Salt‐ and sequence‐dependence of the secondary structure of DNA in Solution by 31P‐nmr spectroscopy

Abstract

AbstractWe examined three sonicated, specific‐seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P‐nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P‐nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche−‐gauche− conformation and shifts upfield in all four monovalent salts used, relative to a single‐stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans‐gauche− conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly‐(dAdT) from a presumed right‐handed dinucleotide‐repeat B‐form to another conformation with a dinucleotide‐repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans‐gauche− conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly‐(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right‐handed regular B‐form to a left‐handed Z‐form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B‐form with a gauche−‐gauche− phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.