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

29.8K
29.8K
RNA Structure01:23

RNA Structure

81.4K
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...
81.4K
RNA Structure01:19

RNA Structure

8.4K
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...
8.4K
Ribosome Profiling02:24

Ribosome Profiling

4.3K
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...
4.3K
RNA-seq03:21

RNA-seq

12.6K
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...
12.6K
Nucleic Acid Structure01:25

Nucleic Acid Structure

10.3K
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...
10.3K

You might also read

Related Articles

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

Sort by
Same author

RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.

Bioinformatics (Oxford, England)·2026
Same author

Construction and validation of a lncRNA/circRNA-miRNA-mRNA ceRNA network in allergic rhinitis pathogenesis.

BMC medical genomics·2026
Same author

Unlocking stable four-electron redox chemistry in aqueous zinc-iodine batteries via solvation structure reconstruction.

Journal of colloid and interface science·2026
Same author

Tailoring Solvation Sheaths and Interfacial Chemistry: A Review of Electrolyte Engineering for Highly Reversible Aqueous Zinc-Iodine Batteries.

Molecules (Basel, Switzerland)·2026
Same author

Characteristics of patients with acute respiratory failure in obesity hypoventilation syndrome in the intensive care unit: A retrospective cohort study.

Respiratory medicine·2026
Same author

From in silico screening to mechanism: computational advances in developing anti-allergic agents for food allergy.

Critical reviews in food science and nutrition·2026

Related Experiment Video

Updated: Apr 6, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K

STAR3D: a stack-based RNA 3D structural alignment tool.

Ping Ge1, Shaojie Zhang2

  • 1Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

Nucleic Acids Research
|July 18, 2015
PubMed
Summary
This summary is machine-generated.

Comparing three-dimensional (3D) RNA structures aids understanding of RNA function and evolution. A new tool, STAR3D, aligns RNA 3D structures efficiently by considering 2D structural relationships, improving accuracy and speed.

More Related Videos

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.5K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.3K

Related Experiment Videos

Last Updated: Apr 6, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.5K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.3K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Non-coding RNAs (ncRNAs) perform diverse functions requiring complex 3D structures.
  • Comparing RNA 3D structures is crucial for understanding functional conservation and evolutionary history.
  • Existing RNA 3D structure alignment tools often do not fully consider the hierarchical formation of RNA secondary structures.

Purpose of the Study:

  • To develop a novel tool, STAR3D, for aligning RNA 3D structures.
  • To address the limitations of existing methods by incorporating 2D structural relationships without complex secondary structure comparisons.
  • To improve the accuracy and efficiency of RNA 3D structure alignment.

Main Methods:

  • STAR3D identifies conserved 3D stacks within input RNA structures.
  • These conserved stacks are integrated into a tree-like consensus structure.
  • Loop regions are compared based on their positions within the consensus tree.

Main Results:

  • STAR3D demonstrates higher prediction accuracy for both homologous and non-homologous RNAs compared to state-of-the-art tools.
  • The tool achieves this accuracy with a significantly shorter running time.
  • STAR3D effectively utilizes 2D structural relationships within the 3D context.

Conclusions:

  • STAR3D offers a more accurate and efficient approach to RNA 3D structure alignment.
  • The method's focus on hierarchical 2D relationships within 3D structures is key to its performance.
  • This tool can advance research in RNA structure-function relationships and evolution.