title: Metal ion-N7 coordination in a ribozyme branch domain by NMR.
abstract: The N7 of purine nucleotides presents one of the most dominant metal ion binding sites in nucleic acids. However, the interactions between kinetically labile metal ions like Mg(2+) and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct (15)N detection, here we have used (2)J-[(1)H,(15)N]-HSQC (Heteronuclear Single Quantum Coherence) NMR experiments as a fast and efficient method to specifically observe and characterize such interactions within larger RNA constructs. Using the 27 nucleotides long branch domain of the yeast-mitochondrial group II intron ribozyme Sc.ai5gamma as an example, we show that direct N7 coordination of a Mg(2+) ion takes place in a tetraloop nucleotide. A second Mg(2+) ion, located in the major groove at the catalytic branch site, coordinates mainly in an outer-sphere fashion to the highly conserved flanking GU wobble pairs but not to N7 of the sandwiched branch adenosine.
authors.affiliation: Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
authors.forename: Michèle C
authors.initials: MC
authors.lastname: Erat
authors.forename: Helena
authors.initials: H
authors.lastname: Kovacs
authors.forename: Roland K O
authors.initials: RK
authors.lastname: Sigel
mesh_terms: D007477:Ions / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism
chemical_list: D007477:Ions; D008670:Metals; D011687:Purines; D016337:RNA, Catalytic