Modified oligonucleotides for mismatch discrimination

1. A method for primer extension, the method comprising incubating a polynucleotide containing a target sequence with one or more oligonucleotide primers complementary to the target sequence, in the presence of a polymerizing enzyme and nucleotide substrates under conditions favorable for polymerization; wherein at least one of the oligonucleotide primers contains a modified base selected from the group consisting of an unsubstituted pyrazolo[3,4-d]pyrimidine, a 3-substituted pyrazolo[3,4-d]pyrimidine and a 5-substituted pyrimidine base, in place of a purine or pyrimidine base.

2. A method in accordance with claim 1 , wherein one of said oligonucleotide primers is extended with a single base.

3. A method in accordance with claim 1 , wherein said at least one of said oligonucleotide primers further comprises an attached minor groove binder.

4. A method in accordance with claim 1 , wherein said incubating is part of an amplification reaction.

5. A method in accordance with claim 4 , wherein said amplification reaction is a polymerase chain reaction.

6. A method in accordance with claim 1 , wherein said modified oligonucleotide further comprises a covalently attached minor groove binder.

7. A method for determining the nucleotide sequence of a polynucleotide, the method comprising:

(a) incubating the polynucleotide with a modified oligonucleotide array under hybridization conditions; and

(b) determining to which of the modified oligonucleotides in the array the polynucleotide hybridizes;

wherein a plurality of the modified oligonucleotides comprise at least one 3-substituted pyrazolo[3,4]pyrimidine in place of a purine base.

8. A method in accordance with claim 7 , wherein said array comprises from 10 to 100,000 different modified oligonucleotides.

9. A method in accordance with claim 7 , wherein said array comprises from 10 to 1000 different modified oligonucleotides.