Molecular dynamics simulation study of the stability and conformation of spin-probe labeled DNAs

Nitroxide based spin-probes, observable by ESR, have been used to study protein structure and protein-substrate interactions. More recently, spin-probe labeled DNAs have been introduced to study its structure and dynamics. Molecular modeling has proven to be an increasingly powerful tool for studying structure and dynamics of biologically interesting, molecules. As part of our work, we have conducted molecular dynamics simulations on both double-stranded (ds) and triple-stranded or triplex (tx) spin-probe labeled DNAs for comparison with unmodified ones and to design new probes. Nitroxide spin-labeled analogue of thymidine in which the methyl group is replaced by an acetylene-tethered nitroxide (T*) was inserted into the middle part of both ds DNA and tx DNA. Molecular mechanics force fields implemented in both Amber and Sybyl programs lack suitable parameters for nitroxides. These force fields were modified to contain new types of atoms designated as N.rad and O.rad with slightly different values than those reported by Barone, et al. for MM3 and MM+ force fields (Barone et al., J. Am. Chem. Soc. 1998, 120, 7069--7078). In addition new type of carbon atom designated as C1 (for sp hybridized carbon) with corresponding parameter was developed and added to Amber force field. We conducted MD simulations on both modified and unmodified DNAs to compare their stabilities and relative motion of the nitroxide with respect to a DNA molecule. Some results are in the process of analysis. We expect to see slower motion of nitroxide associated with triplex, rather than with duplex. The simulations will also be correlated with experimental studies conducted on different DNA sequences. (Supported by NIH Grant R15 GM7630)