Detection of nucleic acid sequences by invader-directed cleavage

Brow, Mary Ann D; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

Title: Detection of nucleic acid sequences by invader-directed cleavage

Patent · Fri Jan 01 00:00:00 EST 1999

OSTI ID:872754

Brow, Mary Ann D ^[1]; Hall, Jeff Steven Grotelueschen ^[1]; Lyamichev, Victor ^[1]; Olive, David Michael ^[1]; Prudent, James Robert ^[1]

Madison, WI

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 5' 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. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

View Patent

Cite

Export

Save

Research Organization:: Third Wave Technologies, Inc., Madison, WI (United States)

DOE Contract Number:: FG02-94ER81891

Assignee:: Third Wave Technologies, Inc. (CA)

Patent Number(s):: US 6001567

OSTI ID:: 872754

Country of Publication:: United States

Language:: English

References (48)

Intervening sequences in an Archaea DNA polymerase gene. Perler, F. B.; Comb, D. G.; Jack, W. E. Proceedings of the National Academy of Sciences, Vol. 89, Issue 12, p. 5577-5581 https://doi.org/10.1073/pnas.89.12.5577	journal	June 1992
Allelic discrimination by nick-translation PCR with fluorgenic probes Lee, Linda G.; Connell, Charles R.; Bloch, Will Nucleic Acids Research, Vol. 21, Issue 16, p. 3761-3766 https://doi.org/10.1093/nar/21.16.3761	journal	August 1993
Recent advances in the polymerase chain reaction Erlich, H.; Gelfand, D.; Sninsky, J. Science, Vol. 252, Issue 5013 https://doi.org/10.1126/science.2047872	journal	June 1991
Compilation and alignment of DNA polymerase sequences Ito, Junetsu; Braithwaite, Dan K. Nucleic Acids Research, Vol. 19, Issue 15 https://doi.org/10.1093/nar/19.15.4045	journal	January 1991
A novel method for the rapid detection of specific nucleotide sequences in crude biological samples without blotting or radioactivity; application to the analysis of hepatitis B virus in human serum Urdea, Mickey S.; Running, Joyce A.; Horn, Thomas Gene, Vol. 61, Issue 3 https://doi.org/10.1016/0378-1119(87)90189-2	journal	January 1987
[21] Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction Mullis, Kary B.; Faloona, Fred A. Methods in Enzymology https://doi.org/10.1016/0076-6879(87)55023-6	book	January 1987
Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements Dunn, John J.; Studier, F. William; Gottesman, M. Journal of Molecular Biology, Vol. 166, Issue 4, p. 477-535 https://doi.org/10.1016/S0022-2836(83)80282-4	journal	June 1983
Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies Kwok, S.; Kellogg, D. E.; McKinney, N. Nucleic Acids Research, Vol. 18, Issue 4 https://doi.org/10.1093/nar/18.4.999	journal	January 1990
Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase Tindall, Kenneth R.; Kunkel, Thomas A. Biochemistry, Vol. 27, Issue 16 https://doi.org/10.1021/bi00416a027	journal	August 1988
Chemical nucleases Sigman, David S.; Mazumder, Abhijit.; Perrin, David M. Chemical Reviews, Vol. 93, Issue 6 https://doi.org/10.1021/cr00022a011	journal	September 1993
Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Kwoh, D. Y.; Davis, G. R.; Whitfield, K. M. Proceedings of the National Academy of Sciences, Vol. 86, Issue 4, p. 1173-1177 https://doi.org/10.1073/pnas.86.4.1173	journal	February 1989
Identification of Hepatitis C Virus Genotypes among Hospitalized Patients in British Columbia, Canada Altamirano, M.; Delaney, A.; Wong, A. Journal of Infectious Diseases, Vol. 171, Issue 4 https://doi.org/10.1093/infdis/171.4.1034	journal	April 1995
Characterization of the 5′ to 3′ exonuclease associated with Thermus aquaticus DNA polymerase Longley, Matthew J.; Bennett, Samuel E.; Mosbaugh, Dale W. Nucleic Acids Research, Vol. 18, Issue 24 https://doi.org/10.1093/nar/18.24.7317	journal	January 1990
48000-fold Acceleration of Hybridization by Chemically Modified Oligonucleotides Corey, David R. Journal of the American Chemical Society, Vol. 117, Issue 36 https://doi.org/10.1021/ja00141a038	journal	September 1995
Isolation, Characterization, and Expression in Escherichia coli of the DNA Polymerase Gene from Thermus aquaticus Lawyer, F. C.; Stoffel, S.; Saiki, R. K. Journal of Biological Chemistry, Vol. 264, Issue 11 https://doi.org/10.1016/S0021-9258(18)83367-1	journal	April 1989
Molecular mechanics of nucleic acid sequence amplification Landegren, Ulf Trends in Genetics, Vol. 9, Issue 6 https://doi.org/10.1016/0168-9525(93)90119-3	journal	June 1993
Molecular cloning and nucleotide sequence of the DNA polymerase gene from Thermus flavus Akhmetzjanov, A. A.; Vakhitov, V. A. Nucleic Acids Research, Vol. 20, Issue 21 https://doi.org/10.1093/nar/20.21.5839	journal	January 1992
Multicopy expression vectors carrying the lac represser gene for regulated high-level expression of genes in Escherichia coli Stark, Michael J. R. Gene, Vol. 51, Issue 2-3 https://doi.org/10.1016/0378-1119(87)90314-3	journal	January 1987
Heat-induced depyrimidination of deoxyribonucleic acid in neutral solution Lindahl, Tomas; Karlstrom, Olle Biochemistry, Vol. 12, Issue 25 https://doi.org/10.1021/bi00749a020	journal	December 1973
Hybridization specificity, enzymatic activity and biological (Ha-ras) activity of oligonucleotides containing 2,4-dideoxy-β-D-erythro-hexopyranosyl nucleosides Augustyns, K.; Godard, G.; Hendrix, C. Nucleic Acids Research, Vol. 21, Issue 20 https://doi.org/10.1093/nar/21.20.4670	journal	January 1993
Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Physical Chemical Studies Doty, P.; Marmur, J.; Eigner, J. Proceedings of the National Academy of Sciences, Vol. 46, Issue 4 https://doi.org/10.1073/pnas.46.4.461	journal	April 1960
Deoxyribonucleic Acid Polymerase: Two Distinct Enzymes in One Polypeptide Setlow, Peter; Kornberg, Arthur Journal of Biological Chemistry, Vol. 247, Issue 1 https://doi.org/10.1016/S0021-9258(19)45780-3	journal	January 1972
Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. Livak, K. J.; Flood, S. J.; Marmaro, J. Genome Research, Vol. 4, Issue 6 https://doi.org/10.1101/gr.4.6.357	journal	June 1995
Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes Studier, F. William; Moffatt, Barbara A. Journal of Molecular Biology, Vol. 189, Issue 1, p. 113-130 https://doi.org/10.1016/0022-2836(86)90385-2	journal	May 1986
Hepatitis C: progress and problems. Cuthbert, J. A. Clinical Microbiology Reviews, Vol. 7, Issue 4 https://doi.org/10.1128/CMR.7.4.505	journal	October 1994
Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase Myers, Thomas W.; Gelfand, David H. Biochemistry, Vol. 30, Issue 31 https://doi.org/10.1021/bi00245a001	journal	August 1991
Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. Holland, P. M.; Abramson, R. D.; Watson, R. Proceedings of the National Academy of Sciences, Vol. 88, Issue 16, p. 7276-7280 https://doi.org/10.1073/pnas.88.16.7276	journal	August 1991
Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat Hirao, Ichiro; Kawai, Gota; Yoshizawa, Satoko Nucleic Acids Research, Vol. 22, Issue 4 https://doi.org/10.1093/nar/22.4.576	journal	January 1994
The ligase chain reaction in a PCR world. Barany, F. Genome Research, Vol. 1, Issue 1 https://doi.org/10.1101/gr.1.1.5	journal	August 1991
Current methods of mutation detection Cotton, R. G. H. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 285, Issue 1 https://doi.org/10.1016/0027-5107(93)90060-S	journal	January 1993
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Woese, C. R.; Gutell, R.; Gupta, R. Microbiological Reviews, Vol. 47, Issue 4 https://doi.org/10.1128/MR.47.4.621-669.1983	journal	January 1983
The DNA polymerase gene from the hyperthermophilic marine archaebacterium, pyrococcus furiosus , shows sequence homology with α-like DNA polymerases Mathur, Eric J.; Adams, Michael W. W.; Callen, Walter N. Nucleic Acids Research, Vol. 19, Issue 24 https://doi.org/10.1093/nar/19.24.6952	journal	January 1991
An active fragment of DNA polymerase produced by proteolytic cleavage Brutlag, Douglas; Atkinson, Maurice R.; Setlow, Peter Biochemical and Biophysical Research Communications, Vol. 37, Issue 6 https://doi.org/10.1016/0006-291X(69)90228-9	journal	December 1969
The Polymerase Chain Reaction in an Anemic Mode: How to Avoid Cold Oligodeoxyribonuclear Fusion Mullis, K. B. Genome Research, Vol. 1, Issue 1 https://doi.org/10.1101/gr.1.1.1	journal	August 1991
Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes. Pontius, B. W.; Berg, P. Proceedings of the National Academy of Sciences, Vol. 88, Issue 18 https://doi.org/10.1073/pnas.88.18.8237	journal	September 1991
Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Guatelli, J. C.; Whitfield, K. M.; Kwoh, D. Y. Proceedings of the National Academy of Sciences, Vol. 87, Issue 5, p. 1874-1878 https://doi.org/10.1073/pnas.87.5.1874	journal	March 1990
Use of conserved sequences from hepatitis C virus for the detection of viral RNA in infected sera by polymerase chain reaction Inchauspe, Genevieve; Abe, Kenji; Zebedee, Suzanne Hepatology, Vol. 14, Issue 4 https://doi.org/10.1002/hep.1840140404	journal	October 1991
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Saiki, R. K.; Gelfand, D. H; Stoffel, S. Science, Vol. 239, Issue 4839, p. 487-491 https://doi.org/10.1126/science.239.4839.487	journal	January 1988
Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Youil, R.; Kemper, B. W.; Cotton, R. G. Proceedings of the National Academy of Sciences, Vol. 92, Issue 1 https://doi.org/10.1073/pnas.92.1.87	journal	January 1995
The ligation amplification reaction (LAR)—Amplification of specific DNA sequences using sequential rounds of template-dependent ligation Wu, Dan Y.; Wallace, R. Bruce Genomics, Vol. 4, Issue 4, p. 560-569 https://doi.org/10.1016/0888-7543(89)90280-2	journal	May 1989
Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Cech, T. R.; Tanner, N. K.; Tinoco, I. Proceedings of the National Academy of Sciences, Vol. 80, Issue 13 https://doi.org/10.1073/pnas.80.13.3903	journal	July 1983
Purification of Thermus aquaticus DNA polymerase expressed in Escherichia coli Engelke, David R.; Krikos, Alexandra; Bruck, Mary E. Analytical Biochemistry, Vol. 191, Issue 2 https://doi.org/10.1016/0003-2697(90)90238-5	journal	December 1990
Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro Leirmo, Sigrid; Harrison, Catherine; Cayley, D. Scott Biochemistry, Vol. 26, Issue 8 https://doi.org/10.1021/bi00382a006	journal	April 1987
Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR. Fahy, E.; Kwoh, D. Y.; Gingeras, T. R. Genome Research, Vol. 1, Issue 1 https://doi.org/10.1101/gr.1.1.25	journal	August 1991
A thermodynamic study of unusually stable RNA and DNA hairpins Antao, Vincent P.; Lai, Sandy Y.; Tinoco, Ignacio Nucleic Acids Research, Vol. 19, Issue 21 https://doi.org/10.1093/nar/19.21.5901	journal	January 1991
Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Biological Studies Marmur, J.; Lane, D. Proceedings of the National Academy of Sciences, Vol. 46, Issue 4 https://doi.org/10.1073/pnas.46.4.453	journal	April 1960
Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases Lyamichev, V.; Brow, M.; Dahlberg, J. Science, Vol. 260, Issue 5109 https://doi.org/10.1126/science.7683443	journal	May 1993
Genetic disease detection and DNA amplification using cloned thermostable ligase. Barany, F. Proceedings of the National Academy of Sciences, Vol. 88, Issue 1, p. 189-193 https://doi.org/10.1073/pnas.88.1.189	journal	January 1991

Similar Records

Detection of nucleic acid sequences by invader-directed cleavage

Patent · Tue Dec 14 00:00:00 EST 1999 · OSTI ID:872754

Brow, M A.D.; Hall, J S.G.; Lyamichev, V; +2 more

Detection of nucleic acids by multiple sequential invasive cleavages

Patent · Fri Jan 01 00:00:00 EST 1999 · OSTI ID:872754

Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; +1 more

Detection of nucleic acids by multiple sequential invasive cleavages 02

Patent · Tue Jan 01 00:00:00 EST 2002 · OSTI ID:872754

Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; +1 more

Related Subjects

detection
nucleic
acid
sequences
invader-directed
cleavage
relates
means
characterization
variations
methods
forming
structure
target
sequence
cleaving
site-specific
manner
nuclease
activity
variety
enzymes
cleave
target-dependent
indicating
presence
specific
devices
separation
molecules
based
charge
acid molecule
cleavage structure
acid molecules
acid sequence
nucleic acid
acid sequences
target sequence
acid cleavage
specific nucleic
molecules based
specific variations
site-specific manner
nuclease activity
target-dependent cleavage
specific manner
/435/999/

Title: Detection of nucleic acid sequences by invader-directed cleavage

Citation Formats

References (48)

Similar Records

Related Subjects