Solid support assay systems and methods utilizing non-standard bases

A method for detecting the presence or absence of a target nucleic acid in a sample comprising:

• (a) producing an amplified target nucleic acid comprising a first non-standard base by amplifying the target nucleic acid using a reaction mixture that comprises a first primer complementary to a first strand of the target nucleic acid and a second primer complementary to a second strand of the target nucleic acid, wherein the second primer further comprises the first non-standard base and wherein the first non-standard base is not complementary with standard bases;
• (b) specifically hybridizing a strand of the amplified target nucleic acid comprising the first non-standard base to a capture oligonucleotide on a solid support, thereby forming a hybridized capture oligonucleotide on the solid support;
• (c) extending the hybridized capture oligonucleotide in a reaction mixture comprising a labeled nucleotide comprising a second non-standard base that is complementary to the first non-standard base of the amplified target nucleic acid, thereby forming an extended hybridized capture oligonucleotide comprising the labeled nucleotide on the solid support;
• and
• (d) detecting the presence or absence of the target nucleic acid in the sample by determining the presence or absence of the extended hybridized capture oligonucleotide comprising the labeled nucleotide on the solid support.