ArticleNature protocols2007
Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.
Article in Nature protocols, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 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
- Frequency and time domainPhysical chemistry chemical physics : PCCP · 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
- Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies.Biomolecules · 2024Article
- A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination.Nucleic acids research · 2023Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM.The CRISPR journal · 2022Article
- Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Orientation and dynamics of CuPhysical chemistry chemical physics : PCCP · 2020Article
- Lanthanide Tagging of Oligonucleotides to Nucleobase for Paramagnetic NMR.Chembiochem : a European journal of chemical biology · 2020Article
- Do the P1 and P2 hairpins of the Guanidine-II riboswitch interact?Nucleic acids research · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
- NMR characterization of RNA small molecule interactions.Methods (San Diego, Calif.) · 2019Review
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Single-DNA electron spin resonance spectroscopy in aqueous solutions.Nature methods · 2018Article
- Insights on the Structure, Molecular Weight and Activity of an Antibacterial Protein-Polymer Hybrid.Chemphyschem : a European journal of chemical physics and physical chemistry · 2018Article
- CRISPR-Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling.ACS chemical biology · 2017Article
- Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling.Cell biochemistry and biophysics · 2017Article
- Complementary-addressed site-directed spin labeling of long natural RNAs.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.
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Registered trials
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