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

79.0K
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...
79.0K
RNA Structure01:19

RNA Structure

7.5K
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...
7.5K
Protein and Protein Structure02:15

Protein and Protein Structure

87.4K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
87.4K
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

3.4K
3.4K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.7K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.7K
RNA Stability01:53

RNA Stability

35.7K
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...
35.7K

You might also read

Related Articles

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

Sort by
Same author

Effect of the cardiac long non-coding RNA Charme depletion on the maturation and paracrine signaling of resident cardiac fibroblasts.

Cell death & disease·2026
Same author

Multimodal Structural Characterization of SARS-CoV-2 Spike Variants: Spectroscopic and Computational Insights.

International journal of molecular sciences·2025
Same author

The MYC-dependent lncRNA MB3 inhibits apoptosis in Group 3 Medulloblastoma by regulating the TGF-β pathway via HMGN5.

Cell death & disease·2025
Same author

N-Heterocyclic Carbenes on a III-V Semiconductor: From Chain Formation to Ordered Monolayers.

Angewandte Chemie (International ed. in English)·2025
Same author

LncRNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyogenesis via splicing regulation.

Nature communications·2025
Same author

TARNAS: A Software Tool for Abstracting and Translating RNA Secondary Structures.

International journal of molecular sciences·2025
Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026
Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026
Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026
Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026
Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026
Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 28, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.2K

Decoding RNA triple helices: identification from sequence and secondary structure.

Margherita A G Matarrese1, Michela Quadrini2, Nicole Luchetti1

  • 1Department of Engineering, Università Campus Bio-Medico di Roma, Via Àlvaro del Portillo, 21, 00128 Rome, Italy.

Briefings in Bioinformatics
|January 26, 2026
PubMed
Summary
This summary is machine-generated.

Researchers developed a new framework and tool, TripleMatcher, to identify RNA triple helices, crucial for gene regulation. This method accurately detects these structures from secondary RNA data, aiding in understanding long non-coding RNA functions.

Keywords:
RNA pattern searchRNA secondary structureRNA structure predictionlong non-coding RNAnon-coding RNA

More Related Videos

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.7K
Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

11.2K

Related Experiment Videos

Last Updated: Jan 28, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.2K
Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.7K
Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

11.2K

Area of Science:

  • Molecular Biology
  • RNA Structure and Function
  • Bioinformatics

Background:

  • Long non-coding RNAs (lncRNAs) regulate gene expression through interactions with DNA, RNA, and proteins.
  • RNA triple helices, involving Hoogsteen base pairing, are critical structural motifs for lncRNA stability and function, exemplified by MALAT1.
  • Accurate detection of RNA triple helices is essential for understanding their regulatory roles.

Purpose of the Study:

  • To develop a secondary-structure-based framework for annotating and detecting RNA triple helices.
  • To introduce TripleMatcher, a computational tool for identifying and filtering potential RNA triple helix candidates.
  • To validate the framework's performance using known triple-helical RNAs and apply it to large-scale RNA screening.

Main Methods:

  • Extended the dot-bracket notation to include a third line for Hoogsteen contacts.
  • Developed TripleMatcher to search for triple-helix patterns, filter by C1'-C1' distance, and merge overlapping regions.
  • Benchmarked against eight predictors and applied prospectively to a large dataset of 4160 RNAs.

Main Results:

  • TripleMatcher successfully localized all experimentally validated triple helices in a test set of 8 RNAs (8/8 detection).
  • Geometric filtering significantly improved precision (0.42 to 0.81) and accuracy (F1 from 0.42 to 0.62) while maintaining sensitivity.
  • Prospective screening identified 97 geometrically feasible triple-helix candidates across 7 molecules, including human telomerase complexes, from 150,990 raw candidates.

Conclusions:

  • The proposed framework and TripleMatcher provide an efficient and accurate method for identifying RNA triple helices from secondary structures.
  • This approach facilitates the discovery of novel triple-helical structures and enhances the understanding of lncRNA regulatory mechanisms.
  • The identified candidates are suitable for targeted experimental validation, advancing research in RNA biology and gene regulation.