Labeling by simultaneous ligation and restriction
First Claim
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1. A method for extending DNA fragments with a ligand comprising:
- combining in a reaction mixture said fragments in the simultaneous presence of ligase and a restriction enzyme which cuts in or near the recognition site, with dsDNA comprising said ligand and having a terminus complementary to a terminus of said fragments, wherein said fragments have predetermined termini as a result of digestions with said restriction enzyme, said fragments have terminal phosphates and said complementary termini of said dsDNA lack a terminal phosphate and ligation of said dsDNA results in sequence different from the sequence recognized and cleaved by said restriction enzyme,whereby said fragments and dsDNA are covalently joined.
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Abstract
Termini of restricted double-stranded DNA fragments are modified by ligating the fragments with terminal phosphate-free double-stranded oligonucleotides having a complementary terminus in the presence of a restriction enzyme and a ligase, where joining of the complementary ends results in loss of the restriction enzyme recognition sequence.
108 Citations
12 Claims
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1. A method for extending DNA fragments with a ligand comprising:
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combining in a reaction mixture said fragments in the simultaneous presence of ligase and a restriction enzyme which cuts in or near the recognition site, with dsDNA comprising said ligand and having a terminus complementary to a terminus of said fragments, wherein said fragments have predetermined termini as a result of digestions with said restriction enzyme, said fragments have terminal phosphates and said complementary termini of said dsDNA lack a terminal phosphate and ligation of said dsDNA results in sequence different from the sequence recognized and cleaved by said restriction enzyme, whereby said fragments and dsDNA are covalently joined. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method for labeling DNA fragments with a ligand or radionuclide comprising:
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combining said fragments in the simultaneous presence of ligase and a restriction enzyme which cuts in or near the recognition site, with ligand or radionuclide labeled dsDNA of fewer than about 200 bp and having a terminus complementary to a terminus of said fragments, wherein said fragments have predetermined termini as a result of digestion with said restriction enzyme, said fragments have terminal phosphates and said complementary termini of said dsDNA lack a terminal phosphate and ligation of said dsDNA results in a sequence different from the sequence recognized and cleaved by said restriction enzyme, whereby said fragments and dsDNA are covalently joined to label said fragments. - View Dependent Claims (8, 9, 10, 11)
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12. A labeling composition for binding to a restricted dsDNA fragment resulting in loss of the restriction recognition site by simultaneous restriction and ligation, said composition comprising:
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a bridging strand and first and second strands hybridized to said bridging strand, wherein said strands hybridize contiguously to said bridging strand; said first strand is a labeling strand providing for a double-stranded DNA sequence of interest and a fluorescent label; said second strand is an adapter strand hybridizing to said bridging strand to provide a cohesive end or blunt end with said bridging strand, and wherein said adapter strand contains a particular sequence necessary to destroy the recognition site of a restriction enzyme of interest.
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Specification