Scalable Force Fields for Metal-Mediated DNA Nanostructures

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