Separation of Preferential Interaction and Crowding Effects on DNA Hairpin and Duplex Formation

Abstract

Solutes affect protein and nucleic acid processes as a consequence of their competition with water for biopolymer surfaces that become exposed (or buried) in the process (“preferential interactions”) and through their ability to occupy space and reduce the available volume of the solution (“crowding”). Here we develop a quantitative analysis of the molecular weight dependence both preferential interaction and crowding effects of flexible coil polymers, with the capability of interpreting or predicting effects of any flexible coil polymer on any biopolymer process. We report dependences of free energies of DNA hairpin helix unfolding and duplex dissociation on PEG concentration (PEG m-values) for EG and a wide range of PEG chain lengths. EG and small PEG oligomers are destabilizing to hairpin and duplex; with increasing PEG size this destabilization decreases so that large PEGs are only slightly destabilizing to the hairpin and stabilizing to the duplex. We conclude that contributions of preferential interactions to PEG m-values increase in proportion to the product of the amount of DNA surface exposed on melting and the amount of surface of PEG accessible to, and therefore able to interact with, this DNA surface. We further conclude that the large stabilizing effect of crowding on the duplex is due to the assembly of two reactants into product while the crowding effect on the hairpin is much weaker because hairpin folding involves only a small change in shape and not assembly of multiple reactants. Finally, we examine the concentrated PEG solution regime where PEG chains interpenetrate. NIH GM47022 and Biophysics training grant.