Hybridization and mismatch discrimination using...

Details Hybridization and mismatch discrimination using... Hybridization and mismatch discrimination using...

2005-04-26

2005-04-26

Whisenant, Ethan (Department: 1634)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091100, C435S091200, C536S025600

Reexamination Certificate

active

06884584

ABSTRACT:
Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides. The MGB-conjugated probes and primers described herein facilitate various analytic and diagnostic procedures, such as amplification reactions, PCR, detection of single-nucleotide polymorphisms, gene hunting, differential display, fluorescence energy transfer, hydrolyzable probe assays and others; by allowing the use of shorter oligonucleotides, which have higher specificity and better discriminatory power.

REFERENCES:
patent: 4358535 (1982-11-01), Falkow et al.
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4800159 (1989-01-01), Mullis et al.
patent: 4835263 (1989-05-01), Nguyen et al.
patent: 4868103 (1989-09-01), Stavrianopoulos et al.
patent: 4868105 (1989-09-01), Urdea et al.
patent: 4883750 (1989-11-01), Whiteley et al.
patent: 5124246 (1992-06-01), Urdea et al.
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5237101 (1993-08-01), Nicolaou et al.
patent: 5419966 (1995-05-01), Reed et al.
patent: 5446137 (1995-08-01), Maag et al.
patent: 5449767 (1995-09-01), Ward et al.
patent: 5492806 (1996-02-01), Drmanac et al.
patent: 5512667 (1996-04-01), Reed et al.
patent: 5525464 (1996-06-01), Drmanac et al.
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 5574142 (1996-11-01), Meyer, Jr. et al.
patent: 5646126 (1997-07-01), Cheng et al.
patent: 5659022 (1997-08-01), Kutyavin et al.
patent: 5776907 (1998-07-01), Kohn et al.
patent: 5786138 (1998-07-01), Swenson
patent: 5801155 (1998-09-01), Kutyavin et al.
patent: 6312894 (2001-11-01), Hedgpeth
patent: 070685 (1985-10-01), None
patent: 320308 (1993-11-01), None
patent: 336731 (1994-05-01), None
patent: WO 9003370 (1990-04-01), None
patent: WO 9014353 (1990-11-01), None
patent: WO 9210588 (1992-06-01), None
patent: WO 9220698 (1992-11-01), None
patent: WO 9303736 (1993-03-01), None
patent: WO 9417092 (1994-08-01), None
patent: WO 9529184 (1995-11-01), None
patent: WO 9617957 (1996-06-01), None
patent: WO 9640711 (1996-12-01), None
patent: WO 9712896 (1997-04-01), None
patent: WO 9802448 (1998-01-01), None
patent: WO 9632496 (1999-10-01), None
Afonina et al., “Sequence-specific arrest of primer extension on single-stranded DNA by an oligonulcleotide-minor groove binder conjugate,” Proc. Natl. Acad. Sci. USA, vol. 93:3199-3204.
Agrawal et al., “Pharmacokinetics, biodistribution, and stability of oligodeoxynucleotide phosphorothioates in mice,” Proc. Natl. Acad. Sci. USA, vol. 88:7595-7599 (1991).
Animati et al., “Synthesis of Two Distamycin Analogues and Their Binding Mode to d(CGCAAATTTGCG)2in the 2:1 Solution Complexes as Determined by Two Dimensional1H-NMR,” J. Med. Chem., vol. 38:1140-1149 (1995).
Asseline et al., “Nucleic acid-binding molecules with high affinity and base sequence specificity: Interacting agents covalently linked to oligodeoxynucleotides,” Proc. Natl. Acad. Sci. USA, vol. 81:3297-3301 (1984).
Atkinson T., and Smith M., “Solid-phase Synthesis of Oligodeoxyribonucleotides by the Phosphite-triester Method,” InOligonucleotide Synthesis, A Practical Approach, M.J. Gait, ed., IRL Press, Oxford, UK, pp. 35-81 (1984).
Boger et al., “Studies on the Total Synthesis of CC-1065: Preparation of a Synthetic, Simplified 3-Carbamoyl-1,2-dihydro-3H-pyrrolo[3,2-e]indole Dimer/Trimer/Tetramer (CDPI Dimer/Trimer/Tetramer) and Developing of Methodology for PDE-I Dimer Methyl Ester Formation,” J. Org. Chem., vol. 52:1521-1530 (1987).
Boger et al., “CC-1065 Partial Structures: Enhancement of Noncovalent Affinity for DNA Minor Groove Binding through Introduction of Stabilizing Electrostatic Interactions,” J. Org. Chem., vol. 57:1277-1284 (1992).
Boger et al., “CC-1065 and the duocarmycins: Unraveling the keys to a new class of naturally derived DNA alkylating agents,” Proc. Natl. Acad. Sci. USA, vol. 92:3642-3649 (1995).
Bolli et al., “Watson-Crick base-pairing properties of bicyclo-DNA,” Nucleic Acids Res., vol. 24:4660-4667 (1996).
Caetano-Anolles et al., “DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers,” Biotechnology, vol. 9:553-557 (1991).
Cardullo et al., “Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer,” Proc. Natl. Acad. Sci. USA, vol. 85:8790-8794 (1988).
Chen et al., “A New DNA Minor Groove Binding Motif: Cross-Linked Lexitropsins,” J. Am Chem. Soc., vol. 116:6995-7005 (1994).
Cosstick et al., “Synthesis of d(GC) and d(CG) Octamers Containing Alternating Phosphorothioate Linkages: Effect of the Phosphorothioate Group on the B-Z Transiton,” Biochemistry, vol. 24:3630-3638 (1985).
Demidov et al., “Kinetics and mechanism of polyamide (“peptide”) nucleic acid binding to duplex DNA,” Proc. Natl. Acad. Sci. USA, vol. 92:2637-2641 (1995).
Dempcy et al., “Synthesis of a thymidyl pentamer of deoxyribonucleic guanidine and binding studies with DNA homopolynucleotides,” Proc. Natl. Acad. Sci. USA, vol. 92:6097-6101 (1995).
Don et al., “‘Touchdown’ PCR to circumvent spurious priming during gene amplification,” Nucleic Acids Res., vol. 19:4008 (1991).
Draper et al., “A Method for Linking Fluorescent Labels-to Polynucleotides: Application to Studies of Ribosome-Ribonucleic Acid Interactions,” Biochemistry, vol. 19:1774-1781 (1980).
Eckstein et al., “Polyribonucleotides Containing a Phosphorothioate Backbone,” Eur. J. Biochem., vol. 13:558-564 (1970).
Fagan et al., Cooperative Binding of Distamycin-A to DNA in the 2:1 Mode, J. Am Chem. Soc., vol. 114:1080-1081 (1992).
Freifelder, “Fluorescence Spectroscopy,” Physical Biochemistry, Second Edition, W.H. Freeman & Co., San Francisco p. 537-542 (1982).
Gamper et al., “Facile preparation of nuclease resistant 3′ modified oligodeoxynucleotides,” Nucleic Acids Res., vol. 21(1):145-150 (1993).
Gibson K.J. & Benkovic, S.J., “Synthesis and application of derivatizable oligonucleotides,” Nucleic Acids Res., vol. 15:6455-6467 (1987).
Giovannangeli et al., “Oligonucleotide clamps arrest DNA synthesis on a single-stranded DNA target,” Proc. Natl. Acad. Sci. USA , vol. 90:10013-10017 (1993).
Godovikova et al., “Reactive Oligonucleotide Derivatives with a Zwitter-Ionic Terminal Phosphate Group for Affinity Reagents and Probe Construction,” Bioorgan. Khim., vol. 15:1246-1259 (1989).
Grehn L., et al., “Novel Efficient Total Synthesis of Antiviral Antibiotic Distamycin A,” J. Org. Chem., vol. 46:3492-3497 (1981).
Gryaznov et al., “Oligodeoxyribonucleotide N3′→P5′ Phosphoramidates: Synthesis and Hybridization Properties,” J. Am. Chem. Soc., vol. 116:31434-3144 (1994).
Gryaznov et al., “Modulation of oligonucleotide duplex and triplex stability via hydrophobic interactions,” Nucleic Acids Res., vol. 21(25):5909-5915 (1993).
Heid et al., “Real Time Quantitative PCR,” Genome Res., vol. 6:986-994 (1996).
Huang et al., “Diagnosis of Glucose-6-Phosphate Dehydrogenase (G6PD) Mutations by DNA Amplification and Allele-Specific Oligonucleotide Probes,” Acta Haematol., vol. 88:92-95 (1992).
Hurley et al., “Reaction of the

Affiliated with

Also associated with

Rating

Hybridization and mismatch discrimination using... does not yet have a rating. At this time, there are no reviews or comments for this patent.

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

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-3419449