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Energetic of Cooperative Binding of Oligonucleotides with Discrete Dimerization Domains to DNA by Triple Helix Formation

Distefano, Michael D. and Dervan, Peter B. (1993) Energetic of Cooperative Binding of Oligonucleotides with Discrete Dimerization Domains to DNA by Triple Helix Formation. Proceedings of the National Academy of Sciences of the United States of America, 90 (4). pp. 1179-1183. ISSN 0027-8424.

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Cooperativity in oligonucleotide-directed sequence-specific recognition of DNA by triple helix formation can be enhanced by the addition of discrete dimerization domains. The equilibrium association constants for cooperative binding of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and occupy adjacent sites on double helical DNA by triple helix formation have been measured by quantitative affinity cleavage titration. For two oligonucleotides that bind unique neighboring 11-bp and 15-bp sites on double helical DNA, and dimerize by formation of an 8-bp Watson-Crick mini-helix, the free energy of binding is -8.0 and -9.7 kcal·mol^-1, respectively, and the cooperative energy of interaction is -2.3 kcal·mol^-1 (1 kcal = 4.18 kJ). The energetics of this artificial nucleic acid cooperative intermolecular assembly can mimic naturally occurring cooperative protein-DNA systems, such as the phage {lambda} repressor.

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Additional Information:Copyright © 1993 by National Academy of Sciences This paper was presented at a colloquium entitled "Molecular Recognition," organized by Ronald Breslow, held September 10 and 11, 1992, at the National Academy of Sciences, Washington, DC. We thank Scott Singleton and Natalia Colocci for helpful discussions. This work was supported by the National Institutes of Health (GM-35724) and a Damon Runyon-Walter Winchell Cancer Research Fund postdoctoral fellowship to M.D.D.
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Deposited On:21 Sep 2005
Last Modified:14 Nov 2014 19:18

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