Double-stranded DNA in methanol-ethanol-buffer solvent system

DNA in a solvent system consisting of roughly equal volumes of methanol and ethanol and 5% buffer has a conservative circular dichroism (CD) spectrum of very low intensity above 220 nm and an increase of epsilon258 comparable to that of denatured DNA (about 40%). A direct comparison of this spectrum with the CD of single-stranded DNA reveals many differences, indicating DNA in this solvent system has a conformation different from that of denatured DNA. When the alcohols are removed, the B form conformation and normal epsilon258 are restored in native DNA, while single-stranded DNA remains denatured. A double-stranded structure of DNA in the methanol-ethanol-buffer solvent system is confirmed by the neutral cesium chloride density gradient centrifugation of DNA in which one chain is labeled with [14C]thymidine and the other [3H]5-bromodeoxyuridine. The doubly labeled DNA exposed to the alcohol solvent system has a centrifugal pattern identical with that of control DNA; the two radioactivities cosediment and form a superimposing band, distinctly different from that of single-stranded DNA; 3H-labeled (thymidine) chains sediment further than 14C-labeled chains (5-bromo-deoxyuridine). Denatured DNA exhibits varying CD spectra depending on solvents. It is suggested that single-stranded DNA in different solvent systems assumes different modes of base stacking.