Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

From DNA to Protein

From DNA to Protein

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...

The Central Dogma

The Central Dogma

The Central Dogma

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...

Complementary DNA

Complementary DNA

Leaky Scanning

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...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

You might also read

Related Articles

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

Sort by

Same author

Large field of view fluorescence imaging of microfluidic devices with a tandem-lens macroscope.

Lab on a chip·2026

Same author

Machine-learning prediction of affinity and epistasis in the bovine pancreatic trypsin inhibitor-chymotrypsin complex.

Protein science : a publication of the Protein Society·2026

Same author

High-throughput biochemical phenotyping of SHP2 variants reveals the molecular basis of diseases and allosteric drug inhibition.

bioRxiv : the preprint server for biology·2026

Same author

FoTO1 orchestrates Taxol biosynthesis through catalytic and non-catalytic mechanisms.

bioRxiv : the preprint server for biology·2026

Same author

Engineering the mechanosensitivity of single DNA molecules via high-throughput microfluidic force spectroscopy.

bioRxiv : the preprint server for biology·2026

Same author

uSort-M: Scalable isolation of user-defined sequences from diverse pooled libraries.

bioRxiv : the preprint server for biology·2026

Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026

Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026

Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026

Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026

Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 26, 2025

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

DeCoDe: degenerate codon design for complete protein-coding DNA libraries.

Tyler C Shimko¹, Polly M Fordyce^1,2,3,4, Yaron Orenstein⁵

¹Department of Genetics.

Bioinformatics (Oxford, England)

|March 17, 2020

Summary

This summary is machine-generated.

We developed DeCoDe, a novel algorithm for optimizing degenerate codon (DC) libraries used in high-throughput protein screening. DeCoDe efficiently designs diverse protein variants, overcoming limitations of previous methods for complex sequence covariation.

More Related Videos

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Related Experiment Videos

Last Updated: Dec 26, 2025

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Area of Science:

Protein engineering and synthetic biology
Computational biology and bioinformatics
Molecular biology and biochemistry

Background:

High-throughput protein screening is essential for protein function analysis and design.
Current methods like mutagenesis and DNA synthesis have limitations, including high costs and low functional variant yields.
Degenerate codons (DCs) offer a cost-effective solution for generating diverse protein libraries, but designing them for covarying sequences is challenging.

Purpose of the Study:

To introduce a novel algorithm, degenerate codon design (DeCoDe), for optimizing degenerate codon libraries.
To address the limitations of existing methods in designing DC libraries with complex sequence covariation and mixed-length proteins.
To provide a broadly applicable tool for various protein engineering and reconstruction applications.

Main Methods:

Development of a novel algorithm, DeCoDe, based on integer linear programming for total degenerate codon library optimization.
Application of DeCoDe to design libraries with complex patterns of covariation, exemplified by the avGFP lineage.
Demonstration of DeCoDe's capability to encode mixed-length protein libraries.

Main Results:

DeCoDe significantly outperforms existing state-of-the-art degenerate codon optimization algorithms.
The algorithm demonstrates scalability for libraries involving over a hundred proteins with intricate covariation patterns.
DeCoDe is the first algorithm capable of designing mixed-length protein libraries using degenerate codons.

Conclusions:

DeCoDe offers a powerful and efficient solution for designing degenerate codon libraries, overcoming previous design challenges.
The algorithm is broadly applicable to diverse protein engineering tasks, including those leveraging mutual information and ancestral protein reconstruction.
DeCoDe represents a significant advancement in the field of protein library design and high-throughput screening.