DNA frayed wires: Differential polymerization of d(A(n)G(m)) oligonucleotides

Oligodeoxyribonucleotides with terminal I-rns of contiguous guanines, d(A(n )G(m)), spontaneously associate into high molecular weight complexes that r esolve on polyacrylamide gels as a regular ladder pattern of bands with low mobility. The aggregates, which we call frayed wires, arise from the inter action between the guanine residues of the oligonucleotides; the adenine tr acts are single stranded and can rake part in Watson-Crick interactions. Ol igonucleotides, with different arm-to-stem ratios and total length, readily associate in the presence of Mg2+ to form aggregates consisting of an inte ger number of strands. The type of the observed aggregates is determined by the length of the guanine run. Oligonucleotides with sir guanines form fou r- and eight-stranded complexes; there is no further polymerization. An inc rease in the number of guanine residues to 10 and 15 lends to polymerizatio n resulting in a ladder pattern of rip to 9 bands and an intense signal at the top of the gel. The relative population of any given species in a fraye d wire sample is governed by the guanine stern length and is riot affected to any substantial extent by arms lip to 40 bases long, The type and concen tration of the cation in the solution affect the degree of aggregation, wit h Na+ and K+ promoting the formation of complexes comprised of 2-4 strands and Mg2+ being the most effective in facilitating polymerization. The elect rophoretic behavior of frayed wires was analyzed in the framework of the Og ston theory. The free mobility of frayed wires in the solution is close to the values reported for single-stranded DNA, indicating the equivalence of the charge density of the two conformations. The retardation coefficients f or frayed wires arising from a single kind of parent strand increase with t he introduction of each additional strand There is ilo correlation between the retardation coefficient and the type of parent strand; rather, the magn itude of the retardation coefficient is determined by the total molecular w eight of the complex. The values of the retardation coefficients ape consis tently higher than those for double-stranded DNA and they display much stro nger dependence on the total molecular weight. Presumably the distinct stru ctural and dynamic characteristics of the two conformations account for the ir different electrophoretic behavior (C) 1999 John Wiley & Sons, Inc.