Base-pair opening dynamics of nucleic acids in relation to their biological function

Abstract Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i ) selective recognition of DNA by proteins; ii ) regulation of RNA cleavage by site-specific mutations; iii ) intermolecular interaction of proteins with their target DNA or RNA; iv ) formation of PNA:DNA hybrid duplexes.