Polynucleotide sequence assay

Details Polynucleotide sequence assay Polynucleotide sequence assay

2001-07-03

2003-01-28

Whisenant, Ethan C. (Department: 1634)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C536S023100, C536S024300

Reexamination Certificate

active

06511810

ABSTRACT:

FIELD OF THE INVENTION
The present invention relates to methods for detecting or quantifying one or more polynucleotide sequences in one or more samples, and to reagents and kits for use therein.
REFERENCES
Albretsen et al.,
Anal. Biochem.
189:40 (1990).
Ausubel et al., eds.,
Current Protocols in Molecular Biology Vol.
1, Chapter 2, Section I, John Wiley & Sons, New York (1993).
Barany et al., PCT Application No. PCT/US91/06103.
Barrett, R. W., et al., U.S. Pat. No. 5,482,867 (1996).
Beaucage and Iyer,
Tetrahedron
48:2223-2311 (1992).
Bergot et al., PCT Application No. PCT/US90/05565 (WO 91/07507).
Boom et al., U.S. Pat. No. 5,234,809.
Brenner, PCT Publications No. WO 96/12014 and WO 96/41011.
Breslauer et al.,
Proc. Natl. Acad. Sci.
83:3746-3750 (1986).
Cantor et al, U.S. Pat. No. 5,482,836.
Dieffenbach et al., in
PCR Primer: A Laboratory Manual
, Dieffenbach and Dveksler, eds., pp. 133-142, CSHL Press, New York (1995).
Drmanac, R., et al.,
Electrophoresis
13:566 (1992).
Drmanac, R., et al.,
Science
260:1649 (1993).
Eckstein, F.,
Oligonucleotides and Analogs: A Practical Approach
, Chapters 8 and 9, IRL Press, Oxford, GB (1991).
Fodor, S. P. A., et al.,
Science
251:767 (1991).
Fodor, S. P. A., et al., U.S. Pat. No. 5,445,934 (1995).
Fung et al, U.S. Pat. No. 4,757,141.
Gait, M. J., ed.,
Oligonucleotide Synthesis: A Practical Approach
, IRL Press, Oxford, (1984 and 1990 editions).
Grossman, P. D., and Colburn, J. C., eds.,
Capillary Electrophoresis: Theory and Practice
, Academic Press, Inc., New York (1992).
Haugland,
Handbook of Fluorescent Probes and Research Chemicals
, Molecular Probes, Inc., Eugene, Oreg. (1992).
Hobbs, Jr., et al., U.S. Pat. No. 5,151,507.
Hunziker, J., et al., “Nucleic Acid Analogues: Synthesis and Properties” in
Modern Synth. Methods
7:331-417 (1995, ISSN 0176-7615).
Ji et al.,
Anal. Chem.
65:1323-1328 (1993).
Johnston, R. F., et al.,
Electrophoresis
11:355 (1990).
Keller and Manak,
DNA Probes,
2
nd Ed
., Stockton Press, New York (1993).
Khrapko, K. R., et al.,
DNA Sequencing
1:375 (1991).
Knudsen, H., et al.,
Nucleic Acids Res.
24:494-500 (1996).
Kricka, L. J., ed.,
Nonisotopic DNA Probe Techniques
, Academic Press, Inc., New York (1992).
Kornberg and Baker,
DNA Replication,
2
nd Ed
., W. H. Freeman, San Francisco, Calif. (1992).
Mathies, R. A., et al., U.S. Pat. No. 5,091,652 (1992).
Matthews et al,
Anal. Biochem.
169:1-25 (1988).
Menchen et al., PCT Publication No. WO 94/05688 (1994).
Menchen et al., U.S. Pat. No. 5,188,934.
Miller et al.,
Nucleic Acids Res.
16(3):9-10 (1988).
Montpetit et al.,
J. Virol. Methods
36:119-128 (1992).
Mullis et al., eds,
The Polymerase Chain Reaction
, BirkHauser, Boston, Mass. (1994).
Osborne,
CABIOS
8:83 (1991).
Pirrung et al., U.S. Pat. No. 5,143,854.
Ploem, J. S., in
Fluorescent and Luminescent Probes for Biological Activity
, Mason, T. W., Ed., Academic Press, London, pp. 1-11 (1993).
Pon et al.,
Biotechniques
6:768-775 (1988).
Rosenblum et al.,
Nucl. Acids Res.
25:4500-4504 (1997).
Rychlik et al.,
Nucleic Acids Res.
17:8543-8551 (1989) and 18:6409-6412 (1990).
Sambrook et al.,
Molecular Cloning: A Laboratory Manual,
2
nd Edition
, Cold Spring Harbor Laboratory, New York (1989).
Scheit,
Nucleotide Analogs
, John Wiley Pub., New York (1980).
Schena, M., et al.,
Science
270:467 (1995).
Shalon, D., Ph.D. Dissertation, Falconer Library, Stanford University, California (1995).
Shoemaker et al., European Pub. No.EP 799,897 A1 (1997).
Taylor, J. S.,
Nucl. Acids Res.
13:8749 (1985).
Uhlman and Peyman,
Chem. Rev.
90:543-584 (1990).
Walsh et al.,
Biotechniques
10(4): 506-513 (1991).
Wetmur,
Crit. Rev. Biochem. Mol. Biol.
26:227-259 (1991).
Yershov, G., et al.,
Proc. Natl. Acad. Sci.
93:4913 (1996).
INTRODUCTION
Methods for detection and analysis of target nucleic acids have found wide utility in basic research, clinical diagnostics, forensics, and other areas. One important use is in the area of genetic polymorphism. Genetic polymorphisms generally concern the genetic sequence variations that exist among homologous loci from different members of a species. Genetic polymorphisms can arise through the mutation of genetic loci by a variety of processes, such as errors in DNA replication or repair, genetic recombination, spontaneous mutations, transpositions, etc. Such mutations can result in single or multiple base substitutions, deletions, or insertions, as well as transpositions, duplications, etc.
Single base substitutions (transitions and transversions) within gene sequences can cause missense mutations and nonsense mutations. In missense mutations, an amino acid residue is replaced by a different amino acid residue, whereas in nonsense mutations, stop codons are created that lead to truncated polypeptide products. Mutations that occur within signal sequences, e.g., for directing exon/intron splicing of mRNAs, can produce defective splice variants with dramatically altered protein sequences. Deletions, insertions, and other mutations can also cause frameshifts in which contiguous residues encoded downstream of the mutation are replaced with entirely different amino acid residues. Mutations outside of exons can interfere with gene expression and other processes.
Genetic mutations underlie many disease states and disorders. Some diseases have been traced directly to single point mutations in genomic sequences (e.g., the A to T mutation associated with sickle cell anemia), while others have been correlated with large numbers of different possible polymorphisms located in the same or different genetic loci (e.g., cystic fibrosis). Mutations within the same genetic locus can produce different diseases (e.g., hemoglobinopathies). In other cases, the presence of a mutation may indicate susceptibility to particular condition for a disease but is insufficient to reliably predict the occurrence of the disease with certainty. Most known mutations have been localized to gene-coding sequences, splice signals, and regulatory sequences. However, it is expected that mutations in other types of sequences can also lead to deleterious, or sometimes beneficial, effects.
The large number of potential genetic polymorphisms poses a significant challenge to the development of methods for identifying and characterizing nucleic acid samples and for diagnosing and predicting disease. In other applications, it is desirable to detect the presence of pathogens or exogenous nucleic acids and to detect or quantify RNA transcipt levels.
In light of the increasing amount of sequence data that is becoming available for various organisms, and particularly for higher organisms such as humans, there is a need for rapid and convenient methods for determining the presence or absence of target mutations. Ideally, such a method should have high sensitivity, accuracy, and reproducibility. Also, the method should allow simultaneous detection of multiple target sequences in a single reaction mixture.
SUMMARY OF THE INVENTION
In one aspect, the invention includes a method for detecting a target polynucleotide sequence. In the method, a target polynucleotide strand region and a target-complementary strand region are reacted with a first probe pair and a second probe pair under conditions effective for the first probe pair to hybridize to the first and second regions in the target strand region, forming a first hybridization complex, and for the second probe pair to hybridize to the first and second regions in the target-complementary strand region, forming a second hybridization complex. In one embodiment, the first probe pair comprises (i) a first polynucleotide probe containing a sequence that is complementary to a first target region in the target strand region and (ii) a second polynucleotide probe comprising a sequence that is complementary to a second target region in the target strand region, wherein the second region is located 5′ to the first region and overlaps the first region by at least one nucleotide base, and the second probe pair may comprise (i) a third polynucleotide probe contain

Affiliated with

Also associated with

Rating

Polynucleotide sequence assay does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Polynucleotide sequence assay, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Polynucleotide sequence assay will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3059224