EFFECT OF TEMPERATURE ON DNA SECONDARY STRUCTURE IN THE ABSENCE AND PRESENCE OF 0.5 M TETRAMETHYLAMMONIUM CHLORIDE

Changes in the average secondary structures of three different linear DNAs over the premelting region from 5 to 60 degrees C were investigat ed by measuring their CD spectra and also their torsion elastic consta nts ([alpha]) by time-resolved fluorescence polarization anisotropy. F or one of these DNAs, the HaeII fragment of pBR322, the apparent diffu sion coefficients [D-app(k)] at small and large scattering vectors (k) were also measured by dynamic light scattering. With increasing tempe rature, all three DNAs exhibited typical premelting changes in their C D spectra, and these were accompanied by 1.4- to 1.7-fold decreases in [alpha]. Also for the 1876 base pair fragment, D-app(k) at large scat tering vectors, which is sensitive to the dynamic bending rigidity, de creased by 17%, even though there was no change at small scattering ve ctors, where D-app(k) = D-0 is the translational diffusion coefficient of the center-of-mass. These observations demonstrate conclusively th at the premelting CD changes of these DNAs are associated with a signi ficant change in average secondary structure and mechanical properties , though not in persistence length. In the presence of 0.5 M tetrameth ylammonium chloride (TMA-Cl) the premelting change in CD is largely su ppressed, and the corresponding changes in [alpha] and D-app(k) at lar ge scattering vectors are substantially diminished. These observations suggest that TMA-Cl, which binds preferentially to A.T-rich regions a nd stabilizes those regions (relative to G.C-rich regions) against mel ting, effectively stabilizes the prevailing low-temperature secondary structure sufficiently that the DNA is effectively trapped in that sta te over the temperature range observed. (C) John Wiley & Sons, Inc.