ArticleNucleic acids research2020
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A Phosphorylation Switch Modulates Configurational Codes in the Oncofetal IGF2BP RNA Binding Paralogs.bioRxiv : the preprint server for biology · 2026Article
- A Conjugated Oligoelectrolyte Exhibiting Room Temperature Spin-Correlated Radical Pair Character for Biological Sensing.Journal of the American Chemical Society · 2025Article
- 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
- Investigating the Conformational Diversity of the TMR-3 Aptamer.Journal of the American Chemical Society · 2025Article
- Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation.Nucleic acids research · 2024Article
- Nanosecond chain dynamics of single-stranded nucleic acids.Nature communications · 2024Article
- Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy.ACS omega · 2023Article
- Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms.The journal of physical chemistry. B · 2022Review
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy.Angewandte Chemie (International ed. in English) · 2021Article
- How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations.Computational and structural biotechnology journal · 2021Review
- Orientation and dynamics of CuPhysical chemistry chemical physics : PCCP · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
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