DEHYDRATING AGENTS SHARPLY REDUCE CURVATURE IN DNAS CONTAINING A-TRACTS

The structural basis of DNA curvature remains elusive, because models for curvature based on crystallographic structures of molecules contai ning A tracts do not agree with any of the models for sequence-directe d curvature based on solution studies, Here we demonstrate that the di fference is probably due to MPD (2-methyl-2,4-pentanediol), the dehydr ating agent commonly used in crystallography, One characteristic signa ture of curved DNA molecules is that they run anomalously slowly on po lyacrylamide gels, appearing to be larger than they actually are, The gel anomalies of three curved DNAs from trypanosome kinetoplast minici rcles drop monotonically with increasing MPD concentration, indicating that MPD straightens molecules that are curved in aqueous solution, T his is not due to some non-specific effect of MPD on poly(dA) or polyp urine tracts, because control molecules containing dA(70) and dG(43) r un normally over the full range of MPD concentrations, Circular dichro ism spectra are not affected by MPD, ruling out a conformational chang e to a structure outside the B-DNA family, The effect is not due to MP D-induced changes in phasing of the curved sequences, because MPD has virtually no effect on the linking numbers of relaxed plasmids contain ing either curved sequences or dA(70). At the concentrations of MPD us ed in X-ray crystallography, the curvature of DNAs containing A tracts is substantially lower than in solution, which probably explains the ongoing discrepancies between the crystallographic results and models based on solution studies.