Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex

The solution structure of an adenosine monophosphate (AMP)-DNA aptamer comp lex has been determined previously [Lin, C. H., and Patel, D.J. (1997) Chem . Biol. 4:817-832]. On a symmetrical aptamer complex containing the same bi nding loop, but with better resolved spectra, we have identified two additi onal hydrogen bond-mediated associations in the binding loop, One of these involves a rapidly exchanging G imino proton. The phosphate group of the AM P ligand was identified as the acceptor by comparison with other aptamer co mplexes. Imino proton exchange measurements also yielded the dissociation c onstants of the stem and binding loop base pairs. This study shows that nuc lear magnetic resonance-based imino proton exchange is a good probe for det ection of weak hydrogen-bond associations.