Analysis of the electrophoretic migration of DNA frayed wires

We analyzed the electrophoretic behaviour of the unusual multi-stranded DNA complexes, frayed wires, in polyacrylamide gels under non-denaturing conditions. Frayed wires arise from the association of several strands of a parent oligonucleotide that possesses long terminal runs of consecutive guanines. According to the structural model proposed for frayed wires, there are two distinct conformational domains, a guanine stem and single stranded arms displaced from the stem. The presence of the two domains affects the electrophoretic migration of the frayed wires, resulting in a greater retardation compared to that of double stranded DNA of the same molecular weight. The degree of retardation is determined by the relative length of the stem and the arms; the complexes with longer arms display a stronger dependence on the total molecular weight. Reptation plots (mobility x molecular weight vs. molecular weight) were used to study the electrophoretic behaviour of frayed wires that arise from the different parent oligonucleotides. The plots are unique for each type of frayed wire. The characteristic parameter, the position of the maximum of the reptation plot, depends on the type of the frayed wire as well as the total gel concentration. The plots become similar when we replot the mobility data taking into account only the single stranded arms of the frayed wires. The positions of the maximum and the overall shape are very close for the four types of frayed wires studied.