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THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY
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 (LIU, H., SPIELMANN, H.P., WEMMER, D.E., & JAMES, T.L. (1995) IN PREPARATION). THE NOE DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS USING THE PROGRAM DISCOVER VERSION 2.9.5 WITH MODIFIED AMBER FORCE-FIELD POTENTIALS AS IMPLEMENTED IN DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES FOR THE FORTY STRUCTURES OF THE COMPLEX WAS 1.4 ANGSTROMS (INCLUDING THE DISORDERED TERMINAL DNA RESIDUES). THE COMPLEX EXHIBITS TWO-FOLD SPECTROSCOPIC SYMMETRY, BUT NO SYMMETRY WAS IMPOSED DURING THE REFINEMENT. DEVIATIONS FROM IDEAL TWO-FOLD SYMMETRY REFLECT THE UNCERTAINTY IN THE NMR DATA. THE 40 STRUCTURES ARE BASED ON 362 INTERPROTON DISTANCE RESTRAINTS FROM NOE MEASUREMENTS, 22 HYDROGEN BOND DISTANCE RESTRAINTS, AND 48 RESTRAINTS TO ENFORCE CHIRALITY IN THE DEOXYRIBOSE RESIDUES. THE FIRST 20 STRUCTURES WERE GENERATED FROM B-FORM DNA STARTING COORDINATES, AND THE
SECOND 20 STRUCTURES WERE GENERATED FROM A-FORM DNA
STARTING COORDINATES.