Methods of using oligonucleotides comprising a molecular switch

A method of genotyping a target nucleic acid in a sample, the method comprising:

• (1) contacting said sample, under conditions suitable for hybridization, with first and second oligonucleotides, each of said first and second oligonucleotides comprising
• (a) a nucleic acid anchor region complementary to a first sequence of nucleic acid residues of the target nucleic acid, and
• (b) a switch domain comprising a bridging domain and a binding domain,
• wherein said binding domain comprises 2-20 nucleic acid bases or analogs thereof complementary to said target nucleic acid and said binding domain has less affinity for said target nucleic acid than said anchor region,
• wherein said bridging domain is located between said anchor region and said binding domain and comprises 2-11 universal, generic or mismatched natural bases or analogs thereof or a mixture of universal and non-hydrogen bonding natural bases that do not form a Watson-Crick hybridization complex with said target nucleic acid, wherein two or more universal or non-hydrogen bonding natural bases or analogs thereof or a mixture of universal and non-hydrogen bonding natural bases in said bridging domain are juxtaposed, and wherein said universal or non-hydrogen bonding natural bases in said bridging domain substitute for bases complementary to nucleotide bases of said target nucleic acid, and
• wherein said switch domain is able to discriminate between (i) a sequence of nucleic acid residues of said target nucleic acid that is complementary to said binding domain and (ii) a second mismatch sequence of nucleic acid residues of said target nucleic acid that contains at least one nucleic acid residue that is not complementary to said binding domain, under conditions wherein said anchor region (a) forms a stable duplex with said first sequence of nucleic acid residues of said target nucleic acid, wherein the at least one nucleic acid residue that is not complementary to said binding domain corresponds to the site of a polymorphism or mutation to be detected;
• wherein the first and second oligonucleotides form a tandem oligonucleotide assembly in which the first and second oligonucleotides are positioned side-by-side when hybridized to the target nucleic acid, and wherein a first detectable label is associated with the first oligonucleotide and a second detectable label is associated with the second oligonucleotide, wherein the amount of signal detectable from said first and/or said second detectable label is altered when the binding domain of each of said first and second oligonucleotides is hybridized to the target nucleic acid, relative to the amount of signal detectable from said first and/or said second detectable label when either binding domain is hybridized to said target nucleic acid individually;
• and
• (2) determining, under the conditions wherein each anchor region (a) forms the stable duplex with the respective first sequence, the hybridization status of each switch domain as an indication of the presence or absence of the mutation or polymorphism corresponding to each binding domain, thereby genotyping the target nucleic acid.