ArticleNucleic acids research2006
Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Rational Design of a Cu(II) Spin Label Improves the Sensitivity of Distance Measurements.The journal of physical chemistry letters · 2025Article
- EPR spectroscopy in the study of ribosomal complexes.Biophysical reviews · 2025Review
- Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination.Nucleic acids research · 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
- Spectroscopically Orthogonal Labelling to Disentangle Site-Specific Nitroxide Label Distributions.Applied magnetic resonance · 2024Article
- Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy.ACS omega · 2023Article
- A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination.Nucleic acids research · 2023Article
- Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion.Biophysical journal · 2022Article
- Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM.The CRISPR journal · 2022Article
- 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
- An EPR Study on the Interaction between the Cu(I) Metal Binding Domains of ATP7B and the Atox1 Metallochaperone.International journal of molecular sciences · 2020Article
- Cu(I) Controls Conformational States in Human Atox1 Metallochaperone: An EPR and Multiscale Simulation Study.The journal of physical chemistry. B · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
- Unraveling the Impact of Cysteine-to-Serine Mutations on the Structural and Functional Properties of Cu(I)-Binding Proteins.International journal of molecular sciences · 2019Article
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy.Nucleic acids research · 2018Article
- The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations.Protein science : a publication of the Protein Society · 2017Article
- Interaction of triarylmethyl radicals with DNA termini revealed by orientation-selective W-band double electron-electron resonance spectroscopy.Physical chemistry chemical physics : PCCP · 2016Article
- Complementary-addressed site-directed spin labeling of long natural RNAs.Nucleic acids research · 2016Article
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9 authors.
Funding
Abstract
In site-directed spin labeling (SDSL), local structural and dynamic information is obtained via electron paramagnetic resonance (EPR) spectroscopy of a stable nitroxide radical attached site-specifically to a macromolecule. Analysis of electron spin dipolar interactions between pairs of nitroxides yields the inter-nitroxide distance, which provides quantitative structural information. The development of pulse EPR methods has enabled such distance measurements up to 70 A in bio-molecules, thus opening up the possibility of SDSL global structural mapping. This study evaluates SDSL distance measurement using a nitroxide (designated as R5) that can be attached, in an efficient and cost-effective manner, to a phosphorothioate backbone position at arbitrary DNA or RNA sequences. R5 pairs were attached to selected positions of a dodecamer DNA duplex with a known NMR structure, and eight distances, ranging from 20 to 40 A, were measured using double electron-electron resonance (DEER). The measured distances correlated strongly (R2 = 0.98) with the predicted values calculated based on a search of sterically allowable R5 conformations in the NMR structure, thus demonstrating accurate distance measurements using R5. Furthermore, distance measurement in a 42 kD DNA was demonstrated. The results establish R5 as a sequence-independent probe for global structural mapping of DNA and DNA-protein complexes.
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