Amplification of RNA sequences using composite RNA-DNA primers and strand displacement
First Claim
1. A method of generating multiple copies of the complementary sequence of an RNA sequence of interest, said method comprising:
- (a) extending a first DNA primer hybridized to a target RNA with an RNA-dependent DNA polymerase, wherein said first primer comprises a 3′
portion which hybridizes to the target RNA and a 5′
portion which does not hybridize to the target RNA, whereby a complex comprising a first primer extension product and the target RNA is produced;
(b) cleaving RNA in the complex of step (a) with an enzyme that cleaves RNA from an RNA/DNA hybrid;
(c) extending a second primer hybridized to the first primer extension product with a DNA-dependent DNA polymerase whereby a complex comprising the first primer extension product and a second primer extension product is produced;
(d) denaturing the complex of step (c);
(e) hybridizing, a composite primer to a single stranded second primer extension product resulting from step (d), wherein the composite primer comprises an RNA portion and a 3′
DNA portion, wherein the composite primer hybridizes to a sequence in said single stranded primer extension product which is complementary to a 5′
portion of the first DNA primer;
(f) extending the composite primer with a DNA-dependent DNA polymerase, whereby a complex comprising a primer extension product and the second primer extension product is formed;
(g) cleaving RNA in the complex of step (f) with an enzyme that cleaves RNA from an RNA/DNA hybrid, such that another composite primer hybridizes to the second primer extension product and repeats primer extension by strand displacement,whereby multiple copies of the complement of the RNA sequence of interest are produced.
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Abstract
The invention provides methods for linear amplification of RNA that has an RNA sequence of interest. The methods are based on using a first DNA primer with a 3′ portion that is complementary to the RNA and a 5′ portion that is not complementary to the RNA in that region. The primer and an RNA-dependent DNA polymerase are used to make a DNA-RNA complex from the RNA. The RNA is cleaved from the complex with an enzyme, then a second primer and a DNA-dependent DNA polymerase are used to make double stranded DNA. The double stranded DNA is then denatured, and an RNA-DNA composite primer, a DNA-dependent DNA polymerase, and strand displacement are used to isothermally produce multiple copies of the complementary sequence to the RNA sequence of interest.
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Citations
14 Claims
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1. A method of generating multiple copies of the complementary sequence of an RNA sequence of interest, said method comprising:
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(a) extending a first DNA primer hybridized to a target RNA with an RNA-dependent DNA polymerase, wherein said first primer comprises a 3′
portion which hybridizes to the target RNA and a 5′
portion which does not hybridize to the target RNA, whereby a complex comprising a first primer extension product and the target RNA is produced;(b) cleaving RNA in the complex of step (a) with an enzyme that cleaves RNA from an RNA/DNA hybrid; (c) extending a second primer hybridized to the first primer extension product with a DNA-dependent DNA polymerase whereby a complex comprising the first primer extension product and a second primer extension product is produced; (d) denaturing the complex of step (c); (e) hybridizing, a composite primer to a single stranded second primer extension product resulting from step (d), wherein the composite primer comprises an RNA portion and a 3′
DNA portion, wherein the composite primer hybridizes to a sequence in said single stranded primer extension product which is complementary to a 5′
portion of the first DNA primer;(f) extending the composite primer with a DNA-dependent DNA polymerase, whereby a complex comprising a primer extension product and the second primer extension product is formed; (g) cleaving RNA in the complex of step (f) with an enzyme that cleaves RNA from an RNA/DNA hybrid, such that another composite primer hybridizes to the second primer extension product and repeats primer extension by strand displacement, whereby multiple copies of the complement of the RNA sequence of interest are produced. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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Specification