Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
First Claim
1. A method of linearly generating multiple copies of a nucleic acid sequence of interest from a template polynucleotide, said method comprising the steps of:
- (a) hybridizing a first oligonucleotide and a second oligonucleotide to non-overlapping portions of the target polynucleotide, wherein a portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said first and second oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest;
(b) optionally extending the first oligonucleotide with a DNA polymerase that lacks strand displacement activity;
(c) attaching the first oligonucleotide and second oligonucleotide to each other when hybridized to said target polynucleotide to generate an attached oligonucleotide combination product; and
(d) cleaving the RNA portion of the attached oligonucleotide combination product of (c) with an enzyme that cleaves RNA from an RNA/DNA hybrid such that the cleaved oligonucleotide combination product dissociates from the target polynucleotide,wherein the attached oligonucleotide combination product is of a size that when the RNA is cleaved from the attached oligonucleotide combination product, the cleaved attached oligonucleotide product dissociates from the target polynucleotide, without strand displacement by an enzyme, under essentially the same conditions as those for hybridization of the composite oligonucleotides to the target and the attachment of the hybridized oligonucleotides,(e) repeating steps (a)-(d) whereby multiple copies of the sequence of interest are produced, wherein said first or second oligonucleotide hybridize only to the template polynucleotide and not to said cleaved oligonucleotide combination product.
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Accused Products
Abstract
The present invention provides novel isothermal methods of generating multiple copies of, detecting and/or quantifying nucleic acid sequences of interest based on limited primer extension or attachment of oligonucleotide pairs using composite RNA/DNA primers. Methods for generating multiple copies of and/or detecting and/or quantifying nucleic acid sequences, wherein products of primer extension or attachment of oligonucleotide pairs comprising a cleavable portion are generated, and wherein cleavage of the products results in dissociation of cleaved products from target polynucleotides, are provided. The invention further provides compositions, kits and systems for practicing these methods.
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Citations
93 Claims
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1. A method of linearly generating multiple copies of a nucleic acid sequence of interest from a template polynucleotide, said method comprising the steps of:
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(a) hybridizing a first oligonucleotide and a second oligonucleotide to non-overlapping portions of the target polynucleotide, wherein a portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said first and second oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest;(b) optionally extending the first oligonucleotide with a DNA polymerase that lacks strand displacement activity; (c) attaching the first oligonucleotide and second oligonucleotide to each other when hybridized to said target polynucleotide to generate an attached oligonucleotide combination product; and (d) cleaving the RNA portion of the attached oligonucleotide combination product of (c) with an enzyme that cleaves RNA from an RNA/DNA hybrid such that the cleaved oligonucleotide combination product dissociates from the target polynucleotide, wherein the attached oligonucleotide combination product is of a size that when the RNA is cleaved from the attached oligonucleotide combination product, the cleaved attached oligonucleotide product dissociates from the target polynucleotide, without strand displacement by an enzyme, under essentially the same conditions as those for hybridization of the composite oligonucleotides to the target and the attachment of the hybridized oligonucleotides, (e) repeating steps (a)-(d) whereby multiple copies of the sequence of interest are produced, wherein said first or second oligonucleotide hybridize only to the template polynucleotide and not to said cleaved oligonucleotide combination product. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 86)
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16. A method of determining whether a nucleic acid sequence of interest is present or absent in a template polynucleotide, said method comprising the steps of:
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(a) hybridizing a first oligonucleotide and a second oligonucleotide to non-overlapping portions of the target polynucleotide, wherein the portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest;(b) optionally extending the first oligonucleotide with a DNA polymerase that lacks strand displacement-activity; (c) attaching the first oligonucleotide and second oligonucleotide to each other when hybridized to said target polynucleotide to generate an attached oligonucleotide combination product comprising a detectable identifying characteristic, whereby the attached oligonucleotide combination product is produced if the sequence of interest is present; and (d) cleaving the RNA portion of the attached oligonucleotide combination product of (c), if any, with an enzyme that cleaves RNA from an RNA/DNA hybrid such that the cleaved attached oligonucleotide combination product dissociates from the target polynucleotide, wherein the attached oligonucleotide combination product is of a size that when the RNA is cleaved the cleaved attached oligonucleotide combination product dissociates from the target polynucleotide, without strand displacement by an enzyme, under essentially the same conditions as those for attachment of the oligonucleotides, whereby detection of the cleaved attached oligonucleotide combination product comprising the detectable identifying characteristic indicates the presence of the sequence of interest, and wherein said first or second oligonucleotide hybridize only to the template polynucleotide and not to said cleaved oligonucleotide combination product. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 87, 88)
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41. A method of linearly generating multiple copies of a nucleic acid sequence of interest from a polynucleotide template comprising incubating a reaction mixture, said reaction mixture comprising:
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(a) a target polynucleotide; (b) a first oligonucleotide and a second oligonucleotide that hybridize to non-overlapping portions of a target polynucleotide, wherein the portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest, and wherein said first or second oligonucleotide hybridizes only to said target polynucleotide and not to any dissociated amplification products thereof;(c) optionally a DNA polymerase that lacks strand displacement activity; (d) an enzyme that cleaves RNA from an RNA/DNA hybrid; and (e) an agent that effects attachment of the first oligonucleotide and second oligonucleotide to each other when said oligonucleotides are hybridized to the target polynucleotide, wherein the incubation is under conditions that permits oligonucleotide hybridization, optionally oligonucleotide extension, RNA cleavage and attachment of the first oligonucleotide and the second oligonucleotide, such that an attached oligonucleotide combination product is produced, and wherein the attached oligonucleotide combination product is of a size such that cleavage of RNA from the attached oligonucleotide combination product results in dissociation of the cleaved attached oligonucleotide product without strand displacement by an enzyme. - View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 89)
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56. A method of determining whether a nucleic acid sequence of interest is present or absent in a target polynucleotide comprising incubating a reaction mixture, said reaction mixture comprising:
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(a) the target polynucleotide; (b) a first oligonucleotide and a second oligonucleotide that hybridize to non-overlapping portions of the target polynucleotide, wherein the portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest;(c) optionally a DNA polymerase that lacks strand displacement activity; (d) an enzyme that cleaves RNA from an RNA/DNA hybrid; and
(e) an agent that effects attachment of the first oligonucleotide and second oligonucleotide to each other when said oligonucleotides are hybridized to the target polynucleotide,wherein the incubation is under conditions that permit oligonucleotide hybridization, optionally oligonucleotide extension, RNA cleavage and attachment of the first oligonucleotide and the second oligonucleotide, such that an attached oligonucleotide combination product comprising a detectable identifying characteristic is produced, and wherein the attached oligonucleotide combination product is of a size such that cleavage of the RNA from the attached oligonucleotide combination product results in dissociating of the cleaved attached oligonucleotide combination product from the target polynucleotide, without strand displacement by an enzyme and wherein said first or second oligonucleotide hybridize only to the target polynucleotide and not to said cleaved oligonucleotide combination product, whereby detection of the cleaved attached oligonucleotide combination product comprising the detectable identifying characteristic indicates presence of the nucleotide sequence of interest. - View Dependent Claims (57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 90, 91)
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- 82. The method of 16 or 56, wherein said method comprises determining whether two or more different sequences of interest are present or absent in a sample, said method using a two or more sets of first and second oligonucleotides, wherein the detectable identifying characteristics of the cleaved oligonucleotide attachment products corresponding to two or more different sequences of interest are different from each other.
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84. A method of identifying an altered sequence of interest in a target polynucleotide, said method comprising incubating a reaction mixture, said reaction mixture comprising:
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(a) the target polynucleotide; (b) a first oligonucleotide and a second oligonucleotide that hybridize to non-overlapping portions of the target polynucleotide, wherein the portion of the target polynucleotide that is hybridizable to the first oligonucleotide is 3′
with respect to the portion of the target nucleotide that is hybridizable to the second oligonucleotide, wherein at least one of said oligonucleotides is a composite primer comprising an RNA portion and a DNA portion such that (i) if said first oligonucleotide is the composite primer, said RNA portion is at the 5′
end of said first oligonucleotide, and (ii) if said second oligonucleotide is the composite primer, said RNA portion is at the 3′
end of said second oligonucleotide, and wherein at least one of said oligonucleotides comprises a sequence that is hybridizable to at least one nucleotide of the sequence of interest;(c) optionally a DNA polymerase that lacks strand displacement activity; (d) an enzyme that cleaves RNA from an RNA/DNA hybrid; and (e) an agent that effects attachment of the first oligonucleotide and second oligonucleotide to each other when said oligonucleotides are hybridized to the target polynucleotide, wherein the incubation is under conditions that permit oligonucleotide hybridization, optionally oligonucleotide extension, RNA cleavage and attachment of the first oligonucleotide and the second oligonucleotide, such that an attached oligonucleotide combination product comprising a detectable identifying characteristic is produced, and wherein the attached oligonucleotide combination product is of a size that when RNA is cleaved from the attached oligonucleotide combination product, the cleaved attached oligonucleotide combination product dissociates from the target polynucleotide, without strand displacement by an enzyme and wherein said first or second oligonucleotide hybridize only to the template polynucleotide and not to said cleaved oligonucleotide combination product, wherein production of detectably fewer cleaved oligonucleotide attachment products from the target as compared to the amount of cleaved oligonucleotide attachment products produced from a reference template comprising the sequence of interest indicates that the target polynucleotide contains an altered sequence of interest. - View Dependent Claims (85, 92, 93)
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Specification