Isothermal nucleic acid amplification methods and compositions
First Claim
Patent Images
1. A method for creating a partial RNA-DNA heteroduplex comprising:
- a) providing a template nucleic acid in a reaction mixture;
b) adding a first primer to said reaction mixture and generating a first primer extension product with said first primer;
c) adding a second primer that is an RNA-DNA chimeric primer to said reaction mixture;
d) adding a DNA polymerase to said reaction mixture, wherein said DNA polymerase comprises RNA-dependent polymerase activity; and
e) degrading a portion of said first primer extension product that is not hybridized to a second primer extension product in a double-stranded first and second primer extension product complex by adding an exonuclease to said reaction mixture;
whereby said partial RNA-DNA heteroduplex is created.
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Abstract
Methods and compositions are provided related to the amplification of target polynucleotide sequences as well as total RNA and total DNA amplification. In some embodiments, the methods and compositions also allow for the immobilization and capture of target polynucleotides with defined 3′ and or 5′ sequences to solid surfaces. The polynucleotides attached to the solid surfaces can be amplified or eluted for downstream processing. In some cases, nucleotides attached to solid surfaces can be used for high throughput sequencing of nucleotide sequences related to target DNA or target RNA.
247 Citations
40 Claims
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1. A method for creating a partial RNA-DNA heteroduplex comprising:
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a) providing a template nucleic acid in a reaction mixture; b) adding a first primer to said reaction mixture and generating a first primer extension product with said first primer; c) adding a second primer that is an RNA-DNA chimeric primer to said reaction mixture; d) adding a DNA polymerase to said reaction mixture, wherein said DNA polymerase comprises RNA-dependent polymerase activity; and e) degrading a portion of said first primer extension product that is not hybridized to a second primer extension product in a double-stranded first and second primer extension product complex by adding an exonuclease to said reaction mixture; whereby said partial RNA-DNA heteroduplex is created.
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2. A method for producing amplified nucleic acid comprising:
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a) providing a template nucleic acid; b) annealing an all-DNA first primer or set of all-DNA first primers comprising a 3′
end whereby a portion of the 3′
end comprises a template annealing sequence and a 5′
tail sequence whereby a portion of the tail sequence comprises a sequence (A);c) extending said first primer or set of first primers with a DNA polymerase to create a first primer extension product or first set of primer extension products; d) dissociating the primer extension product or products from the template nucleic acid; e) annealing a second primer comprising a 3′
DNA sequence and a 5′
RNA sequence, whereby a portion of the 3′
end comprises a randomized annealing sequence and a portion of the 5′
end comprises sequence (A) or a sequence (B), to said primer extension product or products, wherein sequence (B) is different from sequence (A); andf) extending said second primer with a DNA polymerase to create a second primer extension product or set of second primer extension products to produce a double stranded DNA product or products comprising an A-A′
DNA duplex at one end, wherein (A′
) is the complement of (A). - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 32, 33, 34, 35, 36, 37, 38, 39)
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20. A method for producing amplified nucleic acid comprising:
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a) providing a template nucleic acid; b) annealing an all-DNA first primer or a set of all-DNA first primers comprising a 3′
end whereby a portion of the 3′
end comprises a template annealing sequence and a 5′
end whereby a portion of the 5′
end comprises a DNA tail sequence (A) that is complementary to a sequence (A′
);c) extending said first primer or set of first primers with a DNA polymerase to create a primer extension product or set of primer extension products; d) dissociation of the primer extension product or products from the template nucleic acid; e) annealing a second primer comprising a 3′
DNA end, whereby a portion of the 3′
end comprises a random template annealing sequence, and a 5′
RNA end, whereby a portion of the 5′
end comprises an RNA tail sequence (A) that is complementary to the sequence (A′
), to said primer extension product or products or to said template nucleic acid;f) extending said second primer with a DNA polymerase to create a second primer extension product or set of second primer extension products, wherein a portion of the 3′
end of said second primer extension product or products comprises sequence (A′
), wherein (A′
) is the complement of (A); andg) denaturing and annealing the second primer extension product or set of second primer extension products to form a stem loop structure comprising an A-A′
RNA-DNA heteroduplex. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40)
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Specification