METHODS AND COMPOSITIONS FOR CAPPING NUCLEIC ACIDS
A method for identifying a nucleic acid template that include (a) providing a plurality of primer-template hybrids, wherein a first hybrid of the plurality includes a first template hybridized to a first primer, and wherein a second hybrid of the plurality includes a second template hybridized to a second primer, the second primer having a ternary complex inhibitor moiety at the 3′ end; (b) delivering polymerases and nucleotides to the plurality, whereby the first hybrid binds a polymerase and nucleotide to form a stabilized ternary complex and whereby the second hybrid does not bind a polymerase and nucleotide to form a stabilized ternary complex; and (c) detecting the stabilized ternary complex to identify the first template.
1 .- 28 . (canceled)
29 . An apparatus, comprising a plurality of primer-template nucleic acid hybrids, wherein a first subset of the primer-template nucleic acid hybrids comprises a blocked nucleotide at the 3′ end of the primer, and wherein a second subset of the primer-template nucleic acid hybrids comprises a ternary complex inhibitor at the 3′ end of the primer.
30 . The apparatus of claim 29 , wherein the blocked nucleotides comprise reversibly terminated nucleotides.
31 . The apparatus of claim 29 , wherein the plurality of primer-template nucleic acid hybrids is attached to a solid support.
32 . The apparatus of claim 31 , wherein the solid support comprises a nucleic acid array.
33 . The apparatus of claim 31 , wherein the plurality of primer-template nucleic acid hybrids is attached to a feature of the array and wherein the templates that are attached to the feature comprise the same sequence.
34 . The apparatus of claim 29 , wherein the plurality of primer-template nucleic acid hybrids is in a manufactured vessel.
35 . The apparatus of claim 34 , wherein the manufactured vessel comprises a flow cell.
36 . The apparatus of claim 29 , wherein primer-template nucleic acid hybrids in the first subset are each bound to a polymerase and cognate nucleotide, thereby forming ternary complexes.
37 . The apparatus of claim 36 , wherein the polymerase is covalently attached to an exogenous label.
38 . The apparatus of claim 36 , wherein the cognate nucleotide is covalently attached to an exogenous label.
39 . The apparatus of claim 36 , wherein the exogenous label comprises a fluorophore.
40 . The apparatus of claim 29 , wherein the primers of the first subset of the primer-template nucleic acid hybrids are the same length.
41 . The apparatus of claim 40 , wherein the primers of the second subset of the primer-template nucleic acid hybrids differ in length.
42 . The apparatus of claim 40 , wherein the primers of the second subset of the primer-template nucleic acid hybrids are shorter than the primers of the first subset of the primer-template nucleic acid hybrids.
43 . The apparatus of claim 40 , wherein the primers of the second subset of the primer-template nucleic acid hybrids are longer than the primers of the first subset of the primer-template nucleic acid hybrids.
44 . The apparatus of claim 29 , wherein the number of primer-template nucleic acid hybrids in the first subset is less than 50% of the number of primer-template nucleic acid hybrids in the plurality.
45 . The apparatus of claim 29 , wherein the ternary complex inhibitor comprises an oligonucleotide moiety.
46 . The apparatus of claim 29 , wherein the ternary complex inhibitor comprises a moiety that inhibits polymerase from binding at the 3′ end of the primer.
47 . The apparatus of claim 29 , wherein the ternary complex inhibitor comprises a moiety that inhibits cognate nucleotide from binding to a polymerase at the 3′ end of the primer.
48 . A system comprising:
(a) the apparatus of claim 29 ; and
(b) a detector configured to detect the plurality of primer-template nucleic acid hybrids.