Cooperative binding of oligonucleotides to DNA by triple helix formation: dimerization via Watson-Crick hydrogen bonds

Abstract

[Introduction] Cooperative binding by proteins to DNA results in higher sequence specificity as well as greater sensitivity to concentration changes. We recently reported cooperative binding of two oligonucleotides at abutting sites by triple helix formation on double helical DNA. However, the enhanced binding observed was modest (a factor of 3.5) and likely due to favorable basestacking interactions between adjacent oligonucleotides and/or induced conformational changes propagated to adjacent binding sites. Thus, the issue arises whether cooperativity in oligonucleotide-directed triple helix formation can be enhanced by the addition of discrete dimerization domains. We report here the binding properties of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and bind neighboring sites on double helical DNA by triple helix formation.