Quasielastic laser light scattering and electron microscopy studies of the conformational transitions and condensation of poly(dA‐dT) · poly(dA‐dT)

Abstract

AbstractPoly(dA‐dT) · poly(dA‐dT) undergoes a reversible conformational transition in the presence of Co(NH3) or spermidine in low salt (10 mM NaCl + 1 mM Na cacodylate). This transition is similar, as judged by changes in the CD spectrum, to the B‐to‐X transition of the polymer provoked by alcohol and Cs+ [Vorlickova et al. (1983) J. Mol. Biol. 166, 85–92; (1982) Nucleic Acids Res. 10, 6969–6979] and by meso‐substituted porphyrin ligands [Carvlin et al. (1983) Nucleic Acids Res. 11, 6141–6154]. Under the salt conditions indicated, the CD transition begins with Co(NH3) at about 70 μM and is complete by 150 μM; with spermidine, it begins at about 300 μM and is complete by 600 μM. Total intensity light scattering shows a marked increase at trivalent cation concentrations somewhat below those at which the CD transition begins. Quasielastic laser light scattering (QLS) measurement of the translational diffusion coefficient, DT, shows that, in the presence of Co(NH3), the hydrodynamic radius, Rh, increases from 260 to 1450 Å over the concentration range of 25 to 200 μM. With spermidine, Rh is 550±50 Å up to 200 μM, then increases rapidly. Values of Rh in this range are generally found for toroidal or other compact condensed forms of DNA. Such forms—toroidal, spheroidal, and rodlike structures—are observed in electron micrographs of poly(dA‐dT) · poly(dA‐dT) when the trivalent cation concentration is in the transition range. Above that range, extensive aggregation of the polymer chains is seen. Taken together, these results suggest a sequenc of related secondary and tertiary structure changes as trivalent cations are added to a low‐salt solution of poly(dA‐dT) · poly(dA‐dT). At very low Co(NH3) or spermidine, condensation of the polymer takes place while it is still in the B‐form. Further additions of trivalent cation provoke a transition from B‐ to X‐form, finally resulting in extensively aggregated polymer. These results are different from those generally observed with native DNA, where condensation with polyamines or Co(NH3) in aqueous solution is not accompanied by secondary structural change. They are also different from those we have seen with poly(dG‐me5dC) · poly(dG‐me5dC), where condensation and the B–Z transition occur at the same ionic conditions. These distinctions are another entry in the growing catalog of sequence‐dependent structural effects that may be important in the regulation of the biological activity of DNA.