IMPROVED RNA STRUCTURE DETERMINATION BY DETECTION OF NOE CONTACTS TO EXCHANGE-BROADENED AMINO PROTONS

A 2D N-15-correlated NOESY experiment is described which makes it possible to obtain distance information for exchange-broadened amino protons in nucleic acids. Little or no NOE distance information is normally obtained for guanine and adenine amino protons because of rotation of the amino group around the C-N bond which leads to extreme broadening of the amino proton resonances. Here NOEs involving amino protons are detected via efficient transfer of heteronuclear magnetization between the amino protons and nitrogens, which is accomplished by application of a train of closely spaced 180 degrees echo pulses. This technique has been applied to a uniformly N-15-labeled lead-dependent ribozyme known-as the leadzyme. The 2D N-15-correlated NOESY experiment allowed 19 NOE constraints to amino protons to be identified that had not been previously observed in standard NOE spectra. Molecular dynamics calculations were performed with and without these additional amino NOE constraints and demonstrated that these amino constraints significantly improved the structure of the GAAA tetraloop in the leadzyme. Such NOE constraints involving amino protons will likely improve structure determinations of many other nucleic acid motifs.