution contains the labeling agent in a concentration of from 0.1 mM to 1 mM.

47. The process according to claim 45, wherein the aqueous solution contains the labeling agent in a concentration of from 0.3 mM to 0.55 mM.

48. The process according to claim 2, wherein the labeling agent contains alkyl halide or haloacetamide reactive functions.

49. The process according to claim 2, wherein the labeling agent is selected from the group consisting of 5-(bromomethyl)fluoroscein, 6-(bromomethyl)fluorescein, 6-iodoacetamidofluorescein and 5-iodoacetamidofluorescein.

17. The process according to claim wherein the fragmenting step for RNA or chimeric DNA-RNA polymer is performed in the presence of at least one multivalent metal cation selected from the group consisting of Cr³⁺, Ce³⁺, Yb³⁺, Tb³⁺, Eu²⁺ and Pb²⁺.