Sequence and Environmental Effects on the Self-Assembly of DNA Oligomers Possessing GxT2Gy Segments

Abstract

It is well-known that DNA oligomers possessing contiguous guanine bases can assume non-Watson−Crick type structures through the formation of four-stranded species. The architecture of these four-stranded structures is highly dependent upon the sequence of the DNA and the conditions (e.g., buffer, pH, ionic strength, cations present, and temperature) under which the DNA is prepared. This lab has previously reported the self-assembly of DNA oligomers of sequence C₄T₄G₄T_1-4G₄ into multistranded high molecular weight species [Dai, T.-Y., Marotta, S. P., & Sheardy, R. D. (1995) Biochemistry 34, 3655−3662]. In order to further investigate the sequence and environmental effects on the self-assembly of DNA oligomers possessing G_xT₂G_y (where x = 1, 3, or 4 and y = 2−5) segments, the synthesis of a number of such oligomers was undertaken. DNA samples were prepared in standard phosphate buffer (10 mM phosphate, pH 7.0) and NaCl, KCl and/or MgCl₂ added to different concentrations in order to evaluate the influence of the cations and their concentrations on the self-assembly of the DNA oligomers. The self-assembly of these oligomers was monitored by nondenaturing polyacrylamide gel electrophoresis and circular dichroism studies. Electrophoresis of the oligomers in either 100 mM K⁺ or 50 mM Na⁺ with 50 mM K⁺ indicated the formation of one or two molecular species for these oligomers. In contrast, electrophoresis of these oligomers in the presence of both 100 mM K⁺ and 20 mM Mg²⁺ give a ladder of multiple bands of high molecular weight indicative of multistanded DNA structure formation. The results presented here indicate that self-assembly into high molecular weight species is favored by the presence of Mg²⁺ as well as the presence of four or more bases in the terminal G_y segment. These results also suggest that the structure of telomeric DNA, which possesses similar sequences, may be quite unusual.