Two-Dimensional ¹H and ³¹P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

Authors

Robert Powers, University of Nebraska - LincolnFollow
Claude R. Jones, Purdue University
David G. Gorenstein, Purdue University

Document Type

Article

Date of this Version

1990

Citation

Published in Journal of Biomolecular Structure and Dynamics 8:2 (1990), pp. 253–294

Comments

Copyright © 1990 Adenine Press. Published by Taylor & Francis. Used by permission.

Abstract

Assignment of the ¹H and ³¹P resonances of a decamer DNA duplex, d(CGCTTAAGCG)₂ was deter-mined by two-dimensional COSY, NOESY, and ¹H-³¹P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experi-ment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approxi-mates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental ma-trix until refinement is complete. JH3′–P coupling constants for each of the phosphates of the decamer were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4′-C3′-O3′-P torsional angles (ε) were obtained. Comparison of the ³¹P chemical shifts and J_H3′–P coupling constants of this sequence has allowed a greater insight into the various factors responsible for ³¹P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the ³¹P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ε and ζ torsional angles from the restrained molecular dynamics refinement agrees quite well with the measured J_H3′–P coupling constants. Thus, the local helical parameters determine the length of the phosphodiester back-bone which in turn constrains the phosphate in various allowed conformations.