Detection of polymorphisms
First Claim
1. A process for producing a nucleic acid fingerprint, the process comprising:
- fragmenting a starting nucleic acid, thus producing a plurality of adapter ligatable nucleic acid fragments having ends that are compatible to at least one adapter;
performing a ligation reaction between said ends of said plurality of adapter ligatable nucleic acid fragments and the at least one adapter, thus producing adapter-ligated nucleic acid fragments;
amplifying said adapter-ligated nucleic acid fragments with at least one amplification primer that is essentially complementary to a nucleotide sequence of said at least one adapter, thus producing amplified adapter-ligated nucleic acid fragments; and
generating a nucleic acid fingerprint from said amplified adapter-ligated nucleic acid fragments.
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Abstract
The present invention provides methods for producing a nucleic acid fingerprint and methods for detecting sequence polymorphisms between one or more genomes. The methods include fragmenting a nucleic acid into nucleic acid fragments with ends that are compatible to ligation with at least one adapter, performing a ligation reaction between the compatible ends of the nucleic acid fragments and at least one adapter, amplifying the nucleic acid fragments by using at least one amplification primer, and generating a nucleic acid fingerprint from the amplified fragments. A method according to the present invention permits high-resolution fingerprinting while maintaining stringency in a PCR reaction. In another aspect, the invention also provides a kit for preparing nucleic acid fingerprints according to methods of the invention.
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Citations
28 Claims
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1. A process for producing a nucleic acid fingerprint, the process comprising:
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fragmenting a starting nucleic acid, thus producing a plurality of adapter ligatable nucleic acid fragments having ends that are compatible to at least one adapter;
performing a ligation reaction between said ends of said plurality of adapter ligatable nucleic acid fragments and the at least one adapter, thus producing adapter-ligated nucleic acid fragments;
amplifying said adapter-ligated nucleic acid fragments with at least one amplification primer that is essentially complementary to a nucleotide sequence of said at least one adapter, thus producing amplified adapter-ligated nucleic acid fragments; and
generating a nucleic acid fingerprint from said amplified adapter-ligated nucleic acid fragments. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 28)
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17. A method for detecting sequence polymorphisms between one or more genomes, the method comprising:
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producing at least one nucleic acid fingerprint from one or more genomes with a process, the process comprising;
fragmenting the one or more genomes, thus producing a plurality of adapter ligatable nucleic acid fragments having ends that are compatible to at least one adapter;
performing a ligation reaction between said ends of said plurality of adapter ligatable nucleic acid fragments and the at least one adapter thus producing adapter-ligated nucleic acid fragments;
amplifying said adapter-ligated nucleic acid fragments with at least one amplification primer that is essentially complementary to a nucleotide sequence of said at least one adapter, thus producing amplified adapter-ligated nucleic acid fragments; and
generating at least one nucleic acid fingerprint from said amplified adapter-ligated nucleic acid fragments; and
comparing the at least one nucleic acid fingerprint for the presence of, the absence of, or differences between said amplified adapter-ligated nucleic acid fragments to determine the presence of sequence polymorphisms. - View Dependent Claims (18, 19, 20, 21, 22)
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23. A method for identifying an unknown organism, the method comprising:
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producing a nucleic acid fingerprint from said unknown organism with a process, the process comprising;
fragmenting a starting nucleic acid thus producing a plurality of adapter ligatable nucleic acid fragments having ends that are compatible to at least one adapter;
performing a ligation reaction between said ends of said plurality of adapter ligatable nucleic acid fragments and the at least one adapter, thus producing adapter-ligated nucleic acid fragments;
amplifying said adapter-ligated nucleic acid fragments with at least one amplification primer that is essentially complementary to a nucleotide sequence of said at least one adapter, thus producing amplified adapter-ligated nucleic acid fragments; and
generating a nucleic acid fingerprint from said amplified adapter-ligated nucleic acid fragments;
comparing said nucleic acid fingerprint with at least one known nucleic acid fingerprint produced from at least one known organism with said process; and
establishing an identity of said unknown organism on the basis of similarity of said nucleic acid fingerprint from said unknown organism with said at least one known nucleic acid fingerprint from said at least one known organism.
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26. A kit comprising:
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at least one set of at least two different restriction endonuclease enzymes capable of producing restriction fragments having ends that are compatible with a single type of adapter; and
at least said one single type of adapter. - View Dependent Claims (27)
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Specification