General criterion for controllable conformational transitions of single and double stranded DNA

Abstract

Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various phenomena, including DNA condensation, protein folding, and the behaviour of polymer solutions. In biological processes such as DNA condensation the collapse is sensitively induced by a small amount of added molecules. Here we derive a general criterion for the effect of such agents on conformational transitions. We find two different scenarios depending on chain stiffness. If the persistence length --the characteristic distance along which the chain retains its direction-- is smaller than the range of attractive correlations induced by the agent (typically up to several nanometres), the chain contracts gradually. Stiffer chains undergo sharp collapse. We thereby suggest that the enhanced rigidity of double-stranded DNA as compared to the single strand is a prerequisite for sharp, controllable conformational transitions.