METHODS AND COMPOSITIONS FOR CAPPING NUCLEIC ACIDS

1 .- 20 . (canceled)

21 . A method for sequencing two template regions in a nucleic acid, comprising

(a) providing a nucleic acid comprising a first primer-template hybrid and a second primer-template hybrid, wherein the first hybrid comprises a first template region hybridized to a first primer, and wherein the second hybrid comprises a second template hybridized to a second primer, the second primer comprising a ternary complex inhibitor moiety at the 3′ end of the second primer;

(b) performing a sequencing process, comprising:

(i) binding the first hybrid to a polymerase and nucleotide to form a stabilized ternary complex;

(ii) detecting the stabilized ternary complex to identify the nucleotide in the stabilized ternary complex;

(iii) extending the first primer to form a modified first hybrid on the nucleic acid; and

(iv) repeating (i), (ii) and (iii) for the modified first hybrid of the nucleic acid, thereby determining a sequence for at least a portion of the first template region;

(c) capping the extended first primer with a second ternary complex inhibitor moiety;

(d) removing the ternary complex inhibitor moiety from the second primer while retaining the second ternary complex inhibitor moiety on the first primer; and

(e) extending the second primer, thereby determining a sequence for at least a portion of the second template region.

22 . The method of claim 21 , wherein (e) comprises

(i) binding the second hybrid to a polymerase and nucleotide to form a stabilized ternary complex;

(ii) detecting the stabilized ternary complex to identify the nucleotide in the stabilized ternary complex;

(iii) extending the second primer along the second template region of the nucleic acid to form a modified second hybrid on the nucleic acid; and

(iv) repeating (i), (ii) and (iii) for the modified second hybrid of the nucleic acid, thereby determining the sequence for the portion of the second template region.

23 . The method of claim 22 , wherein (e)(iv) comprises repeating (i), (ii) and (iii) at least 10 times for the modified second hybrid of the nucleic acid, thereby determining the sequence for the portion of the second template region.

24 . The method of claim 21 , wherein (e) comprises extending the second primer along the second template region in a sequencing by synthesis process or sequencing by ligation process.

25 . The method of claim 21 , wherein (a)(iv) comprises repeating (i), (ii) and (iii) at least 10 times for the modified first hybrid of the nucleic acid, thereby determining the sequence for the portion of the first template region.

26 . The method of claim 21 , wherein the capping of the extended first primer comprises incorporating a nucleotide comprising a ligand and then binding the ligand to a receptor to form the ternary complex inhibitor moiety.

27 . A method for identifying a nucleic acid template, comprising

(a) providing a plurality of nucleic acids, the plurality comprising a primer-template hybrid;

(b) capping the primer with a ternary complex inhibitor moiety, thereby forming a capped primer-template hybrid;

(c) hybridizing a primer to a second template of the plurality of nucleic acids, whereby the plurality of nucleic acids comprises the capped primer-template hybrid and a second primer-template hybrid;

(d) delivering polymerases and nucleotides to the plurality of nucleic acids, whereby the second primer-template hybrid binds a polymerase and nucleotide to form a stabilized ternary complex and whereby the capped primer-template hybrid does not bind a polymerase and nucleotide to form a stabilized ternary complex; and

(e) detecting the stabilized ternary complex to identify the second template.

28 . The method of claim 27 , further comprising

(f) extending the second primer to form a modified second hybrid on the nucleic acid; and

(g) repeating (d), (e) and (f) for the modified second hybrid of the nucleic acid, thereby determining a sequence for at least a portion of the second template.