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Metal ion-N7 coordination in a ribozyme branch domain by NMR

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Erat MC, Kovacs H, Sigel RKO,
Project Coordination Chemistry within the Core of Large RNAs: Regulating Tertiary Contacts and Function
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Original article (peer-reviewed)

Journal JOURNAL OF INORGANIC BIOCHEMISTRY
Volume (Issue) 104(5)
Page(s) 611 - 613
Title of proceedings JOURNAL OF INORGANIC BIOCHEMISTRY

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 Mg2+ and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct 15N detection, here we have used 2J-[1H,15N]-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.ai5c as an example, we show that direct N7 coordination of a Mg2+ ion takes place in a tetraloop nucleotide. A second Mg2+ 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.
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