Methods for searching polynucleotide probe targets in databases

Details Methods for searching polynucleotide probe targets in databases Methods for searching polynucleotide probe targets in databases

2006-08-01

2006-08-01

Brusca, John S. (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C435S006120

Reexamination Certificate

active

07085652

ABSTRACT:
Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.

REFERENCES:
Kaderali et al. Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics vol. 18, No. 10, pp. 1340-1349 (2002).
Hyndman et al. Software to Determine Optimal Oligonucleotide Sequences Based on Hybridization Simulation Data. BioTechniques, 1996, vol. 20, No. 6, pp. 1090-1097, especially p. 1090.
PCT International Search Report, mailed Aug. 15, 2003. For International Application No. PCT/US03/04354.
Lockhart, D.J.; et al., “Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays.” Nature Biotechnology, vol. 14, (1996): pp. 1675-1680.
Myers, G. “A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming.” Journal of the ACM vol. 46, No. 3, (1999): pp. 395-415.
Peyret, N., and SantaLucia, J., Jr. “Prediction of Nucleic Acid Hybridization: Parameters and Algorithms.” Abstract of Dissertation, Wayne State University, Detroit, MI: pp. 353-354.
Gotoh, O., “An Improved Algorithm For Matching Biological Sequences.” J. Mol Biol. vol. 162, (1982): pp. 705-708.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. “Basic Local Alignment Search Tool.” J. Mol. Biol., vol. 215, (1990): pp. 403-410.
Smith, T.F. and Waterman, M.S. “Identification of Common Molecular Subsequences.” J. Mol. Biol., vol. 147, (1981): pp. 195-197.
Pearson, W.R., and Lipman, D.J. “Improved Tools for Biological Sequence Comparison.” Proc. Nat'l. Acad. Sci. USA, vol. 85, (1988): pp. 2444-2448.
Peterson, J.C., et al., “Sequence Information Signal Processor for Local and Global String Comparisons,” California Institute of Technology, Pasadena, CA, USA: U.S. Appl. No. 5,632,041 (1997).
Cherry, J.M., et al, SGD: Saccharomyces Genome Database. Nucleic Acids Res., vol. 26, (1998), No. 1; pp. 73-79.
Kane, M.D. et al., “Assessment of Sensitivity and Specificity of Oligonucleotide (50mer) Microarrays.” Nucleic Acids Research,•vol. 28, No. 22, (2000): pp. 4552-4557.
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs.” Nucleic Acids Research, vol. 25, No. 17. (1997): pp. 3389-3402.
Lockhart, D.J., and Winzeler, E.A. “Genomics, Gene Expression and DNA Arrays.” Nature vol. 405, (2000): pp. 827-836.
Roses, A. “Pharmacogenetics and the Practice of Medicine.” Nature, vol. 405, (2000): pp. 857-865.
Duggan, D.J. et al., “Expression Profiling Using cDNA Microarrays.” Nature Genetics Supplement, vol. 21, (1999): pp. 10-14.
Gray, D.M., and Tinoco, I. , Jr. “A New Approach to the Study of Sequence Dependent Properties of Polynucleotides.” Biopolymers, vol. 9, (1970): pp. 223-244.
Allawi, H.T. and SantaLucia, J., Jr. “Thermodynamics and NMR of Internal G•T Mismatches in DNA.” Biochemistry, vol. 36, (1997): pp. 10581-10594.
Allawi, H.T. and SantaLucia, J., Jr. “Nearest Neighbor Thermodynamic Parameters for Internal G•A Mismatches in DNA.” Biochemistry, vol. 37, (1998): pp. 2170-2179.
Allawi, H.T. and SantaLucia, J., Jr. “Thermodynamics of Internal C•T Mismatches in DNA.” Nucleic Acids Research, vol. 26, No. 11, (1998): pp. 2694-2701.
Allawi, H.T. and SantaLucia, J., Jr. “Nearest Neighbor Thermodynamics of Internal A•C Mismatches in DNA: Sequence Dependence and pH Effects.” Biochemistry, vol. 37, (1998): pp. 9435-9444.
Peyret, N., et al., “Nearest Neighbor Thermodynamics and NMR of DNA Sequences with Internal A•A, C•C, G•G, and T•T Mismatches.” Biochemistry, vol. 38, (1999): pp. 3468-3477.
SantaLucia, J., Jr. “A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics.” Proc. Nat'l. Acad. Sci. USA, vol. 95, (1998): pp. 1460-1465.
Li, Fugen and Stormo, Gary D. “Selecting Optimum DNA Oligos for Microarrays.” 2000 IEEE: pp. 200-207.
Ahsen, Nicholas von, et al. “Application of a Thermodynamic Nearest-Neighbor Model to Estimate Nucleic Acid Stability and Optimize Probe Design: Prediction of Melting Points of Multiple Mutations of Apolipoprotein B-3500 and Factor V with a Hybridization Probe Genotyping Assay on the LightCycler.”, Clinical Chemistry—von Ahsen et al. 45 (12): 2094: pp. 1-13, 1999.
Rognes, T., and Seeberg, E. “Six Fold Speed-up of Smith-Waterman Sequence Database Searches Using Parallel Processing on Common Microprocessors.” Bioinformatics vol. 16, No. 8., (2000), pp. 699-706.
Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C., “A Model of Evolutionary Change in Proteins.” Atlas of Protein Sequence and Structure, 1978, pp. 345-352.
Henikoff, S., and Henikoff, J. G. “Amino Acid Substitutions Matrices From Protein Blocks.” (1992) Proc. Natl. Acad. Sci. USA, vol. 89, pp. 10915-10919.

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