Scalable Force Fields for Metal-Mediated DNA Nanostructures

Force fields were developed for metal-mediated DNA (mmDNA) structures, using ab initio methods to parametrize metal coordination. Two mmDNA structures were considered, using cytosine/thymine mismatches with coordinated Ag and Hg metal atoms. These base pairs were parametrized with the proposed computational framework and subjected to multiple validation steps. The generated force fields showed enhanced structural stability within the metalated base pairs, with the coordinated metal rotating into the major groove. Our findings show a higher propeller angle associated with the metalated base pair, which agrees with previously reported experimental data. The developed force fields have the potential to unveil the structural dynamics of long metalated DNA nanowires, while results have been demonstrated on a chain of three mmDNA base pairs.