ArticleBiophysical journal2007
Nanometer distance measurements in RNA using site-directed spin labeling.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- EPR spectroscopy in the study of ribosomal complexes.Biophysical reviews · 2025Review
- Caught in the Middle: A Rigid DNA Label That Provides an Incisive Picture of DNA Conformational Flexibility in Protein-DNA Complexes.Journal of the American Chemical Society · 2025Article
- Pulsed EPR Methods in the Angstrom to Nanometre Scale Shed Light on the Conformational Flexibility of a Fluoride Riboswitch.Angewandte Chemie (International ed. in English) · 2024Article
- Article
- Conformational Selection and Submillisecond Dynamics of the Ligand-binding Domain of the N-Methyl-d-aspartate Receptor.The Journal of biological chemistry · 2016Article
- High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides.Chemical science · 2016Article
- Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.Biochemistry · 2016Article
- Doubly Spin-Labeled RNA as an EPR Reporter for Studying Multicomponent Supramolecular Assemblies.Biophysical journal · 2015Article
- Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.Biophysical journal · 2015Article
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.BMC biophysics · 2015Article
- Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.Nucleic acids research · 2014Article
- Computational modeling of RNA 3D structures, with the aid of experimental restraints.RNA biology · 2014Review
- Pulsed EPR distance measurements in soluble proteins by site-directed spin labeling (SDSL).Current protocols in protein science · 2013Article
- Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease.Biochemistry · 2013Article
- Pulsed electron double resonance in structural studies of spin-labeled nucleic acids.Acta naturae · 2013Article
- A toolkit and benchmark study for FRET-restrained high-precision structural modeling.Nature methods · 2012Article
- The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.Biochemistry · 2012Article
- Preparation and spectral characterization of fluorescence probes based on 4-N,N-dimethylamino benzoic acid and sterically hindered amines.Journal of fluorescence · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The method of site-directed spin labeling (SDSL) utilizes a stable nitroxide radical to obtain structural and dynamic information on biomolecules. Measuring dipolar interactions between pairs of nitroxides yields internitroxide distances, from which quantitative structural information can be derived. This study evaluates SDSL distance measurements in RNA using a nitroxide probe, designated as R5, which is attached in an efficient and cost-effective manner to backbone phosphorothioate sites that are chemically substituted in arbitrary sequences. It is shown that R5 does not perturb the global structure of the A-form RNA helix. Six sets of internitroxide distances, ranging from 20 to 50 A, were measured on an RNA duplex with a known X-ray crystal structure. The measured distances strongly correlate (R(2) = 0.97) with those predicted using an efficient algorithm for determining the expected internitroxide distances from the parent RNA structure. The results enable future studies of global RNA structures for which high-resolution structural data are absent.
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