Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2008-01-07
2011-11-08
Borin, Michael (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C435S006120
Reexamination Certificate
active
08055451
ABSTRACT:
The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.
REFERENCES:
patent: 5510270 (1996-04-01), Fodor et al.
patent: 6889143 (2005-05-01), Behlke et al.
Sigel. “Interatctions of Metal Ions with Nucleotides and Nucleic Acids and their Constituents”, Chem. Soc. Rev.I 1993, 22:255-267.
Record.Biopolymers1967, 5:993-1008.
Owczarzy et al.,Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures,Biochemistry2004, 43:3537-3554.
Moreira et al., “Effects of Fluorescent dyes, quenchers, and dangling ends on DNA duplex stability”, Biochem. Biophys. Res. Commun. 2005, 327:473-484.
William H. Press et al., Numerical Recipes in C: The Art of Scientific Computing 659-61 (2d Ed. 1992.
Peyret, Ph.D. Thesis, “Prediction of Nucleic Acid Hybridization: Parameters and Algorithms”, Wayne State University, Detroit, Michigan, pp. 128, section 5.4.2 (2000).
Mitsuhashi, “Technical Report: Part 1. Basic Requirements for Designing Optimal Oligonucleotide Probe Sequences”,J. Clin. Lab. Analysis, 1996, 10:277-284.
Efron,B., Tibshirani,R.J., 1993,An Introduction to the Bootstrap. Chapman & Hall/CRC, Boca Raton, FL, pp. 45-123.
Owczarzy et al., “Effects of Sodium Ions on DNA Duplex Oligomers” Improved Predictions of Melting Temperatures,Biochemistry2004, 43:35367-3554.
Plum & Breslauer, “Calorimetry of proteins and nucleic acids”,Curr. Opinion Struct. Biol., 1995, 5:682-690.
Cooper, “Thermodynamic analysis of biomolecular interactions”,Curr. Opinion Chem. Biol., 1999, 3:557-563.
Fasman ed., “Optical Properties of Nucleic Acids, Absorption, and Circular Dichroism Spectra”,Handbook of Biochemistry and Molecular Biology, vol. 1, CRC Press: Cleveland, Ohio, 1975, p. 589.
Warshaw et al., “Optical Properties of Sixteen Dinucleoside Phosphates”,J. Mol. Biol. 1966, 20:29-38.
Caruthers et al., “Chemical Synthesis of Deoxyoligonucleotides and Deoxyoligonucleotide Analogs”,Methods Enzymol. 1992, 211:3-20.
Tan et al., “Nucleic Acid Helix Stability: Effects of Sale Concentration, Cation Valence and Size, and Chain Length”, Biophysical Journal, vol. 90, Feb. 2006, pp. 1175-1190.
Owczarzy et al., “Predicting Sequence-Dependent Melting Stability of Short Duplex DNA Oligomers”,Biopolymers1997, 44:217-239.
Breslauer et al., “Predicting DNA Duplex Stability from the Base Sequence”, Proc. Natl. Acad. Sci. U.S.A. 1986, 83:3746-3750.
Sambrook et al., 1989infra, 11.7-11.8.
Sambrook et al., 1989,infra, 9.50-9.51.
Record, “Effects of Na and Mg Ions on the Helix-Coil Transition of DNA”,Biopolymers1975, 14:2137-2158.
Williams et al., “Laser Temperature-Jump, Spectroscopic, and Thermodynamic Study of Sale Effects on Duplex Formation by dGCATGC”,Biochemistry1989, 28:4283-4291.
SantaLucia, “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics”,Proc. Natl. Acad. Sci. U.S.A. 1998, 95:1460-1465.
Wetmur, “DNA Probes: Applications of the Principles of Nucleic Acid Hybridization”, Critical Review in Biochemistry and Molecular Biology 1991, 26:227-259.
Ivanov & AbouHaidar, “Thermal Stability of Oligodeoxynucleotide Duplexes Bound to Nitrocellulose Filters”,Analytical Biochemistry1995, 232:249-251.
Rychlik et al., “Optimization of the annealing temperature fo DNA amplification in vitro”,Nucleic Acids Res.1990, 18:6409-6412.
Schildkraut et al., “Dependence of the Melting Temperature of DNA on Salt Concentration”,Biopolymers1965, 3:195-208.
SantaLucia et al., “The Thermodynamics of DNA Structural Motifs”,Biophys. Biomol. Struct. 2004, 33:415-440.
Lockhart et al., “Expression monitoring by hybridization to high-density oligonucleotide arrays”Nature Biotech. 1996, 14:1675.
Schena et al., “Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray”,Science1995, 270:467-470.
DeRisi et al., “Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale”,Science1997, 278:680-686.
Meinhoth & Wahl, “Review Hybridization of Nucleic Acids Immobilized on Solid Supports”,Anal. Biochem. 1984, 138:267-284.
Denhardt, “A Membrane-Filter Technique for the Detection of Complementary DNA”, Biochem. Biophys. Res. Commun. 1966, 23:641-646.
Southern, “Detection of Specific Sequences Among DNA Fragments Separated by Gel Electrophoresis”,J. Mol. Biol. 1975, 98:503-517.
Henegariu et al., Multiplex PCR : Critical Parameters and Ste-by-Step Protocol,Biotechniques1997, 23(3):504-11.
Markouatos et al., Multiplex Polymerase Chain Reaction : A Practical Approach,J. Clin. Lab Anal. 2002, 16(1):47-51.
Saiki et al., “Enzymatic Amplification of $/beta $-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Amemia”,Science1985, 230:1350-1354.
Kleppe et al., “Studies on Polynucleotides XCVI. Repair Replication of Short Synthetic DNA's as catalyzed by DNA Polymerases”,J. Mol. Biol.1971, 56:341-361.
Nanko et al. “Nucleic acid duplex stability: influence of base composition on cation effects”, Nucleic Acids Research, (1999), vol. 27, No. 14, pp. 2957-2965.
Nakano et al., Nucleic Acid Duplex Stability: Influence of Base Composition on Cation Effects. Nucleic Acids Research, 1999, vol. 27, pp. 2957-2965.
Tan et al., Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length. Biophysical Journal, Feb. 2006, vol. 90, pp. 1175-1190.
Ahsen et al., Oligonucleotide Melting Temperatures under PCR Conditions: Nearest-Neighbor Corrections for Mg2+, Deoxynucleotide triphosphate, and Dmethyl Sulfoxide Concentrations with Comparison to Alternative Empirical Formulas. Clinical Chemistry, 2001, vol. 47, pp. 1956-1961.
Behlke Mark Aaron
Moreira Bernardo
Owczarzy Richard
Walder Joseph Alan
You Yong
Borin Michael
Integrated DNA Technologies, Inc.
McDonnell Boehnen & Hulbert & Berghoff LLP
LandOfFree
Method for estimating a melting temperature of a nucleic... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method for estimating a melting temperature of a nucleic..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for estimating a melting temperature of a nucleic... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4266759