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

Types of RNA01:20

Types of RNA

6.1K
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
6.1K
RNA Stability01:53

RNA Stability

33.9K
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...
33.9K
RNA-seq03:21

RNA-seq

10.4K
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...
10.4K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

30.3K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
30.3K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

13.4K
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,...
13.4K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.8K
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...
6.8K

You might also read

Related Articles

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

Sort by
Same author

GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.

PLoS computational biology·2026
Same author

Automated Cephalometric Points Marking System.

Diagnostics (Basel, Switzerland)·2026
Same author

A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.

Nucleic acids research·2026
Same author

FRET-guided selection of RNA 3D structures.

Nucleic acids research·2026
Same author

Detecting polynucleotide motifs: Pentads, hexads, and beyond.

PLoS computational biology·2025
Same author

Updates to the CASP Infrastructure in 2024.

Proteins·2025
Same journal

OmicsTransformer: Self-Supervised Masked Consistency and Uncertainty-Aware Fusion for Robust Multi-Omics Prediction.

Bioinformatics (Oxford, England)·2026
Same journal

Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection.

Bioinformatics (Oxford, England)·2026
Same journal

ARISE: RNA-Anchored Shared-Edge Topology and Hierarchical Fusion for Spatial Multi-Omics Integration.

Bioinformatics (Oxford, England)·2026
Same journal

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

Bioinformatics (Oxford, England)·2026
Same journal

PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides.

Bioinformatics (Oxford, England)·2026
Same journal

ARGscape: A modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Sep 5, 2025

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

10.7K

RNAloops: a database of RNA multiloops.

Jakub Wiedemann1, Jacek Kaczor1, Maciej Milostan1,2

  • 1Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland.

Bioinformatics (Oxford, England)
|July 9, 2022
PubMed
Summary
This summary is machine-generated.

RNAloops is a new database for analyzing multi-branched loops in RNA structures. This resource aids in understanding RNA function and designing new therapeutics by providing detailed structural data.

More Related Videos

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K

Related Experiment Videos

Last Updated: Sep 5, 2025

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

10.7K
Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Molecular biology

Background:

  • Understanding RNA's 3D structure is vital for function discovery and therapeutic design.
  • Local RNA substructures, like multi-branched loops, significantly influence overall molecular shape.
  • Computational modeling of these multi-branched loops remains a challenge in structural bioinformatics.

Purpose of the Study:

  • To establish a comprehensive, self-updating database of multi-branched loops in RNA.
  • To facilitate the analysis of multi-branched loop features and spatial arrangements.
  • To address the limitations in computational modeling of RNA substructures.

Main Methods:

  • Collected multi-branched loops from Protein Data Bank (PDB) deposited RNA structures.
  • Computed angular data (planar and Euler angles) between adjacent helices for each loop.
  • Developed a database system for searching, analyzing, and visualizing loop structures and statistics.

Main Results:

  • RNAloops database provides detailed angular data for multi-branched loops.
  • The database enables numerical and visual presentation of loop structure details.
  • It facilitates statistical analysis of loop features and spatial arrangements.

Conclusions:

  • RNAloops serves as a valuable resource for studying RNA multi-branched loops.
  • The database aids in understanding the spatial organization of RNA substructures.
  • It supports advancements in RNA structure-based drug design and functional studies.