Complexity management of genomic DNA
First Claim
1. A method for selective amplification of a nucleic acid sample, the method comprising:
- fragmenting the nucleic acid sample using a first restriction enzyme and a second restriction enzyme and producing a digested nucleic acid sample comprising fragments;
ligating a double stranded first adaptor and a double stranded second adaptor to the fragments and producing ligated fragments, wherein the 3′
end of a first strand of the first adaptor is blocked from ligating to the 5′
ends of the fragments such that only a second strand of the first adaptor can ligate to the fragments, and wherein the 5′
end of a first strand of the second adaptor is blocked from ligating to the 3′
ends of the fragments such that only a second strand of the second adaptor can ligate to the fragments, wherein a subset of the ligated fragments comprises ligated fragments having a single strand which is ligated to the first adaptor at its 3′
end and the second adaptor at its 5′
end; and
subjecting the ligated fragments to amplification conditions, and selectively and exponentially amplifying the ligated fragments having a single strand which is ligated to the first adaptor at its 3′
end and the second adaptor at its 5′
end, thereby selectively amplifying the nucleic acid sample.
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Accused Products
Abstract
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.
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Citations
20 Claims
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1. A method for selective amplification of a nucleic acid sample, the method comprising:
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fragmenting the nucleic acid sample using a first restriction enzyme and a second restriction enzyme and producing a digested nucleic acid sample comprising fragments; ligating a double stranded first adaptor and a double stranded second adaptor to the fragments and producing ligated fragments, wherein the 3′
end of a first strand of the first adaptor is blocked from ligating to the 5′
ends of the fragments such that only a second strand of the first adaptor can ligate to the fragments, and wherein the 5′
end of a first strand of the second adaptor is blocked from ligating to the 3′
ends of the fragments such that only a second strand of the second adaptor can ligate to the fragments, wherein a subset of the ligated fragments comprises ligated fragments having a single strand which is ligated to the first adaptor at its 3′
end and the second adaptor at its 5′
end; andsubjecting the ligated fragments to amplification conditions, and selectively and exponentially amplifying the ligated fragments having a single strand which is ligated to the first adaptor at its 3′
end and the second adaptor at its 5′
end, thereby selectively amplifying the nucleic acid sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification