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 Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

You might also read

Related Articles

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

Sort by
Same author

Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging.

Genome biology·2020
Same author

Increased Burden of Rare Sequence Variants in GnRH-Associated Genes in Women With Hypothalamic Amenorrhea.

The Journal of clinical endocrinology and metabolism·2020
Same author

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.

PLoS computational biology·2020
Same author

Growth kinetics of single-walled carbon nanotubes with a (2<i>n</i>, <i>n</i>) chirality selection.

Science advances·2019
Same author

The possibility of using effluent ionized calcium to assess regional citrate anticoagulation in continuous renal replacement therapy.

The International journal of artificial organs·2019
Same author

Antifouling and pH-Responsive Poly(Carboxybetaine)-Based Nanoparticles for Tumor Cell Targeting.

Frontiers in chemistry·2019
Same journal

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026
Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026
Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026
Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026
Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026
Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026
See all related articles

Related Experiment Video

Updated: May 23, 2026

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting
13:41

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

Published on: October 17, 2011

Three-dimensional RNA structure refinement by hydroxyl radical probing.

Feng Ding1, Christopher A Lavender, Kevin M Weeks

  • 1Department of Biochemistry and Biophysics, University of North Carolina, USA.

Nature Methods
|April 17, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a new method using hydroxyl radical probing (HRP) to quantitatively refine RNA structures. This approach enhances molecular modeling for complex RNAs, improving structure prediction accuracy.

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: May 23, 2026

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting
13:41

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

Published on: October 17, 2011

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • Determining 3D structures of complex RNAs is challenging with high-resolution methods.
  • Hydroxyl radical probing (HRP) offers nucleotide-level solvent accessibility data.
  • Current HRP applications are limited to qualitative model evaluation.

Purpose of the Study:

  • To develop a quantitative method for RNA structure refinement using HRP data.
  • To integrate HRP measurements into discrete molecular dynamics simulations.
  • To improve 3D structure determination for complex RNAs.

Main Methods:

  • Utilized hydroxyl radical probing (HRP) for quantitative solvent accessibility measurements.
  • Employed discrete molecular dynamics simulations driven by HRP data.
  • Applied the method to RNAs ranging from 80 to 230 nucleotides.

Main Results:

  • Successfully identified RNAs with extensive helical packing interactions using HRP reactivities.
  • Achieved highly significant RNA structure predictions with sequence and base pairing inputs.
  • Demonstrated a robust HRP-directed tertiary structure refinement approach.

Conclusions:

  • HRP can be quantitatively used to refine RNA molecular models.
  • This method provides robust structural hypotheses for RNA structure-function studies.
  • Enables better understanding of complex RNA molecules.