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THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT
SOLUTION NMR
NMR Refinement
Method
Details
Software
MOLECULAR DYNAMICS, MATRIX RELAXATION
REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (H.LIU, H.P.SPIELMANN, D.E.WEMMER, AND T.L.JAMES (1995) IN PREPARATION). THE NOE-DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WITH AMBER FORCEFIELD POTENTIALS AS IMPLEMENTED IN DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES FOR THE FORTY STRUCTURES OF THE DUPLEX WAS 0.82 ANGSTROMS.