Richard Owczarzy papers

Richard Owczarzy High-throughput DNA biophysics
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Biopolymers, 1999, Vol. 52, pp 29-56.

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Spink C.H. (2008) Differential scanning Calorimetry. Methods Cell. Biol. 84, 115-141.
Li X.M., Ng M.T.T., Wang Y.F., Liu X.Q., Li T.H. (2007) Dumbbell-shaped circular oligonucleotides as inhibitors of human topoisomerase I. Bioorg. Med. Chem. Lett. 17, 4967-4971.
Fujimoto B.S., Brewood G.P., Schurr J.M. (2006) Torsional rigidities of weakly strained DNAs. Biophys. J. 91, 4166-4179.
Mandell K.E., Vallone P.M., Owczarzy R., Riccelli P.V., Benight A.S. (2006) Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences. Biopolymers 82, 199-221.
Yakovchuk P., Protozanova E., Frank-Kamenetskii M.D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564-574.
Owczarzy R. (2005) Melting temperatures of nucleic acids: Discrepancies in analysis. Biophys. Chem. 117, 207-215.
Frappat L., Sciarrino A. (2005) Sum rules for free energy and frequency distribution of DNA dinucleotides. Physica A 351, 448-460.
Bayer J., Radler J.O., Blossey R. (2005) Chains, dimers, and sandwiches: Melting behavior of DNA nanoassemblies. Nanoletters 5, 497-501.
Ng P.S., Bergstrom D.E. (2004) Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides. Nucleic Acids Res. 32, e107.
Ding Y., Chan C.Y., Lawrence C.E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32, W135-W141 Suppl. 2.
SantaLucia J., Hicks D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415-440.
Owczarzy R., You Y., Moreira B.G., et al. (2004) Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry 43, 3537-3554.
Escaja N., Gomez-Pinto I., Rico M., et al. (2003) Structures and stabilities of small DNA dumbbells with Watson-Crick and Hoogsteen base pairs. Chembiochem 4, 623-632.
Miramontes P., Cocho G. (2003) DNA dimer correlations reflect in vivo conditions and discriminate among nearest-neighbor base pair free energy parameter measures. Physica A 321, 577-586.
Riccelli P.V., Hall T.S., Pancoska P., et al. (2003) DNA sequence, context and multiplex hybridization reactions: Melting studies of heteromorphic duplex DNA complexes. J. Am. Chem. Soc. 125, 141-150.
Shen Y.Q., Kuznetsov S.V., Ansari A. (2001) Loop dependence of the dynamics of DNA hairpins. J. Phys. Chem. B 105, 12202-12211.
Hall T.S., Pancoska P., Riccelli P.V., et al. (2001) Sequence context and thermodynamic stability of a single base pair mismatch in short deoxyoligonucleotide duplexes. J. Am. Chem. Soc. 123, 11811-11812.
Dubins D.N., Lee A., Macgregor R.B., et al. (2001) On the stability of double stranded nucleic acids. J. Am. Chem. Soc. 123, 9254-9259.
Benight A.S., Pancoska P., Owczarzy R., et al. (2001) Calculating sequence-dependent melting stability of duplex DNA oligomers and multiplex sequence analysis by graphs. Methods Enzymol. 340, 165-192.
Ansari A., Kuznetsov S.V., Shen Y.Q. (2001) Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc. Natl. Acad. Sci. USA 98, 7771-7776.
Kuhn H., Frank-Kamenetskii M.D., Demidov V.V. (2001) High-purity preparation of a large DNA dumbbell. Antisense Nucleic Acids 11, 149-153.