MONTE-CARLO ESTIMATION OF ERRORS IN C-13-NMR RELAXATION STUDIES OF A DNA OLIGOMER DUPLEX

An analysis of errors has been done with the Monte Carlo method for na tural abundance C-13-NMR relaxation studies of a DNA duplex. Repeated measurements of the longitudinal relaxation time, T-1, and the heteron uclear NOE were made at 90.6 MHz on the duplexed DNA pentanucleotide, [d(TCGCG)](2).(1) The deviations averaged over all carbons were 13% fo r T-1 and 9% for NOE. These relative deviations were applied to genera te 100 values of T-1 and NOE with normal distributions about the measu red mean values for each carbon. A new version of MOLDYN,(2) called Mc MOLDYN, has been written, which was used to generate 100 values of T-1 and NOE with normal distributions corresponding to the measured error s; the same error distributions were also applied to measurements at 1 25.8 MHz. The order parameter, S-2, and the effective internal correla tion time, tau(e), in the Model-Free Approach(3) have been optimized f rom the distributions simulated by McMOLDYN. McMOLDYN also permits the automated entry of multiple sets of initial guesses for the output pa rameters S-2, tau(e), and tau(m). In addition, McMOLDYN adds cross-rel axation terms from chemical shift anisotropy, increasingly important a s spectrometer magnetic fields get higher. Between the two parameters optimized, S-2 has the smallest relative error, estimated at 15% on av erage, which means that S-2 is a well-defined parameter. However, tau( e) is very poorly defined with the average relative error estimated 85 %; it is typically found in the range of 30-300 ps.