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

Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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 has a double-helix structure. The...
Improving Translational Accuracy02:07

Improving Translational Accuracy

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...
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...

You might also read

Related Articles

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

Sort by
Same author

Splenial corpus callosum lesions in Boucher-Neuhäuser syndrome: a case series and comprehensive literature review with exploratory analysis of disease duration.

Neuroradiology·2026
Same author

Comparison of alpha-particle track characteristics in GAGG and biological tissues for microdosimetry using experimentally validated GATE simulations with high-resolution track imaging.

Physics in medicine and biology·2026
Same author

Indoor discomfort from ground transportation traffic vibration and noise-Comparison between Vietnamese and Japanese young participants.

The Journal of the Acoustical Society of America·2026
Same author

Usefulness of Superselective Arterial Spin Labeling for Evaluating Feeding Arteries and Brain Invasion in Meningiomas.

AJNR. American journal of neuroradiology·2026
Same author

CRISPR/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in Lithospermum erythrorhizon.

Plant & cell physiology·2026
Same author

Sex-Stratified Association of Regional Dopamine Transporter Binding With Disease Progression in Amyotrophic Lateral Sclerosis.

Annals of clinical and translational neurology·2026

Related Experiment Video

Updated: Jul 10, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Partial base pairing between 5' and 3' UTRs artificially regulates IVT mRNA expression levels.

Nao Hosoda1, Atsushi Takasu1, Kohei Nakanishi1

  • 1Synplogen Co., Ltd, Kobe, Hyōgo, Japan.

Nucleosides, Nucleotides & Nucleic Acids
|July 8, 2026
PubMed
Summary

Engineered mRNA circularization via 5' and 3' untranslated region (UTR) base pairing boosts expression. This finding offers a new method for designing and predicting in vitro-transcribed (IVT) mRNA levels using thermodynamic parameters.

Keywords:
Gibbs free energy changeIVT mRNAcircularizationeukaryotetranslation

More Related Videos

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
09:44

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

Related Experiment Videos

Last Updated: Jul 10, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
09:44

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Biotechnology

Background:

  • Eukaryotic mRNAs feature a 5' cap and 3' poly(A) tail crucial for expression regulation.
  • mRNA circularization, mediated by proteins like eIF4E, PABPC1, and eIF4G, underlies this regulation.
  • In vitro-transcribed (IVT) mRNA expression is a key area in biotechnology.

Purpose of the Study:

  • To investigate the impact of 5'-3' untranslated region (UTR) base pairing on IVT mRNA expression.
  • To explore the relationship between UTR pairing patterns and mRNA expression levels.
  • To establish a thermodynamic framework for designing and predicting IVT mRNA expression.

Main Methods:

  • Designing and transcribing IVT mRNAs with varying 5' and 3' UTR base-pairing potentials.
  • Quantifying the expression levels of these IVT mRNAs.
  • Analyzing the correlation between UTR pairing thermodynamics (Gibbs free energy) and expression levels.

Main Results:

  • Partial base pairing between 5' and 3' UTRs of IVT mRNAs promotes mRNA circularization.
  • This induced circularization artificially enhances mRNA expression levels.
  • Expression levels are influenced by the lengths of complementary and non-complementary regions within UTRs.
  • A sigmoidal relationship exists between expression levels and the Gibbs free energy of UTR pairing.

Conclusions:

  • Engineered 5'-3' UTR base pairing is a viable strategy to enhance IVT mRNA expression.
  • The study provides a novel framework for rational design of IVT mRNA UTRs.
  • Thermodynamic parameters, specifically Gibbs free energy of UTR pairing, can predict IVT mRNA expression levels.