Nucleic acid indexing
First Claim
1. A method for indexing double-stranded nucleic acid fragments from a mixture of double-stranded nucleic acid fragments, said method comprises the steps of:
- (a) treating nucleic acids with one or more restriction endonucleases selected from the group consisting of Type IIS restriction endonuclease and interrupted palindrome (IP) restriction endonuclease to generate fragments having at least one 3′
- or 5′
-protruding single strand;
(b) incubating a C-indexer with said fragments generated in step (a) to allow selective hybridization between complementary protruding single strand of said fragments and said C-indexers, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 3′
- or a 5′
-protruding single strand on said first strand and said second strand, wherein the lengths of the 3′
- or 5′
-protruding single strands of said C-indexer correspond to the lengths of the 3′
- or 5′
-protruding single strands of the fragments, wherein said C-indexer is selected from a collection of C-indexers whose 3′
- or 5′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T;
(c) adding ligase to selectively ligate said C-indexer to those fragments whose 3′
- or 5′
-protruding single strands are fully complementary to the 3′
- or 5′
-protruding protruding single strands of said C-indexer; and
(d) obtaining circular indexed nucleic acid fragments, wherein the first strand of said C-indexer is ligated to the fragments to form a closed circular strand, and wherein the second strand of said C-indexer is ligated to the fragments to form a discontinuous strand.
0 Assignments
0 Petitions
Accused Products
Abstract
The present invention describes methods to construct circularization indexers and use them to selectively circularize, purify, and manipulate nucleic acids from a complex nucleic acid mixture. An assay is provided to detect nucleic acid without any amplification. Kits for preparing indexing nucleic acid targets and for high-level multiplexing DNA amplification are provided. The present invention also describes a method to construct a nucleic acids amplification assembly, in which the nucleic acid amplification is self-primed without the need for external primers. In this method, double stranded oligonucleotides with two cohesive ends (C-indexers) are used to circularize double-stranded or single-stranded nucleic acid targets in such a way that one of the strands is completely circularized while the other strand either contains a nick (if the targets are double-stranded) or is only hybridized to part of the targets (if the targets are single-stranded). At the presence of a polymerase, the un-circularized-strand can serve as primer to amplify the circularized strand without any external primer.
-
Citations
58 Claims
-
1. A method for indexing double-stranded nucleic acid fragments from a mixture of double-stranded nucleic acid fragments, said method comprises the steps of:
-
(a) treating nucleic acids with one or more restriction endonucleases selected from the group consisting of Type IIS restriction endonuclease and interrupted palindrome (IP) restriction endonuclease to generate fragments having at least one 3′
- or 5′
-protruding single strand;
(b) incubating a C-indexer with said fragments generated in step (a) to allow selective hybridization between complementary protruding single strand of said fragments and said C-indexers, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 3′
- or a 5′
-protruding single strand on said first strand and said second strand, wherein the lengths of the 3′
- or 5′
-protruding single strands of said C-indexer correspond to the lengths of the 3′
- or 5′
-protruding single strands of the fragments, wherein said C-indexer is selected from a collection of C-indexers whose 3′
- or 5′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T;
(c) adding ligase to selectively ligate said C-indexer to those fragments whose 3′
- or 5′
-protruding single strands are fully complementary to the 3′
- or 5′
-protruding protruding single strands of said C-indexer; and
(d) obtaining circular indexed nucleic acid fragments, wherein the first strand of said C-indexer is ligated to the fragments to form a closed circular strand, and wherein the second strand of said C-indexer is ligated to the fragments to form a discontinuous strand. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
-
-
12. A method of amplifying circular indexed nucleic acid fragments, said method comprises the steps of:
-
(a) treating nucleic acids with one or more restriction endonucleases selected from the group consisting of Type IIS restriction endonuclease and interrupted palindrome (IP) restriction endonuclease to generate fragments having at least one 3′
- or 5′
-protruding single strand;
(b) incubating a C-indexer with said fragments generated in step (a) to allow selective hybridization between complementary protruding single strand of said fragments and said C-indexers, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 3′
- or a 5′
-protruding single strand on said first strand and said second strand, wherein the lengths of the 3′
- or 5′
-protruding single strands of said C-indexer correspond to the lengths of the 3′
- or 5′
-protruding single strands of the fragments, wherein said C-indexer is selected from a collection of C-indexers whose 3′
- or 5′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T;
(c) adding ligase to selectively ligate said C-indexer to those fragments whose 3′
- or 5′
-protruding single strands are fully complementary to the 3′
- or 5′
-protruding protruding single strands of said C-indexer;
(d) obtaining circular indexed nucleic acid fragments, wherein the first strand of said C-indexer is ligated to the fragments to form a closed circular strand, and wherein the second strand of said C-indexer is ligated to the fragments to form a discontinuous strand; and
(e) amplifying the closed strand of said circular indexed nucleic acid fragments by rolling circle amplification. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
-
-
26. A kit for indexing double-stranded nucleic acid fragments from a mixture of double-stranded nucleic acid fragments, said kit comprising:
- (a) one or more Type IIS or IP restriction/endonucleases;
(b) a C-indexer, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 3′
- or a 5′
-protruding single strand on said first strand and said second strand, wherein the lengths of the 3′
- or 5′
-protruding single strands of said C-indexer correspond to the lengths of the 3′
- or 5′
-protruding single strands of nucleic acid fragments generated by Type IIS or IP restriction endonucleases digestion, wherein said C-indexer is selected from a collection of C-indexers whose 3′
- or 5′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T; and
(c) ligase and ligase buffer. - View Dependent Claims (27, 28, 29, 30)
- (a) one or more Type IIS or IP restriction/endonucleases;
-
31. A method for indexing single-stranded nucleic acid fragments from a mixture of single-stranded nucleic acid fragments, said method comprises the steps of:
-
(a) incubating a C-indexer with single-stranded nucleic acid fragments to allow selective hybridization between complementary protruding single strands of said C-indexer with the 5′
end and 3′
end of said single-stranded nucleic acid fragments;
wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 5′
- and a 3′
-protruding single strand on said second strand, wherein said C-indexer is selected from a collection of C-indexers whose 5′
- and 3′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T;
(b) adding ligase to selectively ligate said C-indexer with those single-stranded nucleic acid fragments whose 5′
- and 3′
-ends are fully complementary, respectively, to the 5′
- and 3′
-protruding single strands of said C-indexer; and
(c) obtaining circular indexed nucleic acid fragments, wherein the first strand of said C-indexer is ligated to the fragments to form a closed circular strand, wherein the second strand of the C-indexer is not closed. - View Dependent Claims (32, 33, 34, 35, 36, 37, 38)
-
-
39. A method of amplifying circular indexed single-stranded nucleic acid fragments, said method comprises the steps of:
-
(a) incubating a C-indexer with single-stranded nucleic acid fragments to allow selective hybridization between complementary protruding single strands of said C-indexer with the 5′
end and 3′
end of said single-stranded nucleic acid fragments;
wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 5′
- and a 3′
-protruding single strand on said second strand, wherein said C-indexer is selected from a collection of C-indexers whose 5′
- and 3′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T;
(b) adding ligase to selectively ligate the first strand of said C-indexer with those single-stranded nucleic acid fragments whose 5′
- and 3′
-ends are fully complementary, respectively, to the 5′
- and 3′
-protruding single strands of said C-indexer;
(c) obtaining circular indexed nucleic acid fragments, wherein the first strand of said C-indexer is ligated to the nucleic acid fragments to form a closed circular strand, wherein the second strand of the C-indexer is not closed; and
(d) amplifying the closed strand of said circular indexed nucleic acid fragments by rolling circle amplification. - View Dependent Claims (40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51)
-
-
52. A kit for indexing single-stranded nucleic acid fragments from a mixture of single-stranded nucleic acid fragments, said kit comprising:
- (a) a C-indexer, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 5′
- and a 3′
-protruding single strand on said second strand, wherein said C-indexer is selected from a collection of C-indexers whose 5′
- and 3′
-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T; and
(b) ligase and ligase buffer. - View Dependent Claims (53, 54, 55, 56, 57, 58)
- (a) a C-indexer, wherein said C-indexer is a double-stranded linear nucleic acid comprising a first strand and a second strand and a 5′
Specification