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

Abstract

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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