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

Leaky Scanning02:28

Leaky Scanning

5.4K
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...
5.4K
Improving Translational Accuracy02:07

Improving Translational Accuracy

12.4K
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...
12.4K
Improving Translational Accuracy02:07

Improving Translational Accuracy

3.3K
3.3K
From DNA to Protein03:06

From DNA to Protein

20.9K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
20.9K
Routh-Hurwitz Criterion II01:19

Routh-Hurwitz Criterion II

613
In the application of the Routh-Hurwitz criterion, two specific scenarios can arise that complicate stability analysis.
The first scenario occurs when a singular zero appears in the first column of the Routh table. This situation creates a division by zero issues. To resolve this, a small positive or negative number, denoted as epsilon (∈), is substituted for the zero. The stability analysis proceeds by assuming a sign for ∈. If ∈ is positive, any sign change in the first...
613
Routh-Hurwitz Criterion I01:15

Routh-Hurwitz Criterion I

404
Consider an electrical power grid, where stability is essential to prevent blackouts. The Routh-Hurwitz criterion is a valuable tool for assessing system stability under varying load conditions or faults. By analyzing the closed-loop transfer function, the Routh-Hurwitz criterion helps determine whether the system remains stable.
To apply the Routh-Hurwitz criterion, a Routh table is constructed. The table's rows are labeled with powers of the complex frequency variable s, starting from the...
404

You might also read

Related Articles

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

Sort by
Same author

Identification of small molecule inhibitors of PPM1D using an integrated drug discovery platform.

iScience·2025
Same author

Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.

Molecular cell·2024
Same author

The ribotoxic stress response drives UV-mediated cell death.

Cell·2024
Same author

Identification of Small Molecule Inhibitors of PPM1D Using a Novel Drug Discovery Platform.

bioRxiv : the preprint server for biology·2024
Same author

Paradoxical Hyperreflexia in a Patient With Classic Guillain-Barré Syndrome.

Cureus·2024
Same author

The Effectiveness of Student-Led Musculoskeletal and Vascular Ultrasound Workshops at a Single Institution: A Retrospective Survey Analysis.

Cureus·2023
Same journal

AGCECDA: attention-guided heterogeneous graph collaborative embedding for circRNA-drug sensitivity association prediction.

BMC biology·2026
Same journal

A decoy receptor antagonizes interferon mediated antiviral responses in teleost fish.

BMC biology·2026
Same journal

Decoding the association between platinum resistance and HPV status in cervical cancer using organoid models.

BMC biology·2026
Same journal

Loss of the RAD-51 isoform A redirects DNA repair and preserves genome stability in FANCD2-deficient Caenorhabditis elegans.

BMC biology·2026
Same journal

Skeletal porosity of a cold-water coral increases with decreasing aragonite saturation state along a depth gradient in the Mediterranean Sea.

BMC biology·2026
Same journal

Diet change reveals asymmetric response in gene expression and microbial composition across the digestive tract of two closely related herbivores.

BMC biology·2026
See all related articles

Related Experiment Video

Updated: Nov 16, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

8.6K

Assessing optimal: inequalities in codon optimization algorithms.

Matthew J Ranaghan1, Jeffrey J Li2, Dylan M Laprise2

  • 1Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. ranaghan@broadinstitute.org.

BMC Biology
|February 20, 2021
PubMed
Summary
This summary is machine-generated.

Custom gene optimization for recombinant protein expression shows variable results. A median codon frequency may better predict soluble yields than the CAI metric, highlighting the need for improved DNA sequence analysis.

Keywords:
%MinMaxAlgorithmCodon optimizationCodon usageKRas4BViolin plot

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.3K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.5K

Related Experiment Videos

Last Updated: Nov 16, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

8.6K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.3K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.5K

Area of Science:

  • Molecular Biology
  • Biotechnology
  • Bioinformatics

Background:

  • Custom gene synthesis is common in recombinant biology, with genes often optimized to non-native sequences for overexpression.
  • Previous studies reported variable protein yields and properties when comparing native and optimized DNA sequences.
  • No studies have practically compared different codon optimization algorithms or their impact on protein yields.

Purpose of the Study:

  • To investigate factors influencing optimized DNA sequence (CDS) performance in recombinant protein expression.
  • To compare the effectiveness of different codon optimization algorithms.
  • To identify better predictors of soluble protein yields.

Main Methods:

  • Developed a method for visualizing, analyzing, and comparing algorithm-optimized DNA sequences.
  • Evaluated codon optimization algorithms and their impact on recombinant yields.
  • Utilized KRas4B as a case study to compare prediction metrics.

Main Results:

  • Little consensus exists among codon optimization algorithms.
  • Algorithm-optimized CDSs have an equal chance of increasing or decreasing recombinant yields compared to native DNA.
  • A median codon frequency may be a better predictor of soluble yields than the commonly used Codon Adaptation Index (CAI).

Conclusions:

  • Researchers should carefully consider the necessity of DNA optimization for their experiments.
  • Improving the reproducibility of recombinant work requires publishing non-native CDS sequences.
  • Further development is needed for more reliable codon optimization strategies.