Detectably labeled, dual conformation oligonucleotide probes, as

Details Detectably labeled, dual conformation oligonucleotide probes, as Detectably labeled, dual conformation oligonucleotide probes, as

1999-03-15

2000-08-15

Campbell, Eggerton A.

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

435 912, C12Q 168, C12P 1934

Patent

active

061034762

ABSTRACT:
Unimolecular and bimolecular hybridization probes for the detection of nucleic acid target sequences comprise a target complement sequence, an affinity pair holding the probe in a closed conformation in the absence of target sequence, and either a label pair that interacts when the probe is in the closed conformation or, for certain unimolecular probes, a non-interactive label. Hybridization of the target and target complement sequences shifts the probe to an open conformation. The shift is detectable due to reduced interaction of the label pair or by detecting a signal from a non-interactive label. Certain unimolecular probes can discriminate between target and non-target sequences differing by as little as one nucleotide. Also, universal stems and kits useful for constructing said probes. Also, assays utilizing said probes and kits for performing such assays.

REFERENCES:
patent: 4261968 (1981-04-01), Ullman et al.
patent: 4725536 (1988-02-01), Fritsch et al.
patent: 4725537 (1988-02-01), Fritsch et al.
patent: 4752566 (1988-06-01), Collins et al.
patent: 4766062 (1988-08-01), Diamond et al.
patent: 4822733 (1989-04-01), Morrison
patent: 4996143 (1991-02-01), Heller et al.
patent: 5082830 (1992-01-01), Brakel et al.
patent: 5118801 (1992-06-01), Lizardi et al.
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5241060 (1993-08-01), Engelhardt et al.
patent: 5260433 (1993-11-01), Engelhardt et al.
patent: 5312921 (1994-05-01), Glazer et al.
patent: 5332659 (1994-07-01), Kidwell
patent: 5348853 (1994-09-01), Wang et al.
patent: 5487972 (1996-01-01), Gelfand et al.
patent: 5491063 (1996-02-01), Fisher et al.
patent: 5527676 (1996-06-01), Vogelstein et al.
patent: 5532129 (1996-07-01), Heller et al.
patent: 5538848 (1996-07-01), Livak et al.
patent: 5565322 (1996-10-01), Heller
patent: 5571673 (1996-11-01), Picone
patent: 5622821 (1997-04-01), Selvin et al.
B.C. Bagwell, et al., "A New Homogenous Assay System For Specific Nucleic id Sequences: Poly-dA And Poly-A Detection," Nucleic Acids Research 22: 2424-2425 (1994).
J. Brand, et al., "Fluorescence Probes For Structure," Ann Rev Biochemistry 41: 843-868 (1972).
K.J. Breslauer, et al., "Predicting DNA Duplex Stability From The Base Sequence," P.N.A.S. (U.S.A.) 83: 3746-3750 (1986).
C.R. Cantor, et al., "Techniques For The Study Of Biological Structure And Function," (W.H. Freeman and Co., San Francisco) (U.S.A) pp. 448-455 (1980).
C.R. Cantor, "Lighting Up Hybridization," Nature Biotechnology 14: 264 (1996).
Cardullo, et al., "Detection Of Nucleic Acid Hybridization By Nonradiative Fluorescence Resonance Energy Transfer," P.N.A.S. (U.S.A.) 85: 8790-8794 (1988).
A. Coghlan, "Brilliant Beacons Colour-Code Genes," New Scientist p. 24 (Mar. 16, 1996).
B.A. Connolly, et al., "Chemical Synthesis Of Oligonucleotides Containing A Free Sulphydryl Group And Subsequent Attachment Of Thiol Probes," Nucleic Acids Research 13: 4485-4502, 1985.
J.P. Cooper, et al., "Analysis Of Fluorescence Energy Transfer In Duplex And Branched DNA Molecules," Biochemistry 29: 9261-9268 (1990).
M.E. DePecol, et al., "Sytheses, Properties, And Use Of Fluorescent N-(5'-Phospho-4'-Pyridoxyl) Amines In Assay Of Pyridoxamine (Pyridoxine) 5'-Phosphate Oxidase," Analytical Biochemistry 101: 435-441 (1980).
H.A. Erlich, et al., "Recent Advances In The Polymerase Chain Reaction," Science 252: 1643-1651 (1991).
D. Gillespie, et al., "A Quantitative Assay For DNA-RNA Hybrids With DNA Immobilized On A Membrane," J. Mol. Biol. 12: 829-842 (1965).
Z. Guo, et al., "Enhanced Discrimination Of Single Nucleotide Polymorphisms By Artificial Mismatch Hybridization," Nature Biotechnology 15: 331-335 (1997).
R.P. Haugland, et al., "Dependence Of The Kinetics Of Singlet-Singlet Energy Transfer On Spectral Overlap," P.N.A.S. (U.S.A.) 63: 23-30 (1969).
P.M. Holland, et al., "Detection Of Specific Polymerase Chain Reaction Product By Utilizing the 5'-3' Exonuclease Activity Of Thermus Aquaticus DNA Polymerase," P.N.A.S. (U.S.A.) 88: 7276-7280 (1991).
P.M. Holland, et al., "Detection Of Specific Polymerase Chain Reaction Product By Utilizing the 5'-3' Exonuclease Activity Of Thermus Aquaticus DNA Polymerase," Clinical Chemistry 38: 462-463 (1992).
E.N. Hudson, et al., "Synthesis And Characterization Of Two Fluorescent Sulfhydryl Reagents," Biochemistry 12: 4154-4161 (1973).
V.M. Ingram, "Gene Mutations In Human Haemoglobin: The Chemical Difference Between Normal And Sickle Cell Haemoglobin," Nature 180: 326-328 (1957).
U. Landegren, et al., "A Ligase-Mediated Gene Detection Technique," Science 241: 1077-1080 (1988).
R. Lathe, "Synthetic Oligonucleotide Probes Deduced From Amino Acid Sequence Data, Theoretical And Practical Considerations," J. Mol. Biol. 183: 1-12 (1985).
L.G. Lee, et al., "Allelic Discrimination By Nick-Translation PCR With Fluorogenic Probes," Nucleic Acid Research 21: 3761-3766 (1993).
P. Lichter, et al., "High-Resolution Mapping Of Human Chromosome 11 By In Situ Hybridization With Cosmid Clones," Science 247: 64-69 (1990).
K.J. Livak, et al., "Towards Fully Automated Genome-Wide Polymorphism Screening," Nature Genetics 9: 341-342 (1995).
H. Lomell, et al., "Quantitative Assays Based On The Use Of Replicatable Hybridization Probes," Clinical Chemistry 35: 1826-1831 (1989).
E.D. Matayoshi, et al., "Novel Fluorogenic Substrates For Assaying Retroviral Proteases By Resonance Energy Transfer," Science 247: 954-958 (1990).
J.A. Matthews, et al., "Analytical Strategies For The Use Of DNA Probes," Analytical Biochemistry 169: 1-25 (1988).
L.E. Morrison, et al., "Sensitive Fluorescence-Based Thermodynamic And Kinetic Measurements Of DNA Hybridization In Solution," Biochemistry 32: 3095-3104 (1993).
L.E. Morrison, et al., "Solution-Phase Detection Of Polynucleotides Using Interacting Fluorescent Labels And Competitive Hybridization," Analytical Biochemistry 183: 231-244 (1989).
N.C. Nelson, et al., "Detection Of All Single-Base Mismatches In Solution By Chemiluminescence," Nucleic Acid Research 24: 4998-5003 (1996).
P.S. Nelson, et al., "Bifunctional Oligonucleotide Probes Synthesized Using A Novel CPG Support Are Able To Detect Single Base Pair Mutations," Nucleic Acids Research 17: 7187-7194 (1989).
Newton, et al., Analysis Of Any Point Mutation In DNA. The Amplification Refractory Mutation System (ARMS) Nucleic Acids Research 17: 2503-2516 (1989).
M. Orita, et al., "Detection Of Polymorphisms Of Human DNA By Gel Electrophoresis As Single-Strand Conformation Polymorphism" P.N.A.S. (U.S.A.) 86: 2766-2770 (1989).
H. Orum, et al., "Single Base Pair Mutation Analysis By PNA Directed PCR Clamping," Nucleic Acids Research 21: 5332-5336 (1993).
K.M. Parkhurst, et al., "Kinetic Studies Of Oligonucleotide-DNA Hybridization In Solution By Fluorescence . . . ," 37th Ann. Meeting of the Biophysical Society, Washington, D.C., Abstract W-Pos97, 1993.
R.K. Saiki, et al., "Genetic Analysis Of Amplified DNA With Immobilized Sequence-Specific Oligonucleotide Probes," P.N.A.S. (U.S.A.) 86: 6230-6234 (1989).
Sambrook, et al., "Molecular Cloning: A Laboratory Manual," Synthetic Oligonucleotide Probes, 1989, Cold Spring Harbor Lab Press pp. 11.47 and 11.55-11.57.
P.R. Selvin, "Fluorescence Resonance Energy Transfer," Methods in Enzymology 246: 300-335 (1995).
D. Shore, et al., "DNA Flexibility Studied By Covalent Closure Of Short Fragments Into Circles," P.N.A.S. (U.S.A.) 78: 4833-4837 (1981).
S. Sixou, et al., "Intracellular Oligonucleotide Hybridization Detected By Fluorescence Resonance Energy Transfer (FRET)," 37th Ann. Meeting of the Biophysical Society, Washington, D.C., Abstract Tu-Pos351, 1993.
S. Sixou, et al., "Intracellular Oligonucleotide Hybridization Detected By Fluorescence Resonance Energy Transfer," Nucleic Acids Research 22: 662-668 (1994).
L. Stryer, "Fluorescence Energy Transfer As A Spectroscopic Ruler," Ann. Rev. Biochem. 47: 819-846 (1978).
N. Tibanyenda, et al., The Effect Of Single Base-Pair Mismatches On The Duplex Stability Of d(T-A-T-T-A-A-T -A-T-C-A-A-G-T-T-G) .cndot. d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A), Eur. J. Biochem. 139: 19-27 (1984).
S. Tyagi, et al., Molecula

Affiliated with

Also associated with

Rating

Detectably labeled, dual conformation oligonucleotide probes, as does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Detectably labeled, dual conformation oligonucleotide probes, as, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Detectably labeled, dual conformation oligonucleotide probes, as will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-2005163