Application of Molecular Dynamics Simulations to Spin-labeled Oligonucleotides

Abstract

The EPR study of spin labeled macromolecules has provided insight into structural and dynamical properties of DNA, proteins, and related systems. While spin labeling has been useful, it is experimentally difficult to determine if the spin label significantly alters the conformation of the macromolecule to which it is attached. Molecular modeling has proven to be a powerful tool for studying structure and dynamics of biologically important molecules. Here, we have conducted molecular dynamics (MD) studies of spin labeled oligonucleotides (ONs) bearing a five (5sp) or six (6sp) membered ring nitroxide, and the corresponding unmodified ON using the suite of programs contained in Amber 5.0 with the Cornell et al. 94 force field (Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, Jr., K. M. Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins and Nucleic Acids. J. Am. Chem. Soc. 117, 5179–5197 (1995)). Quantum mechanical calculations employing the B3LYP method with the standard 6–31G1 basis set using Gaussian98 were performed and, together with available crystallographic data for analogous nitroxides, new parameters for the nitrogen, oxygen, nitroxide α-carbon, and sp-hybridized carbon atoms have been developed suitable for the Cornell et al. 94 force field. MD simulations on the double-stranded (ds) spin labeled ONs, along with the corresponding unmodified analogues, have been studied over the course of 4 ns and conformational properties of all ONs are described based on the analysis of the trajectories. The spin labels were found to alter the global conformation of the ONs to which they were attached to accommodate the spin labels. The major changes include widening the major groove, decreasing helical twist, and more negative X-displacement of the base pairs. The magnitude of the effect was dependent on the specific structure of the spin label. Average and ‘most representative’ structures derived from the molecular dynamics simulations correlate with the experimental data on the spin labeled ONs.