Patent ID: 6977161

Claim:
A method of assaying a target oligonucleotide comprising steps of: (a) contacting an analyte comprising an analyte-specific sequence with a first primer and a second primer, the first primer comprising a tagging sequence and a sequence complementary to a first sequence of the analyte, the second primer comprising a sequence complementary to a second sequence of the analyte and a non-standard base; (b) enzymatically extending the first and second primers to form a target oligonucleotide and a second oligonucleotide, wherein one of the target oligonucleotide and the second oligonucleotide comprises the analyte-specific sequence and the other comprises a sequence complementary to the analyte-specific sequence; and incorporating a complementary non-standard base into the extended first primer opposite the non-standard base of the second primer; (c) contacting a capture oligonucleotide coupled to a support with the target oligonucleotide under hybridizing conditions to hybridize a target oligonucleotide, the target oligonucleotide comprising the tagging sequence and the analyte-specific sequence or a complement of the analyte-specific sequence, the capture oligonucleotide comprising a molecular recognition sequence that is complementary to the tagging sequence of the target oligonucleotide; and (d) detecting hybridization of target oligonucleotide to the capture oligonucleotide.