Structure of DNA Hexamer Sequence d-CGATCG by Two-dimensional Nuclear Magnetic Resonance Spectroscopy and Restrained Molecular Dynamics

Abstract

Solution conformation of self-complementary DNA duplex d-CGATCG, containing 5′d- CpG 3′ site for intercalation of anticancer drug, daunomycin and adriamycin, has been investigated by nuclear magnetic resonance (NMR) spectroscopy. Complete resonance assignments of all the protons (except some H5′/H5” protons) have been obtained following standard procedures based on double quantum filtered correlation spectroscopy (dQF COSY) and two-dimensional nuclear Overhauser effect (NOE) spectra. Analysis of sums of coupling constants in one-dimensional NMR spectra, cross peak patterns in dQF COSY spectra and inter proton distances shows that the DNA sequence assumes a conformation close to the B-DNA family. The deoxyribose sugar conformation is in dynamic equilibrium with predominantly S-type conformer and a minor N-type conformer with N↔S equilibrium varying with temperature. At 325 K, the mole fraction of the N-conformer increases for some of the residues by ∼ 9%. Using a total of 10 spin-spin coupling constants and 112 NOE intensities, structural refinement has been carried out using Restrained Molecular Dynamics (rMD) with different starting structures, potential functions and rMD protocols. It is observed that pseudorotation phase angle of deoxyribose sugar for A3 and T4 residues is ∼ 180° and ∼ 120°, respectively while all other residues are close to C2′endo-conformation. A large propeller twist (∼ −18°) and smallest twist angle (∼ 31°) at A3pT4 step, in the middle of the sequence, a wider (12 Å) and shallower (3.0 Å) major groove with glycosidic bond rotation as high anti at both the ends of hexanucleotide are observed. The structure shows base-sequence dependent variations and hence strong local structural heterogeneity, which may have implications in ligand binding.