Molecular dynamics simulations on G-quadruplexes

Guanine-rich DNA/RNA sequences have the potential to form four-stranded structures called G-quadruplexes. Because of the rigidity and glycosidic bond orientation diversity in the stems, the flexibility of loops, and the featured alignment of several cations within one quadruplex channel, G-quadruplexes can serve as a sensitive benchmark to assess and validate current force fields for nucleic acids in molecular dynamics (MD) simulations.