SOLUTION STRUCTURE OF THE CONSERVED SEGMENT OF THE MYB COGNATE DNA-SEQUENCE BY 2D NMR, SPECTRAL SIMULATION, RESTRAINED ENERGY MINIMIZATION,AND DISTANCE GEOMETRY CALCULATIONS

Solution structure of a self-complementary DNA duplex d-ACCGTTAACGGT c ontaining the TAACGG recognition segment of Myb protein has been obtai ned by NMR spectroscopy. Complete resonance assignments of all the pro tons (except H5', H5'' protons) have been obtained following standard procedures based on two-dimensional NMR techniques. Using a total of 7 2 coupling constants, and 95 NOE intensities, restrained energy minimi zation has been carried out, with the X-PLOR force field. The distance constraint set has been iteratively refined, for better fits with exp erimental NOE intensities. Using the final constraint set thus obtaine d, and explicit H-bond constraints for A . T, G . C base pairs in the duplex, distance geometry calculations have been carried in the torsio n angle space with the program TANDY-2S to identify the family of stru ctures consistent with the NMR data. We observe that the constraint se t does indeed define a unique structure for the DNA segment. The struc tural details have been analyzed, and the sequence-dependent variation s in torsion angles, base pair geometries, and helicoidal parameters h ave been documented. We observed that the helix axis displays a nonreg ular 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 b een observed for the helix axis and the groove widths at the recogniti on site. The base pairs exhibit high negative propeller twists. The st ructure is characterized by O4'-endo geometry for all the sugar rings (expect G10), and the other torsion angles belong to the B-DNA familie s.