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 condi tions. Frayed wires arise from the association of several strands of a pare nt oligonucleotide that possesses long terminal runs of consecutive guanine s. According to the structural model proposed for frayed wires, there are t wo distinct conformational domains, a guanine stem and single stranded arms displaced from the stem. The presence of the two domains affects the elect rophoretic migration of the frayed wires, resulting in a greater retardatio n 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 fra yed wires that arise hom different parent oligonucleotides. The plots are u nique for each type of frayed wire. The characteristic parameter, the posit ion 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 a rms of the frayed wires. The positions of the maximum and the overall shape are very close for the four types of frayed wires studied. (C) 1998 Elsevi er Science B.V. All rights reserved.