ArticleChemical science2016
High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides.
Article in Chemical science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 57 citations in OpenAlex.
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- Investigating the Conformational Diversity of the TMR-3 Aptamer.Journal of the American Chemical Society · 2025Article
- Frequency and time domainPhysical chemistry chemical physics : PCCP · 2025Article
- Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy.Biophysical journal · 2022Article
- The Hydrates of TEMPO: Water Vibrations Reveal Radical Microsolvation.Angewandte Chemie (International ed. in English) · 2021Article
- Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy.Angewandte Chemie (International ed. in English) · 2021Article
- Covalent labeling of nucleic acids.Chemical Society reviews · 2020Review
- Orientation and dynamics of CuPhysical chemistry chemical physics : PCCP · 2020Article
- Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.Chemical science · 2020Article
- Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin.Biochemistry · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
- EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription.Angewandte Chemie (International ed. in English) · 2020Article
- 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.Nucleic acids research · 2020Article
- High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label.Nucleic acids research · 2020Article
- Measurement of Angstrom to Nanometer Molecular Distances withAngewandte Chemie (International ed. in English) · 2020Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- "End-to-end" stacking of small dsRNA.RNA (New York, N.Y.) · 2019Article
- Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling.Molecules (Basel, Switzerland) · 2018Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural information at atomic resolution of biomolecular assemblies, such as RNA and RNA protein complexes, is fundamental to comprehend biological function. Modern spectroscopic methods offer exceptional opportunities in this direction. Here we present the capability of pulse EPR to report high-resolution long-range distances in RNAs by means of a recently developed spin labeled nucleotide, which carries the TEMPO group directly attached to the nucleobase and preserves Watson-Crick base-pairing. In a representative RNA duplex with spin-label separations up to 28 base pairs (≈8 nm) we demonstrate that the label allows for a model-free conversion of inter-spin distances into base-pair separation (Δbp) if broad-band pulse excitation at Q band frequencies (34 GHz) is applied. The observed distance distribution increases from ±0.2 nm for Δbp = 10 to only ±0.5 nm for Δbp = 28, consistent with only small deviations from the "ideal" A-form RNA structure. Molecular dynamics (MD) simulations conducted at 20 °C show restricted conformational freedom of the label. MD-generated structural deviations from an "ideal" A-RNA geometry help disentangle the contributions of local flexibility of the label and its neighboring nucleobases and global deformations of the RNA double helix to the experimental distance distributions. The study demonstrates that our simple but strategic spin labeling procedure can access detailed structural information on RNAs at atomic resolution over distances that match the size of macromolecular RNA complexes.
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