Oligonucleotides containing pyrazolo[3,4-d]pyrimidines for hybridization and mismatch discrimination

• US 6,485,906 B2
• Filed: 11/01/1999
• Issued: 11/26/2002
• Est. Priority Date: 04/03/1998
• Status: Expired due to Term

• Current Assignee: ELITechGroup B.V. (ELITech Group SAS)
• Original Assignee: Epoch Pharmaceuticals, Inc.
• Inventors: Meyer, Rich B. Jr., Kutyavin, Igor V., Afonina, Irina A.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US09/431,385
• Publication Number:
  US 20020146690A1
• Time in Patent Office: 1,121 Days
• Field of Search: 435/6, 435/78, 435/77, 435/88, 435/24.31, 435/24.32, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/25.32, 422/50, 422/68.1
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm

Abstract

Oligonucleotides in which one or more purine residues are substituted by pyrazolo[3,4-d]pyrimidines exhibit improved hybridization properties. Oligonucleotides containing pyrazolo[3,4-d]pyrimidine base analogues have higher melting temperatures than unsubstituted oligonucleotides of identical sequence. Thus, in assays involving hybridization of an oligonucleotide probe to a target polynucleotide sequence, higher signals are obtained. In addition, mismatch discrimination is enhanced when pyrazolo[3,4-d]pyrimidine-containing oligonucleotides are used as hybridization probes, making them useful as probes and primers for hybridization, amplification and sequencing procedures, particularly those in which single- or multiple-nucleotide mismatch discrimination is required.

Claims

1. A method for detecting the presence of a target sequence in a plurality of polynucleotides, wherein the plurality of polynucleotides differ from one another by a single nucleotide within the target sequence, the method comprising the following steps:

(a) providing the plurality of polynucleotides which are to be tested for the presence of the target sequence;

(b) providing an oligonucleotide having a sequence that is substantially complementary to the target sequence, wherein one or more purine residues of the oligonucleotide are substituted by a pyrazolo[3,4-d]pyrimidine;

(c) incubating the plurality of polynucleotides and the oligonucleotide under hybridization conditions; and

(d) identifying hybridized nucleic acids;

wherein the presence of hybridized nucleic acids is indicative of the presence of the target sequence in the plurality of polynucleotides.

2. The method according to claim 1, wherein the oligonucleotide further comprises a minor groove binding moiety.

3. The method according to claim 1 wherein the oligonucleotide is a primer comprising an extendible 3′

-hydroxyl group.

4. The method according to claim 3, wherein hybridized nucleic acids are identified by extending the primer with a polymerizing enzyme.

5. The method according to claim 4 wherein the polymerizing enzyme is a thermostable enzyme.

6. The method according to claim 3, wherein the oligonucleotide is a primer in an amplification reaction.

7. The method according to claim 6, wherein the amplification reaction is a polymerase chain reaction.

13. The method according to claim 2, wherein the minor groove binding moiety is selected from the group consisting of the trimer of 3-carbamoyl-1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI₃) and the pentamer of N-methylpyrrole-4-carbox-2-amide (MPC₅).

8. A method for identifying a mutation in a target sequence of a gene of interest, the method comprising the following steps:

(a) providing a polynucleotide that comprises the target sequence,

(b) providing an array of oligonucleotides of different sequences, wherein one or more purine residues in at least one of the oligonucleotides are substituted by a pyrazolo[3,4-d]pyrimidine, and wherein the different sequences include the wild-type target sequence and different mutant target sequences,

(c) incubating the polynucleotide with the array under hybridization conditions, and

(d) determining which of the oligonucleotides in the array become hybridized to the polynucleotide;

wherein hybridization of the polynucleotide to oligonucleotides including the wild-type sequence indicates the lack of a mutation, and hybridization of the polynucleotide to oligonucleotides including a mutant sequence indicates the presence of a mutation whose sequence is defined by the particular oligonucleotide to which the polynucleotide is hybridized.

9. A method for identifying a variant of a target sequence, the method comprising the following steps:

(a) providing a sample comprising one or more polynucleotides to be tested for the presence of the variant sequence;

(b) providing at least two oligonucleotides of known sequence wherein one or more purine residues of the oligonucleotides are substituted by a pyrazolo[3,4-d]pyrimidine, and wherein one of the at least two oligonucleotides has a sequence that is perfectly complementary to the target sequence and one or more of the other oligonucleotides has a sequence that is perfectly complementary to one or more variant sequences;

(c) separately incubating each of the oligonucleotides with the polynucleotide under hybridization conditions; and

(d) determining the degree of hybridization between each of the oligonucleotides and the polynucleotide;

wherein hybridization of the polynucleotide to the oligonucleotide having a sequence that is perfectly complementary to the target sequence indicates the absence of a variant, and hybridization of the polynucleotide to an oligonucleotide having a sequence that is perfectly complementary to a particular variant sequence indicates the presence of a variant whose sequence is defined by the oligonucleotide to which the polynucleotide is hybridized.

10. The method of claim 9 wherein the variant sequence is a mutant.

11. The method of claim 9 wherein the variant sequence is a single nucleotide polymorphism.

12. The method of claim 9 wherein the oligonucleotides constitute part of an oligonucleotide array.