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 for molecular self-organization. A prominent example is the biological cell where a myriad of different molecular receptor pairs recognize their binding partners with astonishing accuracy within a highly crowded molecular environment. 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 can prevail against a disproportionally more concentrated competitor with reduced affinity due to a mismatch. We investigate the situation using fluorescence-based techniques, among them Förster resonance energy transfer and total internal reflection fluorescence excitation. We find that the affinity of certain strands appears considerably reduced only as long as a better matching competitor is present. Compared to the simple Boltzmann picture above we observe increased specificity, up to several orders of magnitude. We interpret our observations based on an energy-barrier of entropic origin that occurs if two competing oligonucleotide strands occupy the same probe simultaneously. Due to their differences in binding microstate distributions, the barrier affects the binding affinities of the competitors differently. Based on a mean field description, we derive a resulting expression for the free energy landscape, a formal analogue to a Landau description of phase transitions reproducing the observations in quantitative agreement as a result of a cooperative transition. The advantage of improved molecular recognition comes at no energetic cost other than the design of the molecular ensemble and the presence of the competitor. As a possible application, binding assays for the detection of single nucleotide polymorphisms in DNA strands could be improved by adding competing strands. It will be interesting to see if mechanisms along similar lines as exposed here contribute to the molecular synergy that occurs in biological systems.

The melting curves of calf thymus-DNA are buffer specific

“…At physiological pH and ionic strength (about 150 mM), DNA is a polyelectrolyte whose behavior has been described by Poisson-Boltzmann and counterion-condensation theories [62,63]. DNA charges are shielded by counterions [35], thus limiting its expansion due to repulsive interactions between charged strands [63]. Polyelectrolyte theory provides a good description for the dependence of Tm on ionic strength [64].…”

“…Hence, DNA-related experiments require the strict control of pH through the use of buffers [35]. Several studies showed that buffers do affect DNA properties [36][37][38][39][40][41][42][43][44].…”

“…Another specific buffer effect involving Tris, Bis-Tris propane (BTP), TES, HEPES, and cacodylate was observed in DNA digestion kinetics by EcoRV endonuclease [46]. Recently, changing from Tris to CAPS (3-(cyclohexylamino)propane-1-sulfonic acid) buffers, a better sedimentation of DNA was obtained [35]. Buffer choice needs also to be considered in nucleotide formulation stability [17].…”