Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Sigel, Roland K. O.; Sashital, Dipali G.; Abramovitz, Dana L; Palmer, Arthur G.; Butcher, Samuel E.; Pyle, Anna Marie

doi:10.1038/nsmb717

Cited by 93 publications

(169 citation statements)

References 39 publications

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“…Remarkably, all resonances change their chemical shift either in the 15 is a well-known effect, 30,33 which has for example been observed in 31 P-NMR studies of ATP derivatives. 11 This effect can be attributed to the fast on-and off-rates of first-shell ligandexchange of Mg 2+ , which is in the order of the NMR time scale.…”

mentioning

confidence: 84%

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

Erat¹,

Kovacs²,

Sigel³

2010

Journal of Inorganic Biochemistry

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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 N-15 detection, here we have used (2)J-H-1,N-15]-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.ai5 gamma 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. (C)

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mentioning

confidence: 84%

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

Erat¹,

Kovacs²,

Sigel³

2010

Journal of Inorganic Biochemistry

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“…Magnesium and potassium, the dominant counterions for RNA folding in vivo, are unfortunately spectroscopically invisible. NMR chemical shift perturbation mapping is a sensitive, but indirect, means of detecting ion association with RNA (Butcher et al 2000;Huppler et al 2002;Sigel et al 2004;Fan et al 2005), and can be difficult to interpret if ion binding simultaneously induces conformational change. Direct methods for detecting sites of metal ion association include Nuclear Overhauser effects (NOEs) to cobalt hexammine, and manganese-induced paramagnetic relaxation enhancement (PRE) (Bertini and Luchinat 1986;Kieft and Tinoco 1997;Gonzalez and Tinoco 1999;Butcher et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Role of metal ions in the tetraloop–receptor complex as analyzed by NMR

Davis

Foster²,

Tonelli³

et al. 2006

RNA

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Metal ions are critical for the proper folding of RNA, and the GAAA tetraloop-receptor is necessary for the optimal folding and function of many RNAs. We have used NMR to investigate the role of metal ions in the structure of the tetraloop-receptor in solution. The NMR data indicate native tertiary structure is formed under a wide range of ionic conditions. The lack of conformational adaptation in response to very different ionic conditions argues against a structural role for divalent ions. Nuclear Overhauser effects to cobalt hexammine and paramagnetic relaxation enhancement induced by manganese ions were used to determine the NMR structures of the tetraloop receptor in association with metal ions, providing the first atomic-level view of these interactions in the solution state. Five manganese and two cobalt hexammine ions could be localized to the RNA surface. The locations of the associated metal ions are similar, but not identical to, those of previously determined crystal structures. The sites of association are in general agreement with nonlinear Poisson-Boltzmann calculations of the electrostatic surface, emphasizing the general importance of diffusely associated ions in RNA tertiary structure.

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“…It does not help that affinities even for the more selective and specific metal ion binding sites in nucleic acids are usually low (10 2 and 10 4 M -1 [6][7][8]) compared to those observed in proteins. Typically most of the coordination sites in an RNA will have very similar metal affinities and are therefore filled more or less simultaneously [7,9,10].…”

Section: Introductionmentioning

confidence: 95%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Sigel

2011

Metal Ions in Life Sciences

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Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

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Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Cited by 93 publications

References 39 publications

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

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

Role of metal ions in the tetraloop–receptor complex as analyzed by NMR

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

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