Chapter 2: Molecular Dynamics and Force Field Based Methods for Studying Quadruplex Nucleic Acids

This chapter firstly introduces the concept of quadruplex nucleic acids, summarizing their major features. Molecular dynamics simulations on these systems are described, outlining the force-fields that have been used and the particular challenges posed by quadruplexes. The treatment of quadruplex electrostatics is uniquely complicated by the presence of an ion channel in these structures. The simulations and theoretical studies of quadruplex folding/unfolding that have been reported in the literature are critically summarized, as are various approaches to studying the energetics of quadruplex ligand complexes.