# US 7,407,782 B2 · Nucleic acid detection compositions > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 7,407,782 B2 - Document ID: US7407782B2 - Status: Granted - Kind: B2 - Application number: 11/103,943 - Filed: 2005-04-12 - Published: 2005-08-18 - Granted: 2008-08-05 - Earliest claimed: 1996-01-24 - Assignees: Third Wave Technologies, Inc. - Inventors: James R. Prudent; Jeff G. Hall; Victor I. Lyamichev; Mary Ann Brow; James L. Dahlberg - Web page: https://patentgrep.com/patent/US7407782B2 ## CPC - C12N 9/22: Ribonucleases {[RNase]; Deoxyribonucleases [DNase]} - C12Q 1/6823: Release of bound markers - C12Q 1/6827: for detection of mutation or polymorphism - C12Q 1/683: involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP] - Y10S 435/81: Packaged device or kit - Y10S 435/822: using bacteria or actinomycetales - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - 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 - Y10S: TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS ## Abstract The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. ## Claims ### Claim 1 A composition for detecting a target nucleic acid, comprising: a) a purified thermostable FEN-1 endonuclease, active at 55° C. or above; b) an oligonucleotide probe, said oligonucleotide probe configured to participate in a FEN-1 endonuclease cleavage structure in the presence of said target nucleic molecule. ### Claim 2 (depends on 1) The composition of claim 1, wherein said oligonucleotide probe comprises a label. ### Claim 3 (depends on 2) The composition of claim 2, wherein said label is configured to be detectable by a method comprising detection of fluorescence. ### Claim 4 (depends on 2) The composition of claim 2, wherein said label is configured to be detectable by a method comprising detection of mass. ### Claim 5 (depends on 2) The composition of claim 2, wherein said label is configured to be detectable by a method comprising detection of fluorescence energy transfer. ### Claim 6 (depends on 2) The composition of claim 2, wherein said label is configured to be detectable by a method comprising detection selected from the group consisting of detection of radioactivity, luminescence, phosphorescence, fluorescence polarization, and charge. ### Claim 7 (depends on 1) The composition of claim 1, wherein said thermostable FEN-1 endonuclease is from an archaebacterium. ### Claim 8 (depends on 7) The composition of claim 7, wherein said archaebacterium is Pyrococcus furiosus. ### Claim 9 (depends on 7) The composition of claim 7, wherein said archaebacterium is Methanococcus jannaschii. ### Claim 10 (depends on 1) The composition of claim 1, further comprising a nucleic acid molecule configured to hybridize to said target nucleic acid upstream of said oligonucleotide probe. ### Claim 11 (depends on 10) The composition of claim 10, wherein said oligonucleotide probe is configured to hybridize to a first region of said target nucleic acid, and wherein said nucleic acid molecule comprises a 5′ portion and a 3′ portion, said 5′ portion being configured to hybridize to a second region of said target nucleic acid, wherein said second region of said target nucleic acid is downstream of and contiguous to said first region of said target nucleic acid. ### Claim 12 (depends on 11) The composition of claim 11, wherein said 3′ portion of said nucleic acid molecule comprises an aromatic ring. ### Claim 13 (depends on 11) The composition of claim 11, wherein said 3′ portion of said nucleic acid molecule comprises a 3′ terminal nucleotide not complementary to said target nucleic acid. ### Claim 14 (depends on 11) The composition of claim 11, wherein said 3′ portion of said nucleic acid molecule consists of a single nucleotide. ### Claim 15 (depends on 14) The composition of claim 14, wherein said single nucleotide is not complementary to said target nucleic acid. ### Claim 16 (depends on 14) The composition of claim 14, wherein said single nucleotide is complementary to said target nucleic acid. ### Claim 17 (depends on 13) The composition of claim 13, wherein said 3′ terminal nucleotide comprises a naturally occurring nucleotide. ### Claim 18 (depends on 13) The composition of claim 13, wherein said 3′ terminal nucleotide comprises a nucleotide analog. ### Claim 19 (depends on 11) The composition of claim 11, wherein said 3′ portion of said nucleic acid molecule is completely complementary to said target nucleic acid. ### Claim 20 (depends on 1) The composition of claim 1, wherein said oligonucleotide probe is attached to a solid support. ### Claim 21 (depends on 10) The composition of claim 10, wherein said nucleic acid molecule is attached to a solid support. ### Claim 22 (depends on 1) The composition of claim 1, further comprising a polymerase enzyme. ### Claim 23 (depends on 22) The composition of claim 22, wherein said polymerase enzyme is altered to have reduced synthetic activity. ### Claim 24 (depends on 1) The composition of claim 1, further comprising said target nucleic acid. ### Claim 25 (depends on 24) The composition of claim 24, wherein said target nucleic acid comprises DNA. ### Claim 26 (depends on 24) The composition of claim 24, wherein said target nucleic acid comprises synthetic nucleic acid. ### Claim 27 (depends on 26) The composition of claim 26, wherein said synthetic nucleic acid comprises an amplified nucleic acid. ### Claim 28 (depends on 27) The composition of claim 27, wherein said amplified nucleic acid is produced using a polymerase chain reaction. ### Claim 29 (depends on 11) The composition of claim 11, wherein said composition further comprises a stacker oligonucleotide, wherein said stacker oligonucleotide is configured to hybridize to a third region of said target nucleic acid, and wherein said third region of said target nucleic acid is upstream of and contiguous to said first region of said target nucleic acid.