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 Structure01:19

RNA Structure

6.9K
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...
6.9K
RNA Structure01:23

RNA Structure

78.7K
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...
78.7K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

14.6K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
14.6K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.3K
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...
8.3K
RNA-seq03:21

RNA-seq

11.7K
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...
11.7K
RNA Splicing01:32

RNA Splicing

60.2K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
60.2K

You might also read

Related Articles

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

Sort by
Same author

A framework for building a synthetic cell from the SynCell Asia Initiative.

Nature biotechnology·2026
Same author

Matrix stiffness induces midnolin-dependent lamin B1 degradation to control myoblast differentiation.

EMBO reports·2026
Same author

Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.

Briefings in bioinformatics·2026
Same author

A general strategy for engineering GU base pairs to facilitate RNA crystallization.

Nucleic acids research·2024
Same author

Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning.

eLife·2024
Same author

MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.

Genomics, proteomics & bioinformatics·2024
Same journal

Real-time Targeted Enrichment in Single-cell Long-read Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Decoding RNA N6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Tranquillyzer: A Neural Network Framework for Long-read Annotation and Demultiplexing.

Genomics, proteomics & bioinformatics·2026
Same journal

Advancing Functional Transcriptomics in Zebrafish with High-accuracy Full-length RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Single-cell Multiomic and Spatiotemporal Dissection of the Liver Circadian Clock.

Genomics, proteomics & bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 8, 2026

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

5.1K

On the Completeness of Existing RNA Fragment Structures.

Xu Hong1, Jian Zhan1,2, Yaoqi Zhou1

  • 1Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.

Genomics, Proteomics & Bioinformatics
|December 19, 2025
PubMed
Summary
This summary is machine-generated.

RNA structure prediction lags behind proteins because its structural space is incomplete. New experimental methods are needed to capture more RNA structures, focusing on stable sugar-ring platforms.

Keywords:
RNA fragmentRNA modelingRNA pseudo-torsion angleRNA reference frameRNA structure

More Related Videos

Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker
08:12

Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker

Published on: January 3, 2019

7.7K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.9K

Related Experiment Videos

Last Updated: Jan 8, 2026

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

5.1K
Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker
08:12

Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker

Published on: January 3, 2019

7.7K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.9K

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Deep learning methods like AlphaFold 2 have revolutionized protein structure prediction.
  • Protein structural space is largely complete, facilitating prediction accuracy.
  • RNA structure prediction faces challenges due to incomplete structural data.

Purpose of the Study:

  • To assess the completeness of RNA structural space at various nucleotide levels (di-, tri-, tetra-, penta-).
  • To compare the completeness of RNA structural space with that of proteins.
  • To identify stable structural motifs in RNA for potential use in prediction models.

Main Methods:

  • Analysis of non-redundant structural fragments of RNA at di-, tri-, tetra-, and penta-nucleotide levels.
  • Examination of structural diversity within RNA fragments.
  • Identification of stable reference frames within RNA structures.

Main Results:

  • The number of non-redundant RNA structural fragments at tetra- and penta-nucleotide levels is increasing exponentially.
  • RNA structural space is far from complete compared to protein structural space.
  • A specific reference frame (O4', C1', C2') shows minimal structural diversity, indicating stability.

Conclusions:

  • Significant efforts are required to enhance experimental determination of RNA structures to expand observed structural space.
  • Improved methods are crucial for advancing RNA structure prediction accuracy.
  • The identified stable sugar-ring reference frame could serve as a foundational element for RNA structure modeling.