DNA amplification and subtraction techniques
DCFirst Claim
1. A method of isolating duplex DNA fragments which are present in a mixture of different-sequence duplex DNA fragments derived from a positive source, but absent from a mixture of different-sequence duplex DNA fragments derived from a negative source, said method comprisingattaching a double-strand linker to the positive-source fragments, and separately, to the negative-source fragments, by ligating the linker to both strands of said positive-source and negative-source fragments, at both ends of said positive-source and negative-source fragments,amplifying the number of each linker-carrying fragment in each fragment mixture by successively repeating the steps of (i) denaturing the fragments to produce single fragment strands with linker regions at each strand end, (ii) hybridizing the single strands with a single-strand primer whose sequence is complementary to the linker region at one end of each strand, to form a strand/primer complex, and (iii) converting the strand/primer complexes to double-strand fragments in the presence of polymerase and deoxynucleotides,denaturing the amplified fragments in the two amplified fragment mixtures and hybridizing the denatured fragments in the two mixtures under conditions in which the linker regions associated with the positive-source strands do not hybridize with the linker regions associated with the negative-source strands, andselectively isolating DNA species which are not hybridized with DNA fragment strands from the negative source.
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Abstract
A method of isolating genomic or RNA-derived duplex fragments which are unique to one of two fragment mixtures. The fragments in positive-source and negative-source mixtures are separately equipped with end linkers, and each mixture is amplified by successive primed-strand replications, using a single primer which is homologous to the associated linker. The second-source linker is biotinylated, and the fragments in this mixture are hybridized in molar excess with the fragments in the positive-source mixture. DNA species which are not hybridized with the biotinylated species, i.e., species that are unique to the positive-source mixture, are isolated after removal of hybridized species by affinity chromatography. Also disclosed is a method of amplifying a mixture of DNA fragments by repeated linker/primer replication.
171 Citations
14 Claims
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1. A method of isolating duplex DNA fragments which are present in a mixture of different-sequence duplex DNA fragments derived from a positive source, but absent from a mixture of different-sequence duplex DNA fragments derived from a negative source, said method comprising
attaching a double-strand linker to the positive-source fragments, and separately, to the negative-source fragments, by ligating the linker to both strands of said positive-source and negative-source fragments, at both ends of said positive-source and negative-source fragments, amplifying the number of each linker-carrying fragment in each fragment mixture by successively repeating the steps of (i) denaturing the fragments to produce single fragment strands with linker regions at each strand end, (ii) hybridizing the single strands with a single-strand primer whose sequence is complementary to the linker region at one end of each strand, to form a strand/primer complex, and (iii) converting the strand/primer complexes to double-strand fragments in the presence of polymerase and deoxynucleotides, denaturing the amplified fragments in the two amplified fragment mixtures and hybridizing the denatured fragments in the two mixtures under conditions in which the linker regions associated with the positive-source strands do not hybridize with the linker regions associated with the negative-source strands, and selectively isolating DNA species which are not hybridized with DNA fragment strands from the negative source.
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12. A method of amplifying a mixture of different sequence duplex DNA fragments, comprising
attaching a double-strand linker to the fragments, by ligating the linkers to both strands of the fragments, at both fragment ends, denaturing the fragments to produce single fragment strands with linker regions at both strand ends, hybridizing the single strands with a primer whose sequence is complementary to a linker region on each fragment strand, to form strand/primer complexes, converting the strand/primer complexes to double-strand fragments in the presence of polymerase and deoxynucleotides, and repeating said denaturing, hybridizing, and converting steps until a desired degree of amplification is achieved.
Specification