# US 2010/0167274 A1 · Methods and kits for identifying nucleic acid sequences > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2010/0167274 A1 - Document ID: US20100167274A1 - Status: Published application - Kind: A1 - Application number: 11/988,714 - Filed: 2006-07-16 - Published: 2010-07-01 - Earliest claimed: 2005-07-15 - Inventors: Joel Stavans; Dror Sagi - Web page: https://patentgrep.com/patent/US20100167274A1 ## CPC - C12Q 1/6818: involving interaction of two or more labels, e.g. resonant energy transfer - C12Q 1/6827: for detection of mutation or polymorphism - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract Methods and kits for detecting a nucleic acid sequence-of-interest in a sample are provided. The methods and kits use RecA-mediated strand exchange which is sensitive to a single-mismatch and which can exchange strands of non-denatured polynucleotide sequences of a sample. Thus the methods and kits of the present invention can be used for the identification of single nucleotide polymorphisms (SNPs), length of telomeric ends, numeration of chromosomes and disease-associated genes in a sample. ## Claims ### Claim 1 A method of detecting a nucleic acid sequence-of-interest in a sample, the method comprising: (a) providing a complex of a polynucleotide sequence of the sample and a recombinase; (b) incubating said complex with a labeled polynucleotide which comprises a nucleic acid sequence complementary to the nucleic acid sequence-of-interest under conditions suitable for exchange between said polynucleotide sequence and said labeled polynucleotide; and (c) measuring a rate and/or amount of said exchange to thereby detect the nucleic acid sequence-of-interest in the sample. ### Claim 2 A kit for detecting a nucleic acid sequence-of-interest in a sample, the kit comprising packaging materials and at least one agent identified by said packaging material as being suitable for measuring a rate and/or amount of a recombinase-mediated exchange between a polynucleotide sequence of the sample and a labeled polynucleotide which comprises a nucleic acid sequence complementary to the nucleic acid sequence-of-interest. ### Claim 3 (depends on 1) The method of claim 1, wherein the nucleic acid sequence-of-interest comprises a single nucleotide polymorphism (SNP). ### Claim 4 A method of detecting a nucleic acid sequence-of-interest in a sample, the method comprising: (a) providing a complex of a labeled polynucleotide which comprises a nucleic acid sequence complementary to the nucleic acid sequence-of-interest and a recombinase and; (b) incubating said complex with the sample under conditions suitable for exchange between said labeled polynucleotide and the polynucleotide sequence of the sample; and (c) measuring a rate and/or amount of said exchange to thereby detect the nucleic acid sequence-of-interest in the sample. ### Claim 5 A kit for detecting a nucleic acid sequence-of-interest in a sample, the kit comprising packaging materials and at least one agent identified by said packaging material as being suitable for measuring a rate and/or amount of a recombinase-mediated exchange between a labeled polynucleotide which comprises a nucleic acid sequence complementary to the nucleic acid sequence-of-interest and a polynucleotide sequence of the sample. ### Claim 6 (depends on 1) The method of claim 1, wherein said recombinase is selected from the group consisting of RecA, Rad51, DMC1, Sin, Cre, RadA and Rec12. ### Claim 7 (depends on 1) The method of claim 1, wherein the polynucleotide sequence is a PCR product. ### Claim 8 (depends on 4) The method of claim 4, wherein said polynucleotide sequence of the sample is a non-denatured fragment of a genomic nucleic acid sequence. ### Claim 9 (depends on 4) The method of claim 4, wherein said measuring of said rate and/or said amount of said exchange is effected in situ. ### Claim 10 (depends on 1) The method of claim 1, wherein said polynucleotide sequence of the sample is a single strand DNA (ssDNA). ### Claim 11 (depends on 4) The method of claim 4, wherein said polynucleotide sequence of the sample is a double strand DNA (dsDNA). ### Claim 12 (depends on 4) The method of claim 4, wherein said detecting is effected in situ. ### Claim 13 (depends on 1) The method of claim 1, wherein said incubating is effected for a time period selected from the range of 1-20 minutes. ### Claim 14 (depends on 1) The method of claim 1, wherein said conditions comprise hydrolysable ATP. ### Claim 15 (depends on 1) The method of claim 1, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is a double stranded DNA (dsDNA) and whereas one strand of said dsDNA is labeled with a fluorescent acceptor and a second strand of said dsDNA is labeled with a fluorescent donor. ### Claim 16 (depends on 1) The method of claim 1, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is a dsDNA and whereas one strand of said dsDNA is labeled at a 5′-end and a second strand of said dsDNA is labeled at a 3′-end. ### Claim 17 (depends on 15) The method of claim 15, wherein said fluorescent acceptor and said fluorescent donor are positioned on said dsDNA such that an average physical distance therebetween is selected from the range of 30-60 Angstrom. ### Claim 18 (canceled) ### Claim 19 (depends on 1) The method of claim 1, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is labeled on one strand and whereas said polynucleotide sequence of the sample is labeled on one strand. ### Claim 20 (depends on 1) The method of claim 1, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is a plurality of labeled polynucleotides and whereas said plurality of labeled polynucleotides are configured as an array. ### Claim 21 (depends on 1) The method of claim 1, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is attached to a solid support. ### Claim 22 (depends on 1) The method of claim 1, wherein the nucleic acid sequence-of-interest is selected from the group consisting of a repeated nucleic acid sequence, a disease-associated nucleic acid sequence and/or a genomic fragment of a chromosome. ### Claim 23 (depends on 3) The method of claim 3, for detecting a presence of said SNP, telomeric instability, and/or DNA or chromosomal aberrations. ### Claim 24 (depends on 4) The method of claim 4, wherein the nucleic acid sequence-of-interest comprises at least 25 nucleic acids. ### Claim 25 (depends on 4) The method of claim 4, wherein said conditions comprise non-denaturing conditions. ### Claim 26 (depends on 4) The method of claim 4, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is a double stranded DNA (dsDNA) and whereas one strand of said dsDNA is labeled with a fluorescent acceptor and a second strand of said dsDNA is labeled with a fluorescent donor. ### Claim 27 (depends on 4) The method of claim 4, wherein said labeled polynucleotide which comprises said nucleic acid sequence complementary to the nucleic acid sequence-of-interest is a dsDNA and whereas one strand of said dsDNA is labeled at a 5′-end and a second strand of said dsDNA is labeled at a 3′-end. ### Claim 28 (depends on 4) The method of claim 4, wherein the nucleic acid sequence-of-interest is selected from the group consisting of a repeated nucleic acid sequence, a disease-associated nucleic acid sequence and/or a genomic fragment of a chromosome. ### Claim 29 (depends on 4) The method of claim 4, for detecting a presence of a SNP, telomeric instability, and/or DNA or chromosomal aberrations.