Ultrahigh molecular recognition specificity of competing DNA oligonucleotide strands in thermal equilibrium: a cooperative transition to order

Abstract

The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize their binding partner with astonishing accuracy. In thermal equilibrium it is usually admitted that the affinity of recognizer pairs only depends on the nature of the two binding molecules. Accordingly, Boltzmann factors of binding energy differences relate the molecular affinities among different target molecules that compete for the same probe. Here, we consider the molecular recognition of short DNA oligonucleotide single strands. We show that a better matching oligonucleotide strand can prevail against a disproportionally more concentrated competitor that exhibits reduced affinity due to a mismatch. The magnitude of deviation from the simple picture above may reach several orders of magnitude. In our experiments the effective molecular affinity of a given strand remains elevated only as long as the better matching competitor is not present. We interpret our observations based on an energy-barrier of entropic origin that occurs if two competing oligonucleotide strands occupy the same probe simultaneously. In this situation the relative binding affinities are reduced asymmetrically, which leads to an expression of the free energy landscape that represents a formal analogue of a Landau description of phase transitions. Our mean field description reproduces the observations in quantitative agreement. The advantage of improved molecular recognition comes at no energetic cost other than the design of the molecular ensemble, and the introduction of the competitor. It will be interesting to see if mechanisms along similar lines as exposed here, contribute to the molecular synergy that occurs in biological systems.