Solution structure of the conserved segment of the Myb cognate DNA sequence by 2D NMR, spectral simulation, restrained energy minimization, and distance geometry calculations

Abstract

Solution structure of a self-complementary DNA duplex d-ACCGTTAACGGT containing the TAACGG recognition segment of Myb protein has been obtained by NMR spectroscopy. Complete resonance assignments of all the protons (except H5', H5" protons) have been obtained following standard procedures based on two-dimensional NMR techniques. Using a total of 72 coupling constants, and 95 NOE intensities, restrained energy minimization has been carried out, with the X-PLOR force field. The distance constraint set has been iteratively refined, for better fits with experimental NOE intensities. Using the final constraint set thus obtained, and explicit H-bond constraints for A.T, G.C base pairs in the duplex, distance geometry calculations have been carried in the torsion angle space with the program TANDY-2S to identify the family of structures consistent with the NMR data. We observe that the constraint set does indeed define a unique structure for the DNA segment. The structural details have been analyzed, and the sequence-dependent variations in torsion angles, base pair geometries, and helicoidal parameters have been documented. We observed that the helix axis displays a nonregular path, and three centered H-bonds have been seen at AA, AC, and CC steps in the major groove of the helix. Substantial variations have been observed for the helix axis and the groove widths at the recognition site. The base pairs exhibit high negative propeller twists. The structure is characterized by O4'-endo geometry for all the sugar rings (expect G10), and the other torsion angles belong to the B-DNA families.