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

Nucleic Acid Structure01:25

Nucleic Acid Structure

7.1K
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...
7.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.9K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.9K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.8K
RNA Editing02:23

RNA Editing

9.2K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.2K
Ribosome Profiling02:24

Ribosome Profiling

3.6K
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...
3.6K
Termination of Translation01:44

Termination of Translation

25.7K
The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
25.7K

You might also read

Related Articles

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

Sort by
Same author

Fine-scale structural information substantially improves mRNA therapeutic stability prediction.

Molecular therapy. Nucleic acids·2026
Same author

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

bioRxiv : the preprint server for biology·2026
Same author

Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.

RNA (New York, N.Y.)·2026
Same author

Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.

bioRxiv : the preprint server for biology·2025
Same author

Fine scale structural information substantially improves multivariate regression model for mRNA in-vial degradation prediction.

bioRxiv : the preprint server for biology·2025
Same author

JAX-RNAfold: scalable differentiable folding.

Bioinformatics (Oxford, England)·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: Sep 13, 2025

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

4.5K

mRNA folding algorithms for structure and codon optimization.

Max Ward1, Mary Richardson2, Mihir Metkar2

  • 1School of Physics, Mathematics, and Computing, The University of Western Australia, WA 6009, Australia.

Briefings in Bioinformatics
|August 4, 2025
PubMed
Summary
This summary is machine-generated.

Messenger RNA (mRNA) stability is crucial for therapies. mRNA folding algorithms enhance mRNA stability and efficacy, improving vaccine development and drug delivery, especially in resource-limited areas.

Keywords:
RNARNA secondary structurealgorithm benchmarkingalgorithmsdynamic programmingmRNA foldingmRNA optimizationmRNA therapeutics

More Related Videos

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.2K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.7K

Related Experiment Videos

Last Updated: Sep 13, 2025

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

4.5K
Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.2K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.7K

Area of Science:

  • Biotechnology and Molecular Biology
  • Bioinformatics and Computational Biology
  • Vaccinology

Background:

  • Messenger RNA (mRNA) technology offers rapid production for vaccines, protein therapies, and cancer immunotherapies.
  • mRNA instability presents significant storage and distribution challenges, particularly in resource-limited settings.
  • Co-optimizing RNA structure and codon choice is a key strategy to improve mRNA stability and efficacy.

Purpose of the Study:

  • To provide an in-depth understanding of mRNA folding algorithms.
  • To identify opportunities for improving mRNA design algorithms.
  • To benchmark current software implementations for scalability, correctness, and features.

Main Methods:

  • Review of specialized algorithms generalizing classical RNA folding algorithms.
  • In silico analysis of underlying principles, performance, and limitations of mRNA folding algorithms.
  • Evaluation of laboratory testing of mRNA folding-optimized vaccines (e.g., SARS-CoV-2 spike, VZV gE).

Main Results:

  • mRNA folding algorithms show promise in enhancing mRNA stability and immunogenicity.
  • Initial laboratory tests indicate improved in-solution stability and immune response for optimized mRNA vaccines.
  • A comprehensive in silico analysis is essential alongside experimental evaluation.

Conclusions:

  • mRNA folding algorithms represent a significant advancement in mRNA-based therapeutics.
  • Further computational analysis and algorithm development are needed to fully realize the potential of mRNA technology.
  • Optimized mRNA design holds promise for more stable, effective, and accessible medical treatments.