Conformational analysis of the single‐helical DNA fragment d(T‐A‐A‐T) in aqueous solution

Abstract

Proton NMR studies at 300 MHz and 500 MHz were carried out on the tetranucleoside trisphosphate d(T-A-A-T). The thermodynamics of the 3 stacking interactions, derived from chemical shift vs. temperature profiles, were used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the fully stacked forms of the molecule. The data were interpreted in terms of N and S pseudorotational ranges. The stacked state of the molecule cannot be described by one conformer, but consists of one major stucture (60%) in which all sugar rings have S-type geometry and another structure (30%) in which residue dT(4) has an N-type sugar. The remainder of the stacked states consists of one or more conformers with 2 or 3 sugar residues in the N-type pseudorotational range. Detailed geometrical models are proposed for the major stacked conformers encountered in aqueous solution.