Indexing linkers
First Claim
1. A method for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said method comprising:
- (i) treating DNA with a restriction endonuclease which is selected from the group consisting of Type IIS restriction endonucleases and restriction endonucleases which recognize interrupted palindromic sequences, to produce DNA fragments having at least one 3'"'"'- or 5'"'"'-protruding single strand;
(ii) adding said DNA fragments to a set of indexing linkers;
each said indexing linker being a DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of said restriction endonuclease, wherein said set comprises a collection of said indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T, and wherein each indexing linker in said set is physically separated from every other indexing linker in said set;
(iii) contacting said DNA fragments added to said set of indexing linkers with a DNA ligase to cause a selective ligation of those indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands are fully complementary to the 3'"'"'- or 5'"'"'-protruding single strands of the DNA fragments; and
(iv) obtaining indexed DNA fragments.
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Abstract
Synthetic nucleic acid molecules are provided which are called indexing linkers and which can be selectively linked to unknown, or non-identical cohesive ends of nucleic acid fragments. Such indexing linkers are useful for the selective isolation, identification, amplification, labelling, and modification, of nucleic acid fragments, especially subsets of such fragments released by cleavage using Type IIS restriction endonucleases or restriction endonucleases recognizing interrupted palindromic sequences. Sets of such indexing linker molecules are described which are useful for indexing fragments released by cleavage of a genome. Methods are described for distinguishing such fragments using said indexing linker molecules for effecting detection, or further modification of such fragments; and for amplifying such fragments by the polymerase chain reaction.
453 Citations
33 Claims
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1. A method for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said method comprising:
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(i) treating DNA with a restriction endonuclease which is selected from the group consisting of Type IIS restriction endonucleases and restriction endonucleases which recognize interrupted palindromic sequences, to produce DNA fragments having at least one 3'"'"'- or 5'"'"'-protruding single strand; (ii) adding said DNA fragments to a set of indexing linkers;
each said indexing linker being a DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of said restriction endonuclease, wherein said set comprises a collection of said indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T, and wherein each indexing linker in said set is physically separated from every other indexing linker in said set;(iii) contacting said DNA fragments added to said set of indexing linkers with a DNA ligase to cause a selective ligation of those indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands are fully complementary to the 3'"'"'- or 5'"'"'-protruding single strands of the DNA fragments; and (iv) obtaining indexed DNA fragments. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A method for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said method comprising:
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(i) treating DNA with a restriction endonuclease which is a member selected from the group consisting of Type IIS restriction endonucleases and restriction endonucleases which recognize interrupted palindromic sequences, to produce DNA fragments having at least one 3'"'"'- or 5'"'"'-protruding single strand; (ii) adding said DNA fragments to two sets of indexing linkers, wherein; each member of a set of indexing linkers is a common DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of said restriction endonuclease, said 3'"'"'- or 5'"'"'-protruding single strand of the member of a set encoding collectively up to all permutations and combinations of nucleotides, A, C, G and T;
said members of a set being physically separated from each other;wherein the common DNA duplex of each of said two sets of indexing linkers is different; and
wherein at least one indexing linker from one set of indexing linkers is physically present with at least one indexing linker from the other set of indexing linkers;(iii) contacting said DNA fragments added to said two sets of indexing linkers with a DNA ligase to cause a selective ligation of those indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands are fully complementary to the 3'"'"'or 5'"'"'-protruding single strands of the DNA fragments; and (iv) obtaining indexed DNA fragments. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
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25. A kit for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments,
said kit comprising two sets of indexing linkers, wherein: -
(i) each member of a set of indexing linkers is a common DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of a 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of a Type IIS restriction endonuclease or restriction endonuclease recognizing interrupted palindromic sequences; (ii) said 3'"'"'- or 5'"'"'-protruding single strands of the members of at least one set encode collectively at least eight different permutations and combinations of the nucleotides, A, C, G and T; (iii) said members of a set being physically separated from each other on the basis of the identity of their 3'"'"'- or 5'"'"'-protruding end; (iv) said two sets of indexing linkers being distinguished from each other on the basis of the identity of their DNA duplexes; and (v) said indexing linkers being arranged in pairwise combinations on the basis of the identity of their DNA duplexes. - View Dependent Claims (26, 27, 28, 29)
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30. A method for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said method comprising:
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(i) treating DNA with a restriction endonuclease which is a member selected from the group consisting of Type IIS restriction endonucleases and restriction endonucleases which recognize interrupted palindromic sequences, to produce DNA fragments having at least one 3'"'"'- or 5'"'"'-protruding single strand; (ii) combining said DNA fragments with a set of indexing linkers and DNA ligase; wherein each said indexing linker being a DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of said restriction endonuclease, wherein said set comprises a collection of said indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T, and wherein said indexing linkers are physically separated from each other; such that indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands are fully complementary to said 3'"'"'- or 5'"'"'-protruding single strands of each DNA fragments are ligated; and (iii) obtaining indexed DNA fragments.
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31. A method for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said method comprising:
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(i) treating DNA with a restriction endonuclease which is a member selected from the group consisting of Type IIS restriction endonucleases and restriction endonucleases which recognize interrupted palindromic sequences, to produce DNA fragments having at least one 3'"'"'- or 5'"'"'-protruding single strand; (ii) combining said DNA fragment with a set of indexing linkers and DNA ligase; wherein each said indexing linker being a DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the length of the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of said restriction endonuclease, wherein said set comprises a collection of said indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands collectively encode up to all possible permutations and combinations of nucleotides, A, C, G and T, and wherein said indexing linkers are physically separated from each other; such that indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands are fully complementary to said 3'"'"'- or 5'"'"'-protruding single strands of each DNA fragments are ligated to form a mixture of indexed dsDNA fragments; and (iii) amplifying at least one of said indexed DNA fragments. - View Dependent Claims (32)
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33. In a polymerase chain reaction kit comprising:
- heat source, oligonucleotide primers, DNA polymerase and a mixture of all four deoxynucleotide precursors, wherein the improvement comprises;
a panel for obtaining indexed DNA fragments from a mixture of DNA fragments, for identifying, isolating, mapping, amplifying, or sequencing said fragments, said panel comprising a set of indexing linkers, each said indexing linker being a DNA duplex having one 3'"'"'- or 5'"'"'-protruding single strand of a length corresponding to the 3'"'"'- or 5'"'"'-protruding single strand of the cleavage site of a Type IIS restriction endonuclease or a restriction endonuclease recognizing interrupted palindromic sequences, wherein said set comprises a collection of indexing linkers whose 3'"'"'- or 5'"'"'-protruding single strands collectively encode up to all possible permutations and combinations of the nucleotides, A, C, G and T, and wherein said indexing linkers are physically separated from each other on the basis of the identity of their 3'"'"'- or 5'"'"'-protruding single strand.
- heat source, oligonucleotide primers, DNA polymerase and a mixture of all four deoxynucleotide precursors, wherein the improvement comprises;
Specification