Hybridization and mismatch discrimination using oligonucleotides conjugated to minor groove binders

• US 7,556,923 B1
• Filed: 04/06/2007
• Issued: 07/07/2009
• Est. Priority Date: 04/03/1995
• Status: Expired due to Fees

• Current Assignee: Epoch Biosciences Inc. (Ngen, Inc.)
• Original Assignee: Epoch Biosciences Inc. (Ngen, Inc.)
• Inventors: Meyer, Rich B. Jr., Lukhtanov, Eugeny A., Kutyavin, Igor V., Hedgpeth, Joel, Belousov, Evgeniy S., Afonina, Irina A.
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US11/784,539
• Time in Patent Office: 823 Days
• Field of Search: 435/6, 536/23.1, 536/24.3
• US Class Current: 435/6.11
• CPC Class Codes: C07H 19/23 Heterocyclic radicals containing two or more heterocyclic rings condensed among themselves or condensed with a common carbocyclic ring system, not provided for in groups C07H19/14 - C07H19/22
• 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 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm

Abstract

Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI₃), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI₃ group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides. The MGB-conjugated probes and primers described herein facilitate various analytic and diagnostic procedures, such as amplification reactions, PCR, detection of single-nucleotide polymorphisms, gene hunting, differential display, fluorescence energy transfer, hydrolyzable probe assays and others; by allowing the use of shorter oligonucleotides, which have higher specificity and better discriminatory power.

Claims

1. A method for hybridizing nucleic acids, comprising the steps of:

(a) providing a first nucleic acid and a second nucleic acid,

(b) incubating the nucleic acids under hybridization conditions, and

(c) identifying hybridized nucleic acids;

wherein at least one of the nucleic acids comprises a minor groove binder (MGB)-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

2. The method according to claim 1, wherein the MGB-oligonucleotide conjugate further comprises an agent that quenches the emission of the first fluorescent label.

3. The method according to claim 2, further comprising the step of altering the spatial relationship between the first fluorescent label and the agent that quenches the emission of said fluorescent label.

4. The method according to claim 1 wherein said minor groove binder is a molecule having a molecular weight of approximately 150 to approximately 2,000 Daltons that binds in a non-intercalating manner into the minor groove of a double-stranded nucleic acid with an association constant of greater than approximately 10³ M⁻

1.

5. The method according to claim 1 wherein the MGB-oligonucleotide conjugate is a primer comprising a free 3′

-hydroxyl group.

6. The method according to claim 5, further comprising the step of extending the primer with a polymerizing enzyme.

7. The method according to claim 6, wherein the polymerizing enzyme is a thermostable enzyme.

8. The method according to claim 5, wherein the MGB-oligonucleotide conjugate is a primer in an amplification reaction.

9. The method according to claim 8, wherein the amplification reaction is a polymerase chain reaction.

21. The method of hybridization according to claim 1, wherein the melting temperature of the hybridized nucleic acid is independent of base composition.

50. The method according to claim 1, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

51. The method of claim 50, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

68. The method according to claim 1, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

10. A method for primer extension, comprising the steps of:

(a) providing a sample containing a target sequence,

(b) providing one or more oligonucleotide primers complementary to regions of the target sequence,

(c) providing a polymerizing enzyme and nucleotide substrates, and

(d) incubating the sample, the oligonucleotide primers, the enzyme and the substrates under conditions favorable for polymerization;

wherein at least one of the primers comprises a MGB-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

11. The method according to claim 10, wherein the method is an amplification reaction.

12. The method according to claim 11, wherein the amplification reaction is a polymerase chain reaction.

69. The method according to claim 10, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

13. A method for discriminating between polynucleotides which differ by a single nucleotide, the method comprising the following steps:

(a) providing a polynucleotide comprising a target sequence,

(b) providing at least two MGB-oligonucleotide conjugates, wherein one of the at least two MGB-oligonucleotide conjugates has a sequence that is perfectly complementary to the target sequence and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels, and at least one other of the MGB-oligonucleotide conjugates has a single-nucleotide mismatch with the target sequence;

(c) separately incubating each of the MGB-oligonucleotide conjugates with the polynucleotide under hybridization conditions; and

(d) determining the hybridization strength between each of the MGB-oligonucleotide conjugates and the polynucleotide.

14. A method for discriminating between polynucleotides which differ by a single nucleotide, the method comprising the following steps:

(a) providing a MGB-oligonucleotide conjugate of defined sequence and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels,

(b) providing at least two polynucleotides, each of which comprises a target sequence, wherein one of the polynucleotides has a target sequence that is perfectly complementary to the MGB-oligonucleotide conjugate and at least one other of the polynucleotides has a target sequence having a single-nucleotide mismatch with the MGB-oligonucleotide conjugate;

(c) separately incubating each of the polynucleotides with the MGB-oligonucleotide conjugate under hybridization conditions; and

(d) determining the hybridization strength between each of the polynucleotides and the MGB-oligonucleotide conjugate.

52. The method according to claim 14, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

53. The method of claim 52, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

70. The method according to claim 14, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

15. A method of ligating two or more oligonucleotides, each of which is hybridized to adjacent sites on a target nucleic acid, comprising the steps of:

(a) providing a sample containing a target sequence,

(b) providing at least two oligonucleotides which are complementary to adjacent sites on the target sequence,

(c) incubating the sample and the oligonucleotides under conditions favorable for ligation, and

(d) identifying ligated nucleic acids;

wherein at least one of the oligonucleotides comprises a MGB-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

16. The method according to claim 15 in which each of the oligonucleotides comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

54. The method according to claim 15, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

55. The method of claim 54, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

71. The method according to claim 15, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

17. A method for primer-dependent nucleotide sequence analysis wherein a MGB-oligonucleotide conjugate further comprising multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels is used as a primer.

56. The method according to claim 17, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

57. The method of claim 56, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

72. The method according to claim 17, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

18. A method for determining the sequence of a polynucleotide comprising the steps of:

(a) providing an array of oligonucleotide probes of different sequences,

(b) incubating the polynucleotide and the array under hybridization conditions, and

(c) determining to which of the oligonucleotide probes in the array the polynucleotide hybridizes;

wherein one or more of the oligonucleotide probes comprises a MGB-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

58. The method according to claim 18, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

59. The method of claim 58, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

73. The method according to claim 18, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

19. A method for examining gene expression comprising the steps of:

(a) providing an array of oligonucleotide probes of different sequences,

(b) incubating a population of polynucleotides with the array under hybridization conditions, and

(c) determining to which of the oligonucleotide probes in the array the population hybridizes;

wherein one or more of the oligonucleotide probes comprises a MGB-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

60. The method according to claim 19, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

61. The method of claim 60, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

74. The method according to claim 19, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

20. A method for identifying one or more mutations in a gene of interest comprising the steps of:

(a) providing an array of oligonucleotide probes of different sequences,

(b) incubating a polynucleotide sample with the array under hybridization conditions, and

(c) determining to which of the oligonucleotide probes in the array the polynucleotide hybridizes;

wherein one or more of the oligonucleotide probes comprises a MGB-oligonucleotide conjugate and further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

22. The method of hybridization according to claim 20 wherein the melting temperature of the hybridized nucleic acid is dependent primarily on the length of the hybridized nucleic acid.

62. The method according to claim 20, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

63. The method of claim 62, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

75. The method according to claim 20, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

23. A method for cDNA synthesis, wherein a MGB-oligonucleotide conjugate further comprising multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels is used as a primer.

24. A method for detecting a target sequence in a polynucleotide, wherein the polynucleotide is present in a mixture of other polynucleotides, and wherein one or more of the other polynucleotides in the mixture comprise sequences that are related but not identical to the target sequence, the method comprising:

(a) contacting the mixture of polynucleotides with a minor groove binder (MGB)-oligonucleotide conjugate, wherein the MGB-oligonucleotide conjugate forms a stable hybrid only with said target sequence that is perfectly complementary to the oligonucleotide and wherein the MGB-oligonucleotide conjugate does not form a stable hybrid with any of the related sequences; and

(b) measuring hybrid formation, whereby hybrid formation is indicative of the presence of said target sequence;

(c) wherein said MGB-oligonucleotide conjugate comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

25. The method according to claim 24, wherein an oligonucleotide that is not conjugated to a MGB does not form a stable hybrid with the target sequence.

26. The method according to claim 25, wherein the related sequence is a single nucleotide mismatch.

27. The method according to claim 26 wherein the polynucleotide is DNA.

28. The method according to claim 26 wherein the polynucleotide comprises a coding region.

29. The method according to claim 26 wherein the polynucleotide comprises a non-coding region.

30. The method according to claim 26 wherein the polynucleotide comprises a mutant sequence.

31. The method according to claim 26 wherein the target sequence comprises an allele of a polymorphic sequence.

32. The method according to claim 31 wherein the other polynucleotides in the mixture comprise different alleles of the polymorphic sequence.

33. The method according to claim 24 wherein the MGB-oligonucleotide conjugate is attached to a solid support.

34. The method according to claim 31 wherein the polynucleotides in said mixture are attached to a solid support.

64. The method according to claim 24, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

65. The method of claim 64, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

76. The method according to claim 24, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

35. A method for detecting one or more sequences related to a target sequence, wherein the one or more related sequences are present in a sample of polynucleotides, the method comprising:

(a) contacting the sample with a Minor Groove Binder (MGB)-oligonucleotide conjugate, wherein the oligonucleotide has a sequence that is complementary to the target sequence, and wherein the MGB-oligonucleotide conjugate forms stable hybrids with the related sequences; and

(b) measuring hybrid formation, wherein hybrid formation is indicative of the presence of the one or more related sequences;

(c) wherein the MGB-oligonucleotide conjugate further comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels.

36. The method according to claim 35, wherein an oligonucleotide that is not conjugated to a MGB does not form stable hybrids with the related sequence.

37. The method according to claim 36, wherein the related sequence has a single nucleotide mismatch with respect to the target sequence.

38. The method according to claim 36 wherein the polynucleotides are DNA.

39. The method according to claim 36 wherein the polynucleotides comprise one or more coding regions.

40. The method according to claim 36 wherein the polynucleotides comprise one or more non-coding regions.

41. The method according to claim 36 wherein the polynucleotides comprise one or more mutant sequences.

42. The method according to claim 36 wherein the polynucleotides comprise a plurality of different mutations in the same gene.

43. The method according to claim 42 wherein the gene is a viral gene.

44. The method according to claim 43 wherein the virus has an RNA genome.

45. The method according to claim 44 wherein the virus is a human immunodeficiency virus.

46. The method according to claim 35 wherein the target sequence comprises an allele of a polymorphic sequence.

47. The method according to claim 46 wherein the polynucleotides in the mixture comprise different alleles of the polymorphic sequence.

48. The method according to claim 35 wherein the MGB-oligonucleotide conjugate is attached to a solid support.

49. The method according to claim 35 wherein the polynucleotides in said mixture are attached to a solid support.

66. The method according to claim 35, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate is a peptide nucleic acid.

67. The method of claim 66, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

77. The method according to claim 35, wherein the oligonucleotide portion of the MGB-oligonucleotide conjugate comprises a peptide linkage.

78. A method for identifying one or more nucleotide polymorphisms in a polynucleotide sample, the method comprising:

providing an array of support-bound oligonucleotide probes of different sequences;

incubating a polynucleotide sample with said array under hybridization conditions;

incubating a plurality of different minor groove binder-oligonucleotide conjugate probes with said polynucleotide sample with said array under hybridization conditions to form one or more minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids, wherein said minor groove binder comprises multiple fluorescent labels wherein the emission wavelengths of one of the fluorescent labels overlaps the absorption wavelengths of another of the fluorescent labels; and

detecting the presence of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids on said array.

79. The method of claim 78 wherein the minor groove binder is a molecule having a molecular weight of approximately 150 to approximately 2,000 Daltons that binds in a non-intercalating manner into the minor groove of a double-stranded nucleic acid with an association constant of greater than approximately 10³ M⁻

1.

80. The method of claim 78, wherein the nucleotide polymorphisms are one or more single-nucleotide polymorphisms.

81. The method of claim 78, wherein the A/T content of said minor groove binder-oligonucleotide conjugate probe ranges from 12.5% to 100%.

82. The method of claim 81, wherein the range of the melting temperatures of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is less than 18°

C.

83. The method of claim 78, wherein the A/T content of said minor groove binder-oligonucleotide conjugate probe ranges from 25% to 87.5%.

84. The method of claim 83, wherein the range of the melting temperatures of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is less than 8°

C.

85. The method of claim 78, wherein the A/T content of said minor groove binder-oligonucleotide conjugate probe ranges from 37.5% to 75%.

86. The method of claim 85, wherein the range of the melting temperatures of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is less than 4°

C.

87. The method of claim 78, wherein the A/T content of said minor groove binder-oligonucleotide conjugate probe ranges from 37.5% to 87.5%.

88. The method of claim 87, wherein the range of the melting temperatures of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is less than 4°

C.

89. The method of claim 78, wherein said minor groove binder is a member selected from the group consisting of:

netropsin;

distamycin;

lexitropsin;

mithramycin;

chromomycin A₃;

olivomycin;

anthramycin;

sibiromycin;

pentamidine;

stilbamidine;

berenil;

CC-1065;

Hoechst 33258;

4′

-6-diamidino-2-phenylindole (DAPI);

a dimer, a trimer, a tetramer and a pentamer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI);

N-methylpyrrole-4-carbox-2-amide (MPC), and a dimer, a trimer, a tetramer and a pentamer of MPC.

90. The method of hybridization according to claim 78, wherein the melting temperature of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is relatively independent of base composition.

91. The method of hybridization according to claim 78 wherein the melting temperature of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids is dependent primarily on the length of the hybridized nucleic acid.