Thermal activation of DNA frayed wire formation

Abstract

Dynamic light scattering has been used to study the formation of stable multistranded DNA complexes called frayed wires. DNA frayed wires arise from the indefinite self-association of oligonucleotides with long terminal tracks of guanines, e.g. d(A 15G 15). The complexes are stabilized via guanine–guanine interactions resulting in the formation of a guanine stem. Non-guanine portions of the oligonucleotide are disposed away from the stem and form single stranded arms. The indefinite nature of the self-association of these oligonucleotides leads to a distribution of aggregate molecular weights. The distribution arises from aggregated species that differ from one another by the number of self-associated oligonucleotides. In light-scattering experiments, the autocorrelation functions collected for frayed wires are bimodal. The slow mode, often observed for samples containing DNA and other polyelectrolytes, has been ascribed to the formation of large unspecific aggregates due to electrostatic or other long-range interactions. We attribute the fast mode to the translational diffusion of the polydisperse population in the frayed wire sample. We use the mean of the fast mode to characterize the growth of the frayed wires. Consistent with the gel electrophoresis studies, the aggregation of frayed wires is promoted by the presence of magnesium ions and incubation at high temperature. The rate of aggregate formation increases with temperature, indicating the positive activation energy for the reaction. We propose an energy diagram for the formation/disruption of frayed wires revealing the catalytic-like role of the complementary strand in the denaturation of high molecular weight complexes.