SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTINEOPLASTIC AGENT ARABINOSYLCYTOSINE - COMBINED USE OF NMR, RESTRAINED MOLECULAR-DYNAMICS, AND FULL RELAXATION MATRIX REFINEMENT

The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT )(araC)d(GCG)](2) was examined by comparing its nuclear magnetic reson ance (NMR)-determined solution structure with that of the control dupl ex d[(CGCGAATTCGCG)](2). H-1 and P-31 resonances in both duplexes were assigned using a combination of 2-D H-1 NMR and a 3-D P-31-H-1 hetero TOCSY-NOESY experiment. Proton-proton distances (determined from NOESY data) and sugar dihedral angles (from NOESY and COSY data) were used in restrained molecular dynamics simulations starting from canonical A - or B-form DNA models. Both the control and araC sets of simulations converged to B-type structures. These structures were subjected to ful l relaxation matrix refinement to produce final structures which were in excellent agreement (R(1/6) < 0.05) With the observed NOE intensiti es. A detailed comparison of the final control and araC structures rev ealed a global similarity (overall RMSD similar to 1.3 Angstrom), with significant differences localized at the araC site and neighboring ba ses. These included changes in sugar pucker, backbone torsion angles, base stacking, and other helical parameters. These findings are in gen eral agreement with the previously published X-ray structure of a deca mer duplex containing araC. One intriguing feature of the NMR solution structure not found in the crystal structure is the presence of an in tramolecular hydrogen bond between the 2' hydroxyl on the araC sugar a nd the 3' phosphate group.