Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2011-07-12
2011-07-12
Strzelecka, Teresa E (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023100, C536S024300
Reexamination Certificate
active
07977053
ABSTRACT:
The present invention provides methods and kits for the rapid exponential amplification of nucleic acid molecules using a padlock probe. The present invention improves upon the existing methods for amplifying padlock probes by eliminating or delaying the appearance of artifact products that cause false positive results, and also increase the sensitivity and speed of the assay. Further provided are nucleic acid amplification primers containing non-informative base analogs.
REFERENCES:
patent: 4518584 (1985-05-01), Mark et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4737462 (1988-04-01), Mark et al.
patent: 4925785 (1990-05-01), Wang et al.
patent: 4996143 (1991-02-01), Heller et al.
patent: 5119801 (1992-06-01), Eizenhoefer et al.
patent: 5124246 (1992-06-01), Urdea et al.
patent: 5312728 (1994-05-01), Lizardi et al.
patent: 5348853 (1994-09-01), Wang et al.
patent: 5409818 (1995-04-01), Davey et al.
patent: 5438131 (1995-08-01), Bergstrom et al.
patent: 5494810 (1996-02-01), Barany et al.
patent: 5532129 (1996-07-01), Heller
patent: 5545522 (1996-08-01), Van Gelder et al.
patent: 5565322 (1996-10-01), Heller
patent: 5593840 (1997-01-01), Bhatnagar et al.
patent: 5714320 (1998-02-01), Kool
patent: 5854033 (1998-12-01), Lizardi
patent: 5866336 (1999-02-01), Nazarenko et al.
patent: 5912124 (1999-06-01), Kumar
patent: 5916750 (1999-06-01), Iyer et al.
patent: 6007994 (1999-12-01), Ward et al.
patent: 6077668 (2000-06-01), Kool
patent: 6090552 (2000-07-01), Nazarenko et al.
patent: 6096880 (2000-08-01), Kool
patent: 6117635 (2000-09-01), Nazarenko et al.
patent: 6143495 (2000-11-01), Lizardi et al.
patent: 6383752 (2002-05-01), Agrawal et al.
patent: 6399304 (2002-06-01), Kilger et al.
patent: 6403319 (2002-06-01), Lizardi et al.
patent: WO-94006810 (1994-03-01), None
patent: WO-00036141 (2000-06-01), None
patent: WO-02068683 (2002-09-01), None
Thomas, D.C. et al., Arch. Pathol. Med., vol. 123, pp. 1170-1176 (1999).
Metzker, M.L. et al., Nucl. Acids Res., vol. 22, pp. 4259-4267 (1994).
In the US Patent and Trademark Office U.S. Appl. No. 10/469,099, Non-Final Office Action dated Jun. 12, 2006, 13 pages.
Aliotta et al.;Thermostable Bst DNA polymerase I lacks a 3′→5′ proofreading exonuclease activity; Genetic Analysis Biomolecular Engineering; 1996; 12(5-6):185-195.
Baner et al.;Signal amplification of padlock probes by rolling circle replication; Nucleic Acids Research; 1998; vol. 26, No. 22; pp. 5073-5078.
Bauer et al.;A genetic enrichment for mutations constructed by oligodeoxynucleotide-directed mutagenesis; Gene.; 1985; vol. 37; pp. 73-81.
Boehmer et al.;Herpes Simplex Virus Type 1 ICP8: Helix-Destabilizing Properties; Journal of Virology; Feb. 1993; vol. 67, No. 2; pp. 711-715.
Craik, Charles S.;Use of Oligonucleotides for Site-Specific Mutagenesis; BioTechniques; Jan./Feb. 1985; pp. 12-19.
Devereux et al.;A comprehensive set of sequence analysis programs for the VAX; Nucleic Acids Research; 1984; IRL Press Limited, Oxford, England; vol. 12, No. 1; pp. 387-395.
Esteller et al.;Inactivation of the DNA-Repair Gene MGMT and the Clinical Response of Gliomas to Alkylating Agents; The New England Journal of Medicine; 2000; vol. 343, No. 19; pp. 1350-1354; correction 1740a; correction 2001; 344:686(3 pages).
Fire et al.;Rolling replication of short DNA circles; Proc. Natl. Acad. Sci. (USA); May 1995; vol. 92; pp. 4641-4645.
Graff et al.;E-Cadherin Expression Is Silenced by DNA Hypermethylation in Human Breast and Prostate Carcinomas; Cancer Research; 1995; vol. 55; pp. 5195-5199.
Gribskov et al.;Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins; Nucleic Acids Research; 1986; vol. 14, No. 1; pp. 6745-6763.
Guo et al.;Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports; Nucleic Acids Research; 1994; vol. 22, No. 24; pp. 5456-5465.
Hatt et al.;Analysis of the entire nucleotide sequence of the cryptic plasmid of Chlamydia trachomatis serovar L1. Evidence for involvement in DNA replication; Nucleic Acids Research; 1988; vol. 16, No. 9; pp. 4053-4067.
Herman et al.;Hypennethylation-associated Inactivation Indicates a Tumor Suppressor Role for pl5INK4B1; Cancer Research; 1996; vol. 56; pp. 722-727.
Herman et al.;Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands; Proc. Natl. Acad. Sci. (USA); 1996; vol. 93; pp. 9821-9826.
Herman et al.;Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma; Proc. Natl. Acad. Sci. (USA); 1994; vol. 91; pp. 9700-9704.
Holland et al.;Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase; Proc. Natl. Acad. Sci. (USA); 1991; vol. 88; pp. 7276-7280.
Kaplan et al.;Rapid Photolytic Release of Adenosine 5′-Triphosphate from a Protected Analogue: Utilization by the Na:K Pump of Human Red Blood Cell Ghosts; 1978; American Chemical Society; vol. 17, No. 10; pp. 1929-1935.
Khrapko et al.;Hybridization of DNA with Oligonucleotides Immobilized in Gel: Convenient Method for Detection of Single Base Changes; Molekuliarnaia Biologiia (USSR); 1991; vol. 25, No. 3; pp. 718-730. (With English Language Abstract).
Kievitis et al.;NASBATMisothermal enzymatic in vitro nucleic acid amplification optimized for the diagnosis of HIV-1 infection; Journal of Virological Methods, 1991; vol. 35; pp. 273-286.
Kunkel et al.;Rapid and Efficient Site-Specific Mutagenesis without Phenotypic Selection; Methods in Enzymology; 1987; vol. 154; pp. 367-382.
Kunkel, Thomas A.;Rapid and efficient site-specific mutagenesis without phenotypic selection; Proc. Natl. Acad. Sci. (USA); 1985; vol. 82; pp. 488-492.
Kwoh et al.;Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format; Proc. Natl. Acad. Sci. (USA); 1989; vol. 86; pp. 1173-1177.
Landegren et al;A Ligase-Mediated Gene Detection Technique; Science; 1988; vol. 241; pp. 1077-1080.
Lee et al.;Allelic discrimination by nick-translation PCR with fluorogenic probes; Nucleic Acids Research; 1993; vol. 21, No. 16; pp. 3761-3766.
Lee et al.;CG Island Methylation Changes Near the GSTP1 Gene in Prostatic Carcinoma Cells Detected Using The Polymerase Chain Reaction: A New Prostate Cancer Biomarker;Cancer Epidemiology, Biomarkers & Prevention; 1997; vol. 6; pp. 443-450.
Lizardi et al.;Mutation detection and single-molecule counting using isothermal rolling-circle amplification; Nature Genetics; 1998; vol. 19; pp. 225-232.
Loakes et al.;3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR; Nucleic Acids Research; 1995; vol. 23, No. 13; pp. 2361-2366.
Lu et al.;Large Fragment of DNA Polymerase I from Bacillus stearothermophilus (Bst Polymerase) is Stable at Ambient Temperature; BioTechniques; 1991; vol. 11, No. 4; pp. 464, 466.
Luo et al.;Improving the fidelity of Thermus thermophilus DNA ligase; Nucleic Acids Research; 1996; vol. 24, No. 14; pp. 3071-3078.
Marras et al.;Multiplex detection of single-nucleotide variations using molecular beacons; Genetic Analysis: Biomolecular Engineering; 1999; vol. 14; pp. 151-156.
McCray et al.;A new approach to time-resolved studies of ATP-requiring biological systems: Laser flash photolysis of caged ATP; Proc. Natl. Acad. Sci. (USA); 1980; vol. 77, No. 12; pp. 7237-7241.
Merlo et al.; 5'CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers; Nature Medicine; 1995; vol. 1, No. 7; pp. 686-692.
Metzker et al.;Termination of DNA synthesis by novel 3'-modified-deoxyribonucleosides 5'-triphosphates; Nucleic Acids Research; 1994; Vol. 22(20); pp. 4259-4267.
Nazarenko et al.;A closed tube format for amplification and detection of DNA based on energy transfer, Nucleic Acids Research; 1997; vol. 25, No. 12; pp. 2516-2521.
Needleman et al.;A General Method Applicable to the Search for Similarit
Patton & Boggs LLP
Strzelecka Teresa E
Virco BVBA
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