Circular Dichroism of DNA Frayed Wires

Abstract

Ultraviolet circular dichroism spectra are reported for the oligonucleotide d(A 15G 15) in aqueous solutions containing 5 mM MgCl 2 at several temperatures and in the presence of partially complementary oligonucleotides. Oligonucleotides with several consecutive terminal guanine residues self-associate to form aggregates, called frayed wires, that consist of integer numbers of strands. A “stem” is formed through interactions between the guanine residues of the associated oligonucleotides, whereas the adenine “arms” remain single stranded. Upon subtracting the circular dichroism spectrum of d(A 15) from that of d(A 15G 15), one obtains a spectrum that closely resembles previously published spectra of poly(G). Subtracting spectra measured at temperatures between 10°C and 60°C reveals the resultant spectra to be independent of temperature, consistent with the extreme thermal stability observed for the aggregated structures. Upon the addition of d(T 15) to the solution, complexes with the adenine portion of the d(A 15G 15) frayed wires are formed. Subtraction of d(A 15):d(T 15) spectra measured at several temperatures from those of the d(A 15G 15):d(T 15) does not significantly alter the spectrum of the guanines. The helix-coil transition temperature of d(A 15):d(T 15) duplex is identical to that of the unbinding of d(T 15) from d(A 15G 15):d(T 15) complexes. Experiments using oligonucleotides in which the adenines were replaced with sequences of bases yielded similar results. By varying the length of the nonguanine tract, it is shown that the solubility of the complexes increases with the length of the nonguanine region of the oligonucleotide.