Highly Visible Chromosome-Specific Probes and Related Methods

• US 20090215643A1
• Filed: 07/25/2008
• Published: 08/27/2009
• Est. Priority Date: 07/26/2007
• Status: Abandoned Application

• Current Assignee: Cellay, LLC
• Original Assignee: Cellay, LLC
• Inventors: Aurich-Costa, Joan, Bradley, Sean P., Moen, Phillip T. JR.
• Application Number:
  US12/179,770
• Publication Number:
  US 20090215643A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/1025 labels being on the same oligonucleotide
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Disclosed are chromosome-specific synthetic oligonucleotides and labeled probe compositions, as well as related methods for preparing and using such compositions. Also disclosed are kits for utilization in methods for preparing or using the labeled probes.

Claims

1. A synthetic oligonucleotide comprising:

a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes.

2. The oligonucleotide of claim 1, wherein the repeat sequence is a member selected from the group consisting of a centromeric repeat, a pericentromeric repeat, a heterochromatin repeat, and a telomeric repeat.

3. The oligonucleotide of claim 1, wherein the consensus repeat sequence is selected from the group consisting of an alpha satellite, beta satellite, gamma satellite, satellite 1, satellite 2 and a satellite 3 repeat.

4. The oligonucleotide of claim 1, wherein the chromosome-specific sequence is less than 84% identical to all other contiguous nucleic acid sequences within the human genome.

5. The oligonucleotide of claim 1, wherein the chromosome-specific sequence is specific for an alpha monomer repeat sequence from a chromosome selected from the group consisting of the Y chromosome, chromosome 2, and chromosome 4.

6. The oligonucleotide of claim 5, wherein the chromosome-specific sequence is selected from the group consisting of:

7. The oligonucleotide of claim 1, further comprising a detectable label.

8. The oligonucleotide of claim 7, wherein the detectable label comprises a fluorophore.

9. The oligonucleotide of claim 7, wherein the fluorophore is selected from the group consisting of fluorescein, rhodamine, Texas Red, phycoerythrin, Cy3, Cy5, Alexa 532, Alexa 546, Alexa 568, and Alexa 594.

10. The oligonucleotide of claim 1, further comprising an oligonucleotide that forms a hairpin structure comprising a stem region and a loop region, wherein a plurality of nucleotides within the hairpin structure have an attached detectable label.

11. The oligonucleotide of claim 10, wherein the stem region has 16-40 nucleotides.

12. The oligonucleotide of claim 10, wherein at least two nucleotides having an attached detectable label are adjacent.

13. The oligonucleotide of claim 10, wherein the nucleotides having an attached detectable label are spaced at least two nucleotides apart.

14. The oligonucleotide of claim 10, wherein the nucleotides having an attached detectable label are spaced three nucleotides apart.

15. A composition comprising a plurality of oligonucleotides according to claim 7.

16. The composition of claim 15, wherein the detectable label for each of the oligonucleotides is a fluorophore having a spectrally distinguishable emission wavelength.

17. A labeled probe comprising:

a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes; and

a detectable label.

18. The probe of claim 17, wherein the detectable label is a direct label.

19. The probe of claim 18, wherein the direct label comprises a fluorophore.

20. The probe of claim 19, wherein the fluorophore is selected from the group consisting of fluorescein, rhodamine, Texas Red, phycoerythrin, Cy3, Cy5, Alexa 532, Alexa 546, Alexa 568, and Alexa 594.

21. The probe of claim 17, wherein the label is an indirect label.

22. The probe of claim 21, wherein the indirect label comprises a fluorophore.

23. The probe of claim 22, wherein the fluorophore is selected from the group consisting of fluorescein, rhodamine, Texas Red, phycoerythrin, Cy3, Cy5, Alexa 532, Alexa 546, Alexa 568, and Alexa 594.

24. The probe of claim 17, further comprising an oligonucleotide that forms a hairpin structure comprising a stem region and a loop region, wherein a plurality of nucleotides within the hairpin structure have an attached detectable label.

25. The probe of claim 24, wherein the stem region has 16-40 nucleotides.

26. The probe of claim 24, wherein at least two nucleotides having an attached detectable label are adjacent.

27. The probe of claim 24, wherein the nucleotides having an attached detectable label are spaced at least two nucleotides apart.

28. The probe of claim 24, wherein the nucleotides having an attached detectable label are spaced three nucleotides apart.

29. A probe cocktail composition comprising:

a plurality of different labeled probes, each different labeled probe comprising a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes and having

(a) a different chromosome-specific oligonucleotide; and

(b) a different detectable label that is distinguishable from each of the other detectable labels.

30. The composition of claim 29, wherein each detectable label is a fluorophore having a spectrally distinguishable emission wavelength.

31. The composition of claim 29, wherein each probe further comprises an oligonucleotide that forms a hairpin structure comprising a stem region and a loop region, wherein a plurality of nucleotides within the hairpin structure have an attached detectable label.

32. A method of identifying a chromosome-specific probe sequence, the method comprising:

(a) comparing a repeat sequence of a specific human chromosome with a consensus repeat sequence of all human chromosomes; and

(b) identifying a nucleic acid sequence consisting of 25-35 contiguous nucleotides within the repeat sequence of the specific human chromosome and having less than 84% identity to the consensus repeat sequence as a potential chromosome-specific probe sequence.

33. The method of claim 32, further comprising

(c) comparing the chromosome specific probe sequence identified in (b) with all other contiguous nucleotide sequences within the human genome;

and

(d) identifying a nucleic acid sequence that has more than 16% mismatch to all other contiguous nucleotide sequences within the human genome as a potential chromosome specific probe sequence.

34. The method of claim 33, further comprising

(e) chemically synthesizing and labeling the chromosome specific probe sequence with a detectable label;

(f) performing in situ hybridization on a member selected from the group consisting of human metaphases and human interphases using the labeled probe sequence of (e);

(g) detecting the signal associated with the label, wherein a chromosome specific probe sequence that produces a signal at least 2 fold higher than the background upon hybridization is selected as a chromosome specific probe.

35. The method of claim 32, wherein the repeat sequence is selected from the group consisting of a centromeric repeat sequence, a pericentromeric repeat sequence, a heterochromatin repeat sequence, and a telomeric repeat sequence.

36. The method of claim 32, wherein the repeat sequence is selected from the group consisting of an alpha satellite, beta satellite, gamma satellite, satellite 1, satellite 2 and a satellite 3 repeat.

37. The method of claim 32, wherein the consensus repeat sequence is selected from the group consisting of a centromeric repeat sequence, a pericentromeric repeat sequence, a heterochromatin repeat sequence, and a telomeric repeat sequence.

38. The method of claim 32, wherein the consensus repeat sequence is selected from the group consisting of an alpha satellite, beta satellite, gamma satellite, satellite 1, satellite 2 and a satellite 3 repeat.

39. The method of claim 32, wherein the specific human chromosome is selected from the group consisting of the Y chromosome, chromosome 2, and chromosome 4.

57. The method of claim 33, which comprises identifying a plurality of nucleic acid sequences in (b) and (d), thereby identifying a plurality of potential chromosome-specific probe sequences.

58. The method of claim 57, further comprising

preparing a plurality of labeled oligonucleotide probes, each probe comprising a detectable label and a different chromosome-specific nucleic acid sequence, each different sequence being one of the chromosome-specific sequences identified in (d);

performing, individually with each of the different oligonucleotide probes, in situ hybridization on a member selected from the group consisting of human metaphases and human interphases;

detecting a signal associated with the label for each of the hybridized probes; and

selecting one or more of the oligonucleotide probes based on the degree of detected signal.

40. A method of detecting a specific human chromosome, the method comprising:

(a) contacting a preparation of human chromosomes with a labeled oligonucleotide comprising a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes;

(b) incubating the chromosome preparation and the oligonucleotide under conditions sufficient to allow the oligonucleotide to hybridize to, if present, a specific human chromosome having a repeat sequence perfectly complementary to the chromosome-specific sequence of the probe; and

(c) detecting the label to detect the specific human chromosome, if present.

41. The method of claim 40, wherein the label comprises a fluorophore.

42. The method of claim 41, wherein the fluorophore is selected from the group consisting of fluorescein, rhodamine, Texas Red, phycoerythrin, Cy3, Cy5, Alexa 532, Alexa 546, Alexa 568, and Alexa 594.

43. The method of claim 40, wherein the label is attached to the hairpin portion of an oligonucleotide that forms a hairpin structure comprising a stem region and a loop region.

44. The method of claim 43, wherein a plurality of the nucleotides in the hairpin structure have an attached label.

45. The method of claim 43, wherein the stem region has 16-40 nucleotides.

46. The method of claim 43, wherein at least two nucleotides having an attached label are adjacent.

47. The method of claim 43, wherein the nucleotides having an attached label are spaced at least two nucleotides apart.

48. The method of claim 43, wherein the nucleotides having an attached detectable label are spaced three nucleotides apart.

49. The method of claim 40, wherein detection of the human chromosome identifies a chromosomal abnormality.

50. The method of claim 40, wherein the chromosome preparation comprises a human cell and the hybridization step is performed in situ on chromosomes within the cell.

51. A method of detecting a specific human chromosome, the method comprising:

(a) contacting a preparation of human chromosomes with a probe cocktail composition comprising a plurality of different labeled oligonucleotides having a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes, wherein each different oligonucleotide has a different chromosome-specific sequence and a different detectable label that is distinguishable from each of the other detectable labels;

(b) incubating the chromosome preparation and the probe cocktail composition under conditions sufficient to allow the oligonucleotides to hybridize to, if present, a specific human chromosome having a repeat sequence perfectly complementary to the chromosome-specific sequence of the oligonucleotide; and

(c) detecting the label(s) to detect the specific human chromosome(s), if present.

52. A method of selecting a chromosome-specific probe sequence, the method comprising:

(a) comparing centromeric repeat sequences of a specific human chromosome with a consensus alpha-monomer repeat sequence of centromeric repeat sequences of all human chromosomes; and

(b) identifying a nucleic acid sequence consisting of 25-35 contiguous nucleotides within the specific centromeric repeat sequence and having less than 84% identity to the consensus alpha-monomer repeat sequence, thereby selecting a chromosome-specific probe sequence.

53. The method of claim 52, further comprising preparing an oligonucleotide probe comprising a chromosome-specific nucleic acid sequence, said sequence consisting of the chromosome-specific sequence selected in (b).

54. The method of claim 52, which comprises identifying a plurality of nucleic acid sequences in (b), thereby selecting a plurality of chromosome-specific probe sequences.

55. The method of claim 54, further comprising preparing a plurality of labeled oligonucleotide probes, each probe comprising a detectable label and a different chromosome-specific nucleic acid sequence, each different sequence being one of the chromosome-specific sequences selected in (b);

performing, individually with each of the different oligonucleotide probes, in situ hybridization on a member selected from the group consisting of human metaphases and human interphases;

detecting a signal associated with the label for each of the hybridized probes; and

selecting one or more of the oligonucleotide probes based on the degree of detected signal.

56. The method of claim 54, further comprising

(c) comparing the nucleic acid sequences identified in (b) with all other contiguous nucleotide sequences within the human genome;

and

(d) discarding any nucleic acid sequences that have more than 84% identity to another contiguous nucleotide sequence within the human genome.

59. A method for preparing a labeled probe, the method comprising:

attaching an oligonucleotide that forms a hairpin structure comprising a stem region and a loop region, wherein a plurality of nucleotides within the hairpin structure have an attached detectable label, to a chromosome-specific nucleic acid sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a centromeric repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus alpha-monomer repeat sequence of centromeric repeat sequences of all human chromosomes.

60. The method of claim 59, wherein the stem region has 16-40 nucleotides.

61. The method of claim 59, wherein at least two nucleotides having an attached detectable label are adjacent.

62. The method of claim 59, wherein the nucleotides having an attached detectable label are spaced at least two nucleotides apart.

63. The method of claim 59, wherein the nucleotides having an attached detectable label are spaced three nucleotides apart.

64. A method of detecting a specific human chromosome, the method comprising:

contacting a preparation of human chromosomes with a labeled probe comprising a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes;

incubating the chromosome preparation and the probe under conditions sufficient to allow the probe to hybridize to, if present, a specific human chromosome having a centromeric repeat sequence perfectly complementary to the chromosome-specific sequence of the probe; and

detecting the label to detect the specific human chromosome, if present.

65. The method of claim 64, which comprises contacting the preparation of human chromosomes with a plurality of different labeled probes, each different labeled probe having a different chromosome-specific sequence and a different detectable label that is distinguishable from each of the other detectable labels.

66. The method of claim 65, wherein each detectable label is a fluorophore having a spectrally distinguishable emission wavelength.

67. The method of claim 64, which is a method for identifying a chromosomal abnormality.

68. The method of claim 64, wherein detecting the label comprises microscopic imaging.

69. The method of claim 64, wherein detecting the label comprises image scanning microscopy.

70. The method of claim 64, wherein the chromosome preparation comprises a human cell and the hybridization step is performed in situ on chromosomes within the cell.

71. A kit for detection of a specific human chromosome in a cell, the kit comprising:

a labeled oligonucleotide comprising a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes.

72. The kit of claim 71, wherein the label is attached to the chromosome-specific sequence via a linker.

73. The kit of claim 71, wherein the labeled oligonucleotide further comprises a sequence that forms a hairpin structure comprising a stem region and a loop region, wherein a plurality of nucleotides within the hairpin structure have an attached detectable label.

74. The kit of claim 73, wherein the stem region has 16-40 nucleotides.

75. The kit of claim 73, wherein at least two nucleotides having an attached detectable label are adjacent.

76. The kit of claim 73, wherein the nucleotides having an attached detectable label are spaced at least two nucleotides apart.

77. The kit of claim 73, wherein the nucleotides having an attached detectable label are spaced three nucleotides apart.

78. A kit for detection of a specific human chromosome in a cell, the kit comprising:

a plurality of different labeled probes, each different labeled probe comprising a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes and having

(a) a different chromosome-specific sequence; and

(b) a different detectable label that is distinguishable from each of the other detectable labels.

79. The kit of claim 78, wherein each detectable label is a fluorophore having a spectrally distinguishable emission wavelength.