Solid support assay systems and methods utilizing non-standard bases

1. 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.

2. The method of claim 1 wherein (c) is conducted at room temperature.

3. The method of claim 1 wherein (c) is not followed by a washing.

4. A method of detecting at least one target oligonucleotide comprising the steps of:

(a) contacting the sample with at least one primer pair comprising a first primer and a second primer under conditions such that the first and second primer of the primer pair hybridizes to the target oligonucleotide;

(b) amplifying the target oligonucleotide;

(c) hybridizing any amplified target oligonucleotide from (b) with at least one tagged primer comprising, in 5′ to 3′ order, a 5′ tagging sequence comprising at least one non-standard nucleotide, and a 3′ sequence capable of hybridizing with the amplified target oligonucleotide from (b);

(d) enzymatically extending the at least one primer of step (c) in the presence of a labeled non-standard triphosphate base to form a labeled extension product, the labeled extension product comprising the tagging sequence comprising at least one non-standard base;

(e) contacting the labeled extension product of step (d) with at least one capture oligonucleotide comprising a molecular recognition sequence complementary to the tagging sequence of the labeled extension product and coupled to a support under suitable hybridization conditions to hybridize the labeled extension product; and

(f) detecting the hybridization of (e).

5. The method of claim 4 wherein (e) is conducted at room temperature.

6. The method of claim 4 wherein (e) is not followed by a washing.

7. A method of assaying at least two target oligonucleotides comprising the steps of:

(a) contacting an analyte comprising an analyte-specific sequence with a first primer and a second primer, the second primer comprising, in 5′ to 3′ order, a sequence that is not complementary to the analyte-specific sequence, a non-standard base, and an analyte-specific sequence;

(b) enzymatically extending the primers of (a) to form extension products;

(c) hybridizing to the extension product of the second primer of step (b) at least one tagged primer comprising, in 5′ to 3′ order, a 5′ tagging sequence comprising at least one non-standard base and a 3′ sequence complementary to the extension product of the second primer;

(d) enzymatically extending the tagged primer of step (c);

(e) hybridizing a reporter oligonucleotide complementary to the sequence that is not complementary to the analyte-specific sequence of the second primer of step (a) to the extension product of step (b)

(f) contacting the hybridization product of step (e) with at least one capture oligonucleotide comprising at least one non-standard nucleotide and coupled to a support under suitable hybridization conditions to hybridize the hybridization product of step (e) to the at least one capture oligonucleotide; and

(g) detecting the hybridization of step (f).

8. The method of claim 7 wherein (f) is conducted at room temperature.

9. The method of claim 7 wherein (f) is not followed by a washing.

10. The method of claim 7 further comprising covalently attaching the extension product of (d) to the reporter oligonucleotide of (e) with a ligase.

11. 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 second primer comprising, in 5′ to 3′ order, a sequence that is not complementary to the analyte-specific sequence, a non-standard base, and an analyte-specific sequence;

(b) enzymatically extending the 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;

(c) hybridizing to the extension product of the second primer of step (b) a tagged, allele-specific primer comprising, in 5′ to 3′ order, a 5′ tagging sequence comprising a non-standard base, a linker, and a 3′ sequence complementary to the extension product of the second primer;

(d) enzymatically extending the allele-specific primer of step (c);

(e) hybridizing a reporter oligonucleotide complementary to the sequence that is not complementary to the analyte-specific sequence of the second primer of step (a) to the extension product of step (d);

(f) contacting a capture oligonucleotide coupled to a support with the hybridization product of step (e); and

(g) detecting hybridization of the reporter oligonucleotide to the capture oligonucleotide.