Jove
Visualize
Contact Us

Related Concept Videos

RNA Structure01:23

RNA Structure

79.2K
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...
79.2K
RNA Structure01:19

RNA Structure

7.6K
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...
7.6K
Protein and Protein Structure02:15

Protein and Protein Structure

88.2K
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...
88.2K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

32.8K
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...
32.8K
RNA Splicing01:32

RNA Splicing

60.7K
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...
60.7K
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

3.5K
3.5K

You might also read

Related Articles

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

Sort by
Same author

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026
Same author

Computational Resources for Molecular Biology 2026.

Journal of molecular biology·2026
Same author

Reparameterization of the Amber RNA Force Field Non-Bonded Terms.

bioRxiv : the preprint server for biology·2026
Same author

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

Motif server: web server for undesignable RNA motifs and structures.

Journal of molecular biology·2026
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 Experiment Video

Updated: Feb 6, 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

Accelerated RNA secondary structure design using preselected sequences for helices and loops.

Stanislav Bellaousov1, Mohammad Kayedkhordeh1, Raymond J Peterson2

  • 1Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA.

RNA (New York, N.Y.)
|August 12, 2018
PubMed
Summary

Designing RNA sequences for nanostructures is accelerated by using preselected databases of helix and loop sequences. This approach significantly reduces trial-and-error, enabling faster and efficient RNA sequence design.

Keywords:
RNA folding thermodynamicsRNA partition functionRNA sequence designensemble defect

More Related Videos

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

9.9K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Related Experiment Videos

Last Updated: Feb 6, 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
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

9.9K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Area of Science:

  • Computational Biology
  • Biotechnology
  • RNA Nanotechnology

Background:

  • Nucleic acids, particularly RNA, serve as versatile building blocks for nanomachines, pharmaceuticals, and probes.
  • RNA secondary structures are fundamental to self-assembling nanostructures.
  • Designing specific RNA structures is challenging due to the limited natural bases and potential for multiple folding outcomes.

Purpose of the Study:

  • To accelerate the design process for RNA sequences that fold into specific structures.
  • To test the hypothesis that preselecting sequence elements can enhance design efficiency.

Main Methods:

  • Developed databases of RNA helix and loop sequences with favorable thermodynamic properties and low cross-hybridization tendencies.
  • Utilized these preselected sequence databases to guide the iterative refinement process for RNA sequence design.
  • Compared design speed and resulting structure accuracy against methods using randomly chosen sequences.

Main Results:

  • Preselected sequence databases significantly accelerated the design of RNA sequences for both natural (36x faster) and random (6x faster) structures.
  • The ensemble defect of sequences designed using the database was comparable to those designed with random sequences.
  • The developed sequence databases are integrated into the RNAstructure package.

Conclusions:

  • Preselected RNA sequence databases offer a substantial acceleration in designing functional RNA nanostructures.
  • This strategy mitigates the trial-and-error inherent in current iterative RNA design methods.
  • The approach yields RNA sequences with comparable structural accuracy, making it a valuable tool for RNA nanotechnology and design.