Separating Excluded Volume and Chemical Effects of PEG on DNA Helix Formation

Abstract

Small solutes affect protein and nucleic acid processes because of favorable or unfavorable chemical interactions of the solute with the biopolymer surface exposed or buried in the process. Large solutes also exclude volume and affect processes where biopolymer molecularity and/or shape changes. We recently developed an analysis to separate and interpret or predict excluded volume and chemical effects of a flexible coil polymer on a process. As a test system, of significance in its own right, we determined effects of the full series from ethylene glycol (EG) to polyethylene glycols (PEG) on the equilibrium constants for all-or-none intramolecular hairpin and intermolecular duplex formation by 12-nucleotide DNA strands. We find that helix-destabilizing chemical effects of PEG and its oligomers on these processes increase in proportion to the product of the amount of DNA surface exposed on melting and the amount of PEG surface that is accessible to this DNA; these chemical effects are completely described as the sum of interactions of PEG end and interior groups with this DNA surface. Helix-stabilizing excluded volume effects, once separated from these chemical effects, are quantitatively described by the analytical theory of Hermans, which predicts the excluded volume between a flexible polymer and a rigid molecule. An increase in PEG size at constant concentration of PEG monomer increases the excluded volume effect but decreases the chemical interaction effect, because in a large PEG coil a smaller fraction of the monomers are accessible to the DNA. Volume exclusion by PEG has a much larger effect on intermolecular duplex formation than on intramolecular hairpin formation.Reference: PNAS 2011 108 (31) 12699-12704 (http://www.pnas.org/content/108/31/12699.long)Supported by NIH grant GM47022 (TR) and a NIH Molecular Biophysics Traineeship to BK.