Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA Structure

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 Structure

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...

RNA Structure

RNA Structure

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

RNA-seq

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...

You might also read

Related Articles

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

Sort by

Same author

De novo design of RNA pseudoknots with deep learning.

bioRxiv : the preprint server for biology·2026

Same author

Engineered CRISPR/Cas12a2 Nanoprobe Imaging in Living Cells for Precise Tumor Diagnosis.

Small methods·2026

Same author

Integrating non-neonatal tetanus vaccination into an emergency department rabies PEP clinic: Real-world workload, documentation gaps, and VAERS-informed observation priorities.

Human vaccines & immunotherapeutics·2026

Same author

DNA-engineered immunosensing platform for ultrasensitive detection of clinical protein biomarkers.

Biosensors & bioelectronics·2026

Same author

A 5-Fluorouracil-Constituted DNA Hydrogel Embedded with Quercetin Remodels Tumor Microenvironment for Robust Chemoimmunotherapy.

Advanced healthcare materials·2026

Same author

Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle.

Nature communications·2026

Search research articles

Related Experiment Video

Updated: Apr 11, 2026

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

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

Published on: December 9, 2022

Consistent global structures of complex RNA states through multidimensional chemical mapping.

Clarence Yu Cheng¹, Fang-Chieh Chou¹, Wipapat Kladwang¹

¹Department of Biochemistry, Stanford University, Stanford, United States.

|June 3, 2015

Summary

This study introduces MOHCA-seq, a new method for determining non-coding RNA (ncRNA) 3D structures. This approach achieves 1-nm accuracy, enabling detailed analysis of complex ncRNA folding and function.

Keywords:

biochemistry biophysics high-throughput next-generation sequencing non-coding RNA none riboswitches ribozymes structural biology structure prediction

More Related Videos

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Related Experiment Videos

Last Updated: Apr 11, 2026

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

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

Published on: December 9, 2022

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Area of Science:

Structural Biology
Molecular Biology
RNA Biology

Background:

Non-coding RNAs (ncRNAs) play crucial roles in biological processes, but their complex 3D structures are challenging to determine.
Existing high-throughput methods struggle to provide high-resolution tertiary structure information for ncRNAs.

Purpose of the Study:

To develop and validate a novel method for accurate, high-throughput determination of ncRNA tertiary structures.
To enable visualization of ncRNA folding at 1-nm resolution for functional motif analysis.

Main Methods:

Integration of MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference.
Application of Rosetta 3D modeling guided by chemical mapping data.
Validation using a blind RNA-puzzle challenge (lariat-capping ribozyme) and various riboswitch aptamers.

Main Results:

Achieved consistent 1-nm accuracy in 3D modeling for intricately folded ncRNAs up to 188 nucleotides.
Resolved unexpected tertiary proximities in cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers.
Determined the structure of the human HoxA9D internal ribosome entry site regulon, revealing a loose conformation.

Conclusions:

The multidimensional chemical mapping (MCM) pipeline, combining MOHCA-seq and modeling, provides a powerful sequencing-based route to uncover ncRNA 3D structures.
This method is applicable to functionally important ncRNAs, even in potentially heterogeneous or ligand-free states.