DNA oligomer binding in competition exhibits cooperativity

Abstract

Binding of two complementary DNA single strands to a double-helix, DNA hybridization, is a sequence specific molecular recognition process that plays important roles in biology and biotechnological applications. In the past much work has been devoted to understand double helix formation, however, DNA binding in complex situations often remains difficult to deal with. Here we use fluorescence anisotropy to assess the binding affinities of DNA oligonucleotide strands that compete for hybridization to the same probe molecule in thermal equilibrium. We find that the ratio of the binding constants in competition can change substantially compared to pairwise assessments. This is a signature of non-trivial interaction among the competitors: the binding microstates of each strand are affected by the presence of the other, but to a different degree. To our knowledge this type of phenomenon is not included in current equilibrium models of oligonucleotide binding. We suggest interactions beyond double helix conformations to cause the observed cooperative behavior. The cooperativity could produce more complex binding phenomena than previously thought.