Single-Molecule Elasticity Measurements Reveal Swelling Transition in PEG and Certain ssDNAs

Abstract

Although long, flexible polymers form self-avoiding random walks when free in solution, most single-molecule stretching experiments elongate the polymer into a highly-aligned geometry, preventing the long-range interactions that lead to polymer swelling. Here, we report single-molecule stretching data at low force and quantify the effects of swelling in synthetic PEG molecules and various sequences of single-stranded DNA (including heterogeneous ssDNA and poly(dA)). These data will be discussed in light of classic polymer scaling theory and electrostatic effects. Synthetic PEG molecules show multiple elastic transitions as force is increased: 1. at low force the polymer forms swollen coils, 2. at intermediate force it forms smaller, ideal coils, and 3. at high force it forms an elongated chain. In contrast, charged, denatured single-stranded DNA, in mono- and divalent salt solutions, shows an immediate transition from a swollen chain at low forces to an extended chain at high forces, lacking the intermediate ideal coils regime. Single-stranded DNA composed entirely of adenine bases (poly(dA)) cooperatively base stacks. Thus, at low forces, poly(dA) has stiff base-stacked domains interspersed with domains of swollen coils, indicated by an elastic response that is intermediate between ideal and self-avoiding. These data permit estimation of microscopic, intensive properties such as the Kuhn length and excluded volume, which have value in understanding the polymer's low (to zero) force structure and how it varies with polymer size and solvent conditions (e.g., salt concentration).