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Literature DB >> 23900919

A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme.

Phuong Nguyen¹, Xuesong Shi, Snorri Th Sigurdsson, Daniel Herschlag, Peter Z Qin.

Abstract

Rigid spinning: Site-directed spin-labeling studies using a rigid nitroxide spin label (Ç) reveal that both length and sequence of a single-stranded junction (J1/2) modulate nanosecond motional ordering of the substrate-recognition duplex (P1) of the 120 kD group I ribozyme. The studies demonstrate an approach for experimental measurements of nanosecond dynamics in high-molecular-weight RNA complexes.

Entities: Chemical Gene Species

Keywords: EPR spectroscopy; RNA; dynamics; motional ordering; spin labeling

Mesh：

Substances：

Year: 2013 PMID： 23900919 PMCID： PMC3817310 DOI： 10.1002/cbic.201300376

Source DB: PubMed Journal: Chembiochem ISSN： 1439-4227 Impact factor: 3.164

18 in total

1. Elastic properties of a single-stranded charged homopolymeric ribonucleotide.

Authors: Yeonee Seol; Gary M Skinner; Koen Visscher
Journal: Phys Rev Lett Date: 2004-09-10 Impact factor: 9.161

2. A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise.

Authors: Nivrutti Barhate; Pavol Cekan; Archna P Massey; Snorri Th Sigurdsson
Journal: Angew Chem Int Ed Engl Date: 2007 Impact factor: 15.336

3. Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach.

Authors: David E Budil; Kenneth L Sale; Khaled A Khairy; Peter G Fajer
Journal: J Phys Chem A Date: 2006-03-16 Impact factor: 2.781

Review 4. Site-directed spin labeling studies on nucleic acid structure and dynamics.

Authors: Glenna Z Sowa; Peter Z Qin
Journal: Prog Nucleic Acid Res Mol Biol Date: 2008

5. Molecular motion of spin labeled side chains in alpha-helices: analysis by variation of side chain structure.

Authors: L Columbus; T Kálai; J Jekö; K Hideg; W L Hubbell
Journal: Biochemistry Date: 2001-04-03 Impact factor: 3.162

6. Probing the dynamics of the P1 helix within the Tetrahymena group I intron.

Authors: Xuesong Shi; Emilia T Mollova; Goran Pljevaljcić; David P Millar; Daniel Herschlag
Journal: J Am Chem Soc Date: 2009-07-15 Impact factor: 15.419

7. Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling.

Authors: Gian Paola G Grant; Nathan Boyd; Daniel Herschlag; Peter Z Qin
Journal: J Am Chem Soc Date: 2009-03-11 Impact factor: 15.419

8. Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking.

Authors: Yeonee Seol; Gary M Skinner; Koen Visscher; Arnaud Buhot; Avraham Halperin
Journal: Phys Rev Lett Date: 2007-04-12 Impact factor: 9.161

9. Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.

Authors: Anna M Popova; Ma'mon M Hatmal; Maria P Frushicheva; Eric A Price; Peter Z Qin; Ian S Haworth
Journal: J Phys Chem B Date: 2012-05-23 Impact factor: 2.991

10. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.

Authors: Deniz Sezer; Jack H Freed; Benoît Roux
Journal: J Am Chem Soc Date: 2009-02-25 Impact factor: 15.419

4 in total