METHODS FOR FRAGMENTATION AND LABELING OF NUCLEIC ACIDS
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Abstract
The invention provides methods, compositions, and kits for fragmentation and labeling of nucleic acids. More particularly, the invention relates to methods for fragmentation of nucleic acids to produce fragments with 3′ end hydroxyl groups within a desired size range. In methods of the invention, nucleic acids are fragmented at abasic sites to produce fragments with blocked 3′ ends. The 3′ ends are unblocked to produce polynucleotide fragments with hydroxyl groups at their 3′ ends. Methods, kits, and compositions for carrying out fragmentation of a polynucleotide template in a single reaction mixture to yield fragments with 3′-hydroxyl ends within the desired size range are disclosed.
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Citations
131 Claims
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1-74. -74. (canceled)
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75. A method for generating a polynucleotide fragment, within a desired size range and comprising a hydroxyl group at the 3′
- end, from a polynucleotide comprising an abasic site, said method comprising;
(a) contacting said polynucleotide comprising an abasic site with a reaction mixture comprising; i. a chemical capable of fragmenting a phosphodiester backbone of a polynucleotide at an abasic site, whereby generating a polynucleotide fragment within the desired size range and comprising a blocked 3′
end; andii. an enzyme capable of unblocking the blocked 3′
end of said fragment, whereby generating a polynucleotide fragment within the desired size range and comprising a hydroxyl group at the 3′
end. - View Dependent Claims (76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116)
- end, from a polynucleotide comprising an abasic site, said method comprising;
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117. A method for fragmenting a polynucleotide comprising an abasic site to generate fragments within a desired size range, said method comprising:
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(a) chemically cleaving a phosphodiester backbone of a polynucleotide comprising an abasic site at the abasic site, whereby a polynucleotide fragment within the desired size range and comprising a blocked 3′
end is generated; and(b) contacting the polynucleotide fragment with an enzyme capable of unblocking the blocked 3′
end of said fragment, whereby a polynucleotide fragment within the desired size range and comprising a 3′
end hydroxyl group is generated;wherein (a) and (b) are performed simultaneously and performed in the same reaction mixture.
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118. A composition or kit comprising:
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(a) a chemical agent capable of cleaving a phosphodiester backbone at an abasic site to produce a polynucleotide fragment with a blocked 3′
end within a desired size range; and(b) an enzyme capable of unblocking a blocked 3′
end to generate a polynucleotide comprising a 3′
hydroxyl group. - View Dependent Claims (119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129)
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- 130. A population of single-stranded polynucleotide fragments of a desired size range representative of a complete genome or complete transcriptome of an organism wherein each of said fragments comprises a hydroxyl group at the 3′
Specification