Capture moieties for nucleic acids and uses thereof
First Claim
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1. A unimolecular probe for hybridization to a molecule comprising a target nucleic acid sequence, the probe comprising:
- (i) a first nucleic acid sequence complementary to the target nuclic acid sequence and comprising a first portion and a second portion;
(ii) a second nucleic acid sequence complementary to the first portion of the first nucleic acid sequence and capable of hybridization therewith to form a first intramolecular duplex comprising a first hairpin structure under a defined set of conditions, the first intramolecular duplex including a portion of the first nucleic acid sequence complementary to the target nucleic acid sequence; and
(iii) third and fourth nucleic acid sequences, the third and fourth nucleic acid sequences being complementary to each other and linked to each other so as to hybridize to form a second intramolecular duplex comprising a second hairpin structure under said set of conditions,wherein the second portion of the first nucleic acid sequence comprises a single standed region covalently attached to the third nucleic acid sequence and is located between the first and second intramolecular duplexes, and under said set of conditions and in the presence of the target nucleic acid sequence, the single standed region acts as a nucleic acid sequence such that hybrization of the target nucleic acid sequence and first nucleic acid sequence disrupts the first intramolecular duplex to form an intermolecular duplex.
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Abstract
A unimolecular probe for hybridization to a molecule comprising a target nucleic acid sequence, the probe includes: a first nucleic acid sequence complementary to the target sequence (target-binding sequence); a second nucleic acid sequence complementary to a portion of the first nucleic acid sequence and capable of hybridization therewith to form a first intramolecular duplex. In use, the target and target-binding sequence hybridize to form a duplex. A probe can be used to detect a molecule containing the target sequence, act as a primer for synthesis or amplification, etc.
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Citations
20 Claims
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1. A unimolecular probe for hybridization to a molecule comprising a target nucleic acid sequence, the probe comprising:
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(i) a first nucleic acid sequence complementary to the target nuclic acid sequence and comprising a first portion and a second portion; (ii) a second nucleic acid sequence complementary to the first portion of the first nucleic acid sequence and capable of hybridization therewith to form a first intramolecular duplex comprising a first hairpin structure under a defined set of conditions, the first intramolecular duplex including a portion of the first nucleic acid sequence complementary to the target nucleic acid sequence; and (iii) third and fourth nucleic acid sequences, the third and fourth nucleic acid sequences being complementary to each other and linked to each other so as to hybridize to form a second intramolecular duplex comprising a second hairpin structure under said set of conditions, wherein the second portion of the first nucleic acid sequence comprises a single standed region covalently attached to the third nucleic acid sequence and is located between the first and second intramolecular duplexes, and under said set of conditions and in the presence of the target nucleic acid sequence, the single standed region acts as a nucleic acid sequence such that hybrization of the target nucleic acid sequence and first nucleic acid sequence disrupts the first intramolecular duplex to form an intermolecular duplex. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A composition comprising a mixture of a plurality of microparticles, each microparticle having a probe attached thereto for detection of a target nucleic acid sequence, each probe comprising a single molecule comprising:
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(i) a first tag sequence complementary to the target nucleic acid sequence; (ii) a nucleic acid second sequence complementary to a portion of the first tag sequence and capable of hybridization therewith to form a first intramolecular duplex under a defined set of conditions, the first intramolecular duplex including a portion of the first tag sequence complementary to the target nucleic acid sequence; wherein; (a) under said set of conditions, hybridization of the target nucleic acid sequence and first tag disrupts the intramolecular duplex to form an intermolecular duplex; (b) said mixture of a plurality of microparticles comprises at least ten different populations of microparticles, each different population of said microparticles having a said different probe attached thereto and being for detection of a said target nucleic acid sequence different from that of each other different population of microparticles; and (c) the first tag sequence of each said probe attached to a population of microparticles is identical to the first tag sequence of every other said probe attached to that population of microparticles.
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10. A repertoire of probes comprising a plurality of populations of unimolecular probes for hybridization to molecules, each molecule comprising a target nucleic acid sequence, each probe comprising:
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(i) a first nucleic acid sequence complementary to the target nucleic acid sequence; and (ii) a second nucleic acid sequence complementary to a first portion of the first nucleic acid sequence and capable of hybridization therewith to form a first intramolecular duplex under a defined set of conditions, the first intramolecular duplex including a portion of the first nucleic acid sequence complementary to the target nucleic acid sequence; and
wherein;(a) under said set of conditions and in the presence of the target nucleic acid sequence, hybridization of the target nucleic acid sequence and first nucleic acid sequence disrupts the first intramolecular duplex to form an intermolecular duplex; (b) each probe of a said population is the same as each other probe in that population; (c) for each probe of the repertoire, the first nucleic acid sequence of the probe is the same length, and; (d) the first nucleic acid sequence of each probe comprises a tag complement that is complementary to a tag sequence of the target nucleic acid and wherein there are at least ten populations of said tag complements, in the repertoire of probes, each said tag complement of one population of said probes having a sequence different from the tag complement sequence of tags in every other population of said probes in the repertoire.
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11. A unimolecular probe for hybridization to a molecule comprising a target nucleic acid sequence, the probe comprising:
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(i) a first nucleic acid sequence complementary to the target nucleic acid sequence; (ii) a second nucleic acid sequence complementary to a first portion of the first nucleic acid sequence and capable of hybridization therewith to form a first intramolecular duplex comprising a first hairpin structure under a defined set of conditions, the first intramolecular duplex including a portion of the first nucleic acid sequence complementary to the target nucleic acid sequence; and (iii) third and fourth nucleic acid sequences being complementary to each other and linked to each other so as to hybridize to form a second intramolecular duplex comprising a second hairpin structure under said set of conditions; wherein one end of the first nucleic acid sequence is covalently attached to the third nucleic acid sequence, and under said set of conditions and in the presence of the target nucleic acid sequence, hybridization of the target nucleic acid sequence and first nucleic acid sequence disrupts the first intramolecular duplex to form an intermolecular duplex. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification