SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT
Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. THREE STRUCTURES WERE GENERATED STARTING FROM CANONICAL A-TYPE DNA AND THREE STRUCTURES STARTING FROM CANONICAL B-TYPE DNA. FOR BOTH CONTROL AND ARAC STRUCTURES, THE RMSD OF THE SIX STRUCTURES WAS < 0.7 ANGSTROM. THE SIX STRUCTURES WERE AVERAGED, MINIMIZED AND REFINED USING RELAXATION MATRIX REFINEMENT IN A DYNAMICAL SIMULATED ANNEALING PROTOCOL. THE X-PLOR DISTANCE CONSTRAINT AND SUGAR DIHEDRAL CONSTRAINT TABLES USED IN THE RESTRAINED MOLECULAR DYNAMICS CALCULATIONS FOR THE ARAC-CONTAINING DODECAMER ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY.
DNA, ARABINOSYLCYTOSINE, ANTI-NEOPLASTIC, DODECAMER