Monte Carlo estimation of errors in 13C-NMR relaxation studies of a DNA oligomer duplex.

An analysis of errors has been done with the Monte Carlo method for natural abundance 13C-NMR relaxation studies of a DNA duplex. Repeated measurements of the longitudinal relaxation time, T1, and the heteronuclear NOE were made at 90.6 MHz on the duplexed DNA pentanucleotide, [d(TCGCG)]2. The deviations averaged over all carbons were 13% for T1 and 9% for NOE. These relative deviations were applied to generate 100 values of T1 and NOE with normal distributions about the measured mean values for each carbon. A new version of MOLDYN, called McMOLDYN, has been written, which was used to generate 100 values of T1 and NOE with normal distributions corresponding to the measured errors; the same error distributions were also applied to measurements at 125.8 MHz. The order parameter, S2, and the effective internal correlation time, tau e, in the Model-Free Approach have been optimized from the distributions simulated by McMOLDYN. McMOLDYN also permits the automated entry of multiple sets of initial guesses for the output parameters S2, tau e, and tau m. In addition, McMOLDYN adds cross-relaxation terms from chemical shift anisotropy, increasingly important as spectrometer magnetic fields get higher. Between the two parameters optimized, S2 has the smallest relative error, estimated at 15% on average, which means that S2 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.