Methods and compositions for identifying nucleic acid molecules using nucleolytic activities and hybridization
First Claim
1. A method of identifying one or more nucleic acid molecules, comprising:
- a) contacting at least one probe nucleic acid molecule with a survey population of nucleic acid molecules under conditions that promote hybridization between nucleic acid molecules to generate a probe-survey population mixture of nucleic acid molecules;
b) treating said probe-survey population mixture of nucleic acid molecules with a nucleolytic acitivity, such that nucleolytic activity-sensitive nucleic acid molecules are digested, to generate a population of nucleolytic activity-protected nucleic acid molecules;
c) contacting said population of nucleolytic activity-protected nucleic acid molecules with a solid support comprising one or more attached nucleic acid molecules under conditions that promote hybridization between nucleic acid molecules to generate attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes; and
d) identifying one or more of said attached nucleic acid molecules or one or more of said nucleolytic activity-protected nucleic acid molecules in one or more attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes.
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Abstract
The present invention recognizes that identifying genes expressed during developmental processes, stress responses, and disease states can advance understanding of these biological functions, and can contribute to identifying targets for therapeutic drugs. In addition, the present invention recognizes that rapid and reliable profiling of genetic variations, such as mutations and SNPs, is of increasing importance to diagnostics, prognostics, forensics, heredity determinations, and pharmacogenetics.
One aspect of the present invention provides a method of identifying one or more nucleic acid molecules that are expressed under a given set of conditions based on their complementarity to known sequences, or one or more mutations or SNPs in a population of nucleic acid molecules. The method includes: contacting at least one probe nucleic acid molecule with a survey population of nucleic acid molecules under conditions that promote nucleic acid hybridization to generate a probe-survey population mixture of nucleic acid molecules, treating the probe-survey population mixture of nucleic acid molecules with a nucleolytic activity, such that nucleolytic activity-sensitive nucleic acid molecules are digested, and contacting the resulting mixture of nucleolytic activity-protected nucleic acid molecules with a solid support comprising one or more attached nucleic acid molecules to generate attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes, and identifying one or more of the attached nucleic acid molecules or one or more of the nucleolytic activity-protected nucleic acid molecules in one or more attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes.
Another aspect of the present invention provides compositions that can be used for carrying out the methods of the present invention. Such compositions can be in the form of kits, and comprise a solid support comprising a first population of attached nucleic acids, and a second population of nucleic acids not attached to the solid support.
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Citations
81 Claims
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1. A method of identifying one or more nucleic acid molecules, comprising:
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a) contacting at least one probe nucleic acid molecule with a survey population of nucleic acid molecules under conditions that promote hybridization between nucleic acid molecules to generate a probe-survey population mixture of nucleic acid molecules;
b) treating said probe-survey population mixture of nucleic acid molecules with a nucleolytic acitivity, such that nucleolytic activity-sensitive nucleic acid molecules are digested, to generate a population of nucleolytic activity-protected nucleic acid molecules;
c) contacting said population of nucleolytic activity-protected nucleic acid molecules with a solid support comprising one or more attached nucleic acid molecules under conditions that promote hybridization between nucleic acid molecules to generate attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes; and
d) identifying one or more of said attached nucleic acid molecules or one or more of said nucleolytic activity-protected nucleic acid molecules in one or more attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 57, 58, 59, 60, 61, 62, 63)
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44. A method of identifying one or more nucleic acid molecules, comprising:
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a) contacting at least one probe nucleic acid molecule with a survey population of nucleic acid molecules to generate a mixture of nucleic acid molecules under conditions that promote hybridization between complementary nucleic acids;
b) treating said mixture of nucleic acid molecules with a nucleolytic activity, such that nucleolytic acitivity-sensitive nucleic acid molecules are digested, to generate a population of nucleolytic activity-protected nucleic acid molecules;
c) contacting said population of nucleolytic activity-protected nucleic acid molecules with a solid support comprising one or more attached nucleic acid molecules to generate attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes;
d) treating said attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes with a nucleolytic activity, such that nucleic acid molecules having single-stranded regions are cleaved; and
e) identifying one or more of said attached nucleic acids that remain bound to said solid support. - View Dependent Claims (45, 46, 47, 48, 49, 50, 51, 52)
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53. A method of identifying one or more nucleic acid molecules, comprising:
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a) contacting a first set of probe nucleic acid molecule with a first survey population of nucleic acid molecules to generate a first probe-survey population mixture of nucleic acid molecules under conditions that promote nucleic acid hybridization;
b) contacting a second set of probe nucleic acid molecules with a second survey population of nucleic acid molecules to generate a second probe-survey population mixture of nucleic acid molecules under conditions that promote nucleic acid hybridization;
c) treating said first and second mixtures of probe-survey population nucleic acid molecules with a nucleolytic activity, such that nucleolytic activity-sensitive nucleic acid molecules are digested, generating two populations of nucleolytic activity-protected nucleic acid molecules;
c) contacting said two populations of nucleolytic activity-protected nucleic acid molecules with a solid support comprising one or more attached nucleic acids to generate attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes; and
d) identifying one or more of said attached nucleic acids that are bound to one or more members of one or both of said two populations of nucleolytic activity-protected nucleic acids in one or more attached nucleic acid molecule/nucleolytic activity-protected nucleic acid molecule complexes. - View Dependent Claims (54, 55, 56)
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64. A composition, comprising:
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a) a solid support comprising a first population of at least two attached nucleic acid molecules immobilized thereon;
b) a second population of at least two nucleic acid molecules that are not bound to a solid support, wherein a majority of the members of said first population of attached nucleic acid molecules are at least partially complementary to one or more members of said second population of probe nucleic acid molecules. - View Dependent Claims (65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81)
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Specification