Does Water Play a Structural Role in the Folding of Small Nucleic Acids?
Eric J. Sorin, Young Min Rhee, and Vijay S. Pande. Biophysical Journal (2005) SUMMARY: While previous studies on the folding of nucleic acid hairpins have employed simplified models of either the nucleic acid or the solvent, this paper reports the first such study using an explicit treatment of the surrounding water and counterions. We show that accounting for water molecules in this manner is necessary to most accurately characterize the energetics of hairpin folding, whereas monovalent ions appear to play only a background role. TECHNICAL ABSTRACT: Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5′-GGGC[GCAA]GCCU-3′) via ensemble molecular dynamics simulati
