title: NMR analysis of base-pair opening kinetics in DNA.
abstract: Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.
authors.affiliation: Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennesee; These authors contributed equally to this work.
authors.forename: Marta W
authors.initials: MW
authors.lastname: Szulik
authors.forename: Markus
authors.initials: M
authors.lastname: Voehler
authors.forename: Michael P
authors.initials: MP
authors.lastname: Stone
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*
chemical_list: D004247:DNA
keywords: T1; base-pair opening; exchange kinetics; high Q-probes; imino-exchange; longitudinal water relaxation NMR; nucleic acids; radiation damping