Nucleotide transient binding for sequencing methods
First Claim
1. A method for identifying a nucleotide bound to a polymerase, comprising:
- a) transiently binding, without polymerizing, a first type of nucleotide to a first polymerase in the presence of a cation that inhibits nucleotide incorporation by the polymerase, wherein the first polymerase is bound to a template nucleic acid molecule that is bound to a polymerization initiation site, wherein the first polymerase lacks exonuclease activity, and wherein the first type of nucleotide includes a detectable moiety;
b) detecting the first type of transiently-bound nucleotide; and
c) identifying the first type of transiently-bound nucleotide.
1 Assignment
0 Petitions
Accused Products
Abstract
Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
96 Citations
85 Claims
-
1. A method for identifying a nucleotide bound to a polymerase, comprising:
-
a) transiently binding, without polymerizing, a first type of nucleotide to a first polymerase in the presence of a cation that inhibits nucleotide incorporation by the polymerase, wherein the first polymerase is bound to a template nucleic acid molecule that is bound to a polymerization initiation site, wherein the first polymerase lacks exonuclease activity, and wherein the first type of nucleotide includes a detectable moiety; b) detecting the first type of transiently-bound nucleotide; and c) identifying the first type of transiently-bound nucleotide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 82)
-
-
29. A method for identifying a nucleotide bound to a polymerase, comprising:
-
transiently binding, without polymerizing, at least a first type of a nucleotide including a detectable moiety to an immobilized complex including a first polymerase, a template nucleic acid strand, and a polymerization initiation site, wherein the transiently binding includes forming a reaction mixture including the first type of nucleotide and the first polymerase and having a concentration of cation that inhibits nucleotide polymerization by the polymerase; b. identifying the first type of nucleotide transiently-bound to the first polymerase; c. removing the transiently-bound first type of nucleotide; d. contacting the complex with at least a second type of nucleotide under suitable conditions for the first polymerase to polymerize the second type of nucleotide at the polymerization initiation site in a template-dependent manner; and e. repeating steps (a)-(c) at least once. - View Dependent Claims (30, 31, 83)
-
-
32. A method for obtaining sequence information from a template nucleic acid molecule, comprising:
-
(a) forming a reaction mixture including a polymerase and a template nucleic acid molecule, wherein the reaction mixture includes a concentration of cation at which nucleotide polymerization by the polymerase is inhibited; (b) contacting, within the reaction mixture, a first type of nucleotide containing a detectable moiety with the polymerase and transiently binding the first type of nucleotide to the polymerase in a template-dependent manner without polymerizing the transiently bound nucleotide at the polymerization initiation site by the polymerase, (c) detecting a signal generated by the detectable moiety while the first type of nucleotide is transiently bound to the polymerase; (d) removing the transiently bound nucleotide from the polymerase; and (e) contacting the polymerase with a second type of nucleotide and polymerizing the second type of nucleotide at the polymerization initiation site using the polymerase. - View Dependent Claims (33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 76, 77, 84)
-
-
53. A method for obtaining sequence information from a template nucleic acid molecule, comprising:
-
(a) transiently binding, without polymerizing, a first type of nucleotide having a detectable moiety to a polymerase, wherein the transiently binding includes forming a reaction mixture having a concentration of cation at which nucleotide polymerization by the polymerase is inhibited; and (b) detecting a signal, the signal being generated by the detectable moiety during the transiently binding; and (c) identifying the first type of nucleotide. - View Dependent Claims (54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 78, 79, 80, 81, 85)
-
Specification