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Literature DB >> 20946796

Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy.

Xiaojun Zhang¹, Pavol Cekan, Snorri Th Sigurdsson, Peter Z Qin.

Abstract

In site-directed spin-labeling (SDSL), a stable nitroxide radical is attached to a specific location within a macromolecule and electron paramagnetic resonance (EPR) spectroscopy is used to interrogate the local environment surrounding the nitroxide. The SDSL strategy enables probing site-specific structural and dynamic features of RNA in solution without being limited by the size of the molecule, thus serving as a unique tool in biophysical studies of RNA. This chapter describes the use of continuous-wave (cw)-EPR to study dynamic features of RNAs as well as to monitor interactions between them. Various approaches for attaching nitroxide spin labels to nucleic acids are described, followed by detailed descriptions of cw-EPR spectral acquisition and processing procedures. Specific examples are subsequently used to illustrate analysis of EPR spectra, showing how information regarding the parent RNA can be extracted.

Entities: Chemical Disease Gene Mutation Species

Mesh：

Substances：
Spin Labels
RNA

Year: 2009 PMID： 20946796 PMCID： PMC2957307 DOI： 10.1016/S0076-6879(09)69015-7

Source DB: PubMed Journal: Methods Enzymol ISSN： 0076-6879 Impact factor: 1.600

42 in total

1. Electron paramagnetic resonance dynamic signatures of TAR RNA-small molecule complexes provide insight into RNA structure and recognition.

Authors: Thomas E Edwards; Snorri Th Sigurdsson
Journal: Biochemistry Date: 2002-12-17 Impact factor: 3.162

Review 2. A new spin on protein dynamics.

Authors: Linda Columbus; Wayne L Hubbell
Journal: Trends Biochem Sci Date: 2002-06 Impact factor: 13.807

3. Monitoring RNA base structure and dynamics using site-directed spin labeling.

Authors: Peter Z Qin; Kálmán Hideg; Juli Feigon; Wayne L Hubbell
Journal: Biochemistry Date: 2003-06-10 Impact factor: 3.162

4. 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

5. HIV-1 nucleocapsid protein NCp7 and its RNA stem loop 3 partner: rotational dynamics of spin-labeled RNA stem loop 3.

Authors: Xiangmei Xi; Yan Sun; Christine B Karim; Vladimir M Grigoryants; Charles P Scholes
Journal: Biochemistry Date: 2008-08-26 Impact factor: 3.162

6. A novel 5 displacement spin-labeling technique for electron paramagnetic resonance spectroscopy of RNA.

Authors: J C Macosko; M S Pio; I Tinoco; Y K Shin
Journal: RNA Date: 1999-09 Impact factor: 4.942

7. A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling.

Authors: Peter Z Qin; Jennifer Iseri; Arisa Oki
Journal: Biochem Biophys Res Commun Date: 2006-03-03 Impact factor: 3.575

8. Nitroxide-labeled guanine as an ESR spin probe for structural study of DNA.

Authors: Akimitsu Okamoto; Takeshi Inasaki; Isao Saito
Journal: Bioorg Med Chem Lett Date: 2004-07-05 Impact factor: 2.823

9. A PELDOR-based nanometer distance ruler for oligonucleotides.

Authors: Olav Schiemann; Nelly Piton; Yuguang Mu; Gerhard Stock; Joachim W Engels; Thomas F Prisner
Journal: J Am Chem Soc Date: 2004-05-12 Impact factor: 15.419

10. EPR spectroscopic analysis of TAR RNA-metal ion interactions.

Authors: Thomas E Edwards; Snorri Th Sigurdsson
Journal: Biochem Biophys Res Commun Date: 2003-04-04 Impact factor: 3.575

19 in total

1. A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.

Authors: Anna M Popova; Peter Z Qin
Journal: Biophys J Date: 2010-10-06 Impact factor: 4.033

2. Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.

Authors: Xiaojun Zhang; Sang Won Lee; Liang Zhao; Tianbing Xia; Peter Z Qin
Journal: RNA Date: 2010-10-27 Impact factor: 4.942

3. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

Authors: Narin S Tangprasertchai; Xiaojun Zhang; Yuan Ding; Kenneth Tham; Remo Rohs; Ian S Haworth; Peter Z Qin
Journal: Methods Enzymol Date: 2015-08-08 Impact factor: 1.600

Review 4. RNA dynamics: perspectives from spin labels.

Authors: Phuong Nguyen; Peter Z Qin
Journal: Wiley Interdiscip Rev RNA Date: 2011-08-22 Impact factor: 9.957

5. Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.

Authors: Yuan Ding; Venkatesan Kathiresan; Xiaojun Zhang; Ian S Haworth; Peter Z Qin
Journal: J Phys Chem A Date: 2019-04-12 Impact factor: 2.781

6. A Straightforward Approach to the Analysis of Double Electron-Electron Resonance Data.

Authors: Richard A Stein; Albert H Beth; Eric J Hustedt
Journal: Methods Enzymol Date: 2015-09-15 Impact factor: 1.600

7. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.

Authors: Yuan Ding; Xiaojun Zhang; Kenneth W Tham; Peter Z Qin
Journal: Nucleic Acids Res Date: 2014-08-04 Impact factor: 16.971