Method for determination of telomere length

• US 20040265815A1
• Filed: 07/26/2004
• Published: 12/30/2004
• Est. Priority Date: 06/23/2001
• Status: Abandoned Application

• Current Assignee: Cancer Research Technology Limited (Cancer Research UK)
• Original Assignee: Cancer Research Technology Limited (Cancer Research UK)
• Inventors: Baird, Duncan Martin
• Application Number:
  US10/482,596
• Publication Number:
  US 20040265815A1
• Time in Patent Office: Days
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer

Abstract

A method is described for determining telomere length of mammalian chromosomal DNA, which method comprises the steps: (a) annealing the 3′ end of a single-stranded oligonucleotide (hereinafter referred to as a ‘telorette’) to a single-stranded overhang of the telomere comprising the G-rich telomere strand (comprising TTAGGG repeat sequences) and covalently binding the telorette to the 5′ end of the C-rich telomeric strand (having CCCTAA repeat sequences) thereby forming a ligation product; (b) amplifying the ligation product formed in step (a) to form a primer extension product; and (c) detecting the length of the primer extension product(s) of step (b). Step (b) is preferably carried out by PCR using: (i) a first primer capable of annealing to a telomere-adjacent region of DNA but which first primer is not capable of annealing to the C-rich telomeric repeat sequence (CCCTAA); and (ii) a second primer (hereinafter referred to as a ‘teltail’ primer) identical to the 5′ end sequence of the telorette of step (a) which amplification is effected under conditions such that the first primer hybridises to the C-rich telomeric strand (comprising the CCCTAA repeats) and is extended to form a first primer extension product; and the teltail primer hybridises to the first primer extension product and is extended to form a second primer extension product. Also described are specific primers, including telorettes and teltails, for carrying out the method; a kit for use in the method; and the use of the method in determining telomere length and assessing biological conditions associated therewith.

Claims

1-30. -30. (canceled).

31. A method for determining telomere length of mammalian chromosomal DNA, which method comprises the steps of:

(a) annealing a 3′

end of a single-stranded oligonucleotide linker or telorette to a single-stranded overhang of a telomere comprising a G-rich telomere strand having TTAGGG repeat sequences, and covalently binding the telorette to a 5′

end of a C-rich telomeric strand having CCCTAA repeat sequences thereby forming a ligation product;

(b) amplifying the ligation product to form at least one primer extension product; and

(c) detecting a length of the primer extension product.

32. The method according to claim 31, wherein the amplification step is carried out using:

(i) a first primer capable of annealing to a telomere-adjacent region of DNA but not capable of annealing to the C-rich telomeric repeat sequence CCCTAA; and

(ii) a second or teltail primer identical to the 5′

end sequence of the telorette;

wherein the amplification step is effected under conditions such that the first primer hybridises to the C-rich telomeric strand comprising CCCTAA repeats and is extended to form a first primer extension product, and further wherein the teltail primer hybridises to the first primer extension product and is extended to form a second primer extension product.

33. The method according to claim 32, wherein the teltail primer comprises a unique sequence of the telorette.

34. The method according to claim 31, wherein the telorette comprises a single-stranded oligonucleotide having from about 6 to about 12 nucleotides at the 3′

end which are complementary to and capable of annealing to a human telomeric repeated sequence TTAGGG.

35. The method according to claim 34, wherein the telorette further comprises a sequence of from 15 to 30 bases at the 5′

end, said sequence lacking substantial homology to human DNA sequences.

36. The method according to claim 34, wherein the 3′

bases of the telorette complementary to the telomere are short enough that, at an annealing temperature of at least about 35°

C., the telorette is not capable of initiating strand synthesis.

37. The method according to claim 35, wherein the remaining 5′

bases of the telorette comprise a sequence lacking substantial homology to human DNA sequences, and which is efficient for PCR amplification only in the presence of first strand synthesis, initiated from either a primer capable of annealing to the sub-telomeric DNA or the variant repeats in the proximal regions of the telomere.

38. The method according to claim 31, wherein the telomere is a human telomere comprising the canonical telomere repeat sequence TTAGGG, and optionally telomere repeat variants selected from the group consisting of TGAGGG, TCAGGG, and TTGGGG, and any mixture thereof.

39. The method according to claim 38, wherein the telomere is that of human chromosomal DNA.

40. The method according to claim 31, wherein the telorette is ligated to the 5′

end of the C-rich telomeric strand using a ligase capable of joining juxtaposed DNA molecules between the 5′

-phosphate and 3′

-hydroxy groups.

41. The method according to claim 31, wherein the telorette is selected from at least one single-stranded oligonucleotide consisting of the group of sequences reading from 3′

to 5′

AATCCC, ATCCCA, TCCCAA, CCCAAT, CCAATC and CAATCC, or any mixture thereof.

42. The method according to claim 31, wherein the ligation reaction is carried out enzymatically at a temperature of from about 35°

C. to about 37°

C.

43. The method according to claim 42, wherein, following the ligation step, the reaction temperature is raised sufficiently to heat-inactivate the ligase enzyme.

44. The method according to claim 31, wherein the ligation product is amplified by PCR.

45. The method according to claim 44, wherein the amplification step is performed under long-range PCR conditions.

46. The method according to claim 44, wherein the amplification step is carried out at a temperature of from about 60°

C. to about 70°

C.

47. The method according to claim 31, wherein the DNA sample has a weight of from about 10 pg to about 1000 pg.

48. A kit for determining telomere length of mammalian chromosomal DNA, comprising at least one telorette sequence according to claim 31, at least one teltail primer identical to the 5′

end of the telorette, or any mixture thereof.

49. The kit according to claim 48, wherein the teltail primer comprises a unique sequence of the telorette.

50. The kit according to claim 48, further including at least one chromosome-specific primer, at least one allele-specific primer, at least one hybridisation probe, or any mixture thereof.

51. The kit according to claim 50, further including at least one ligase, at least one component specific for long-range PCR, at least one buffer, or any mixture thereof.

52. The kit according to claim 51, further including computer software and/or a spreadsheet adapted for calculation of mean telomere length.

53. The kit according to claim 52, further including instructions for using said kit to calculate a mean telomere length.

56. A method for determining telomere length of mammalian chromosomal DNA as described in claim 31, for use in assessing a potential anti-cancer treatment or other cancer related procedure, for use in the analysis of a biopsy sample, for assessing the effect of stem cells in bone marrow transplantation, for assessing telomere dynamics with age, for assessing the effect of modulating telomerase activity, or for assessing, treating, or diagnosing male infertility.

57. A kit for determining telomere length of mammalian chromosomal DNA as described in claim 48, for use in assessing a potential anti-cancer treatment or other cancer related procedure, for use in the analysis of a biopsy sample, for assessing the effect of stem cells in bone marrow transplantation, for assessing telomere dynamics with age, for assessing the effect of modulating telomerase activity, or for assessing, treating, or diagnosing male infertility.

54. A primer for use in determining telomere length of mammalian chromosomal DNA, comprising a 3′

terminal having 6 to 12 nucleotide bases which are complementary to and capable of annealing to a G-rich telomeric overhang, and a 5′

terminal comprising 15 to 30 bases which are selected so as not to be complementary to the telomere but to be suitable for PCR amplification.

55. The primer according to claim 54, wherein said primer is selected from the group of sequences consisting of:

58. A primer for determining telomere length of mammalian chromosomal DNA as described in claim 54, for use in assessing a potential anti-cancer treatment or other cancer related procedure, for use in the analysis of a biopsy sample, for assessing the effect of stem cells in bone marrow transplantation, for assessing telomere dynamics with age, for assessing the effect of modulating telomerase activity, or for assessing, treating, or diagnosing male infertility.