Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Structures of Cas9-Bound Double-Stranded DNA Mini-Circle Reveal Impacts of DNA Shape on Cas9 Target Interrogation.

bioRxiv : the preprint server for biology·2026
Same author

Cryo-EM Structure of a 95-Basepair Double-Stranded DNA Minicircle at 5.3 Å Resolution.

bioRxiv : the preprint server for biology·2026
Same author

Helicity of the bridge helix of Cas12a regulates on-target DNA cleavage efficiency and off-target cleavage propensity.

Biochemical and biophysical research communications·2026
Same author

Advancing Pharmacoequity in Low- and Middle-Income Countries via Model Informed Drug Development.

Clinical and translational science·2026
Same author

Cardiac arrest caused by acute gastric dilatation in a bulimia patient: a case report.

Frontiers in medicine·2026
Same author

Associations of Systemic Inflammatory Response Index (SIRI) and Systemic Inflammatory Index (SII) with Cerebral Atherosclerosis.

Journal of inflammation research·2026

Related Experiment Video

Updated: Jul 14, 2026

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels
11:19

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels

Published on: July 4, 2016

Nanometer distance measurements in RNA using site-directed spin labeling.

Qi Cai1, Ana Karin Kusnetzow, Kálmán Hideg

  • 1Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA.

Biophysical Journal
|May 29, 2007
PubMed
Summary

Site-directed spin labeling (SDSL) with the R5 probe accurately measures distances in RNA structures. This method provides reliable structural insights for RNA molecules lacking high-resolution data.

More Related Videos

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

Related Experiment Videos

Last Updated: Jul 14, 2026

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels
11:19

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels

Published on: July 4, 2016

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Site-directed spin labeling (SDSL) is a powerful technique utilizing nitroxide radicals to probe biomolecular structure and dynamics.
  • Measuring dipolar interactions between nitroxide pairs provides internitroxide distances, enabling quantitative structural analysis.
  • Accurate distance measurements are crucial for understanding the complex architectures of biomolecules like RNA.

Purpose of the Study:

  • To evaluate the efficacy of SDSL for determining structural information in RNA molecules.
  • To assess the R5 nitroxide probe's compatibility with RNA and its impact on global helical structure.
  • To validate SDSL-derived internitroxide distances against known RNA structures.

Main Methods:

  • Utilized site-directed spin labeling (SDSL) with a novel R5 nitroxide probe attached to phosphorothioate sites in RNA.
  • Synthesized RNA duplexes with chemically substituted backbone phosphorothioate sites for probe attachment.
  • Measured internitroxide distances using Electron Paramagnetic Resonance (EPR) spectroscopy on RNA duplexes.
  • Compared experimentally determined distances with those predicted from X-ray crystal structures.

Main Results:

  • The R5 probe was efficiently and cost-effectively attached to arbitrary RNA sequences without perturbing the A-form helical structure.
  • Six sets of internitroxide distances, ranging from 20 to 50 Å, were accurately measured on an RNA duplex.
  • A strong correlation (R² = 0.97) was observed between experimentally measured and computationally predicted internitroxide distances.
  • The results demonstrate the reliability of SDSL for RNA structural analysis.

Conclusions:

  • SDSL using the R5 probe is a validated and robust method for measuring internitroxide distances in RNA.
  • This technique provides accurate structural information, particularly valuable for RNA structures lacking high-resolution experimental data.
  • The findings pave the way for future investigations into the global structures of diverse RNA molecules.