codon Archives

Outline of construction of plasmids carrying LUCA and E. coli tRNA genes and codon test genes. A LUCA and E. coli tRNA genes. Pairs of tRNA genes from E. coli and LUCA with identical anticodon sequences were synthesized. Primers (Supplementary Table S2) were used to amplify the transcription templates for in vitro synthesis. B Codon test genes. The constructs were based on the pET23a vector. Test genes were inserted between the NdeI and BamHI sites, with the start codons included in the NdeI site. -- [Journal of Molecular Evolution]

Resurrecting tRNAs of the Last Universal Common Ancestor (Commonote) Toward Rebuilding the Ancient Translation System

by Keith CowingJuly 14, 2026July 14, 2026

[Journal of Molecular Evolution] Ancestral sequence reconstruction (ASR) was used to study the evolution of the translational system by inferring tRNA sequences of the Last Archaeal Common Ancestor (LACA), the […]

Relationships between amino acid composition, physicochemical properties, and proteome elemental composition across cellular and viral life. (A) Heatmap showing Spearman rank correlations (ρ) between amino acid frequencies and normalized elemental composition for carbon (C), hydrogen (H), nitrogen (N), oxygen (O), sulfur (S), and selenium (Se) across cellular domains and viral realms. Amino acids are shown on the yaxis using standard three and one-letter abbreviations. (B) Heatmap showing Spearman correlations between aggregated amino acid physicochemical property classes and elemental composition across the same groups. Properties include aliphatic, aromatic, non-polar, polar, charged, basic, and acidic residues. Colors indicate correlation strength and direction from negative (yellow) to positive (blue), with gray cells indicating absent values. -- q-bio.PE

Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Deep-time Consistency In Proteome Elemental Composition Across Cellular And Viral Life

by Keith CowingMay 27, 2026May 27, 2026

Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved.

Model accuracy in terms of predicted DSSP secondary structure. A. DSSP sequence percent identity of predicted sequences to target, input, secondary structure. B. Example target structures of low (green) medium (orange) and high (blue) structure complexity proteins (top) displayed in ribbon format. Histograms (bottom) of results for DSSP sequence percent identity of predicted sequences to target, input, secondary structures for low404 (green) medium- (orange) and high- (blue) complexity protein targets. C. DSSP sequence percent identity for predicted sequences across protein sequence length and alphabet size. --biorxiv.org

AI - Data - Apps - Cybernetics, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

Artificial Intelligence Aided Design Of Peptides With Custom Secondary Structure Motifs And Reduced Amino Acid Alphabets

by Keith CowingMay 20, 2026May 20, 2026

Proteins are highly diverse functional polymers where the specific sequence of amino acids, selected from a standard genetically-encoded alphabet of twenty (C20), determines the structure and ultimately the function of […]

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

The Origin Of The Genetic Code Is Encrypted In The Structure Of Present-day Transfer RNAs

by Keith CowingApril 21, 2026April 21, 2026

Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, […]

The experimental pipeline, from design to characterization, of peptides comprising the Xeno 1 and Xeno 2 amino acid alphabets. Design begins with a library of commercially available amino acids. The physicochemical properties (Van der Waals volume and hydrophobicity at pH 7) are then estimated for a xeno alphabet heuristic search. The potential energy surfaces for each amino acid which returns in the search is calculated and two xeno amino acid alphabets, Xeno 1 and Xeno 2, are selected based on post-search metrics (e.g. PCA and EMD). The similarity of these alphabets to the E10 is further assessed via calculation of HOMO-LUMO gaps and LogS: their ability to form secondary structures is measured in vitro with ECD, IR, and NMR spectroscopy for random combinatorial 25-mer libraries and for designed sequences. -- biorxiv.org

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Press Release

Xeno Amino Acid Alphabets Form Peptides With Familiar Secondary Structure

by Keith CowingFebruary 10, 2026

The central dogma of molecular biology describes how genetic information stored in nucleic acids guides the formation of structured proteins from a single molecular alphabet of twenty amino acids (C20)1,2.

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

All Life Copies DNA Unambiguously Into Proteins. Archaea May Be The Exception.

by Keith CowingDecember 2, 2025December 2, 2025

The beauty of the DNA code is that organisms interpret it unambiguously. Each three-letter nucleotide sequence, or codon, in a gene codes for a unique amino acid that’s added to […]

Codons for the amino acids serine and alanine plus one stop codon were eliminated, requiring over 101,000 recoding events. -- MRC Laboratory of Molecular Biology

AI - Data - Apps - Cybernetics, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

Synthetic Biology: Syn57 Represents A New Chapter In The Genetic Code Of Life

by Keith CowingAugust 27, 2025

The genetic code, which has been nearly universal across all known life for billions of years, utilises 64 triplets of DNA and RNA bases, known as codons, to encode 20 […]

Liquid brine veins, where RNA molecules can replicate, surround solid ice crystals in water ice, as seen with an electron microscope. Credit Philipp Holliger, MRC LMB

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

Chemists Recreate How RNA Might Have Reproduced For The First Time

by Keith CowingMay 29, 2025May 28, 2025

Chemists at UCL and the MRC Laboratory of Molecular Biology have demonstrated how RNA (ribonucleic acid) might have replicated itself on early Earth – a key process in the origin […]

A codon, a sequence of three nucleotides in DNA and RNA that codes for a specific amino acid, acts like an “instruction manual” for protein synthesis, telling the cell which of the 20 natural amino acids to add to a growing protein chain — or, in the case of the three “stop” codons (known as TAG, TGA, and TAA), signaling the termination of protein synthesis. Yale scientists recoded a cell to have a single, non-degenerative TAA codon. The newly “free” TGA and TAG codons have been reassigned to encode nonstandard amino acids into synthetic proteins that possess new chemistries with innumerable applications. Credit Yale University / Michael S. Helfenbein

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

Recoding A Genome For Programmable Synthetic Proteins

by Keith CowingFebruary 11, 2025

Synthetic biologists from Yale were able to re-write the genetic code of an organism — a novel genomically recoded organism (GRO) with one stop codon — using a cellular platform […]

The evolutionary history of a protein domain may date back further in time than that of the whole-gene ortholog that it is part of. Multidomain genes 3 and 4 originated around the same time. However, they are made up of two protein domains (blue and orange boxes) that emerged and diverged at different points in time—domain 1 is older than domain 2. -- PNAS

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Habitable Zones, Origin & Evolution of Life, Press Release

Study Sheds Light On The Origin Of The Genetic Code

by Keith CowingDecember 13, 2024

Despite awe-inspiring diversity, nearly every lifeform – from bacteria to blue whales – shares the same genetic code. How and when this code came about has been the subject of […]

codon

Resurrecting tRNAs of the Last Universal Common Ancestor (Commonote) Toward Rebuilding the Ancient Translation System

Deep-time Consistency In Proteome Elemental Composition Across Cellular And Viral Life

Artificial Intelligence Aided Design Of Peptides With Custom Secondary Structure Motifs And Reduced Amino Acid Alphabets

The Origin Of The Genetic Code Is Encrypted In The Structure Of Present-day Transfer RNAs

Xeno Amino Acid Alphabets Form Peptides With Familiar Secondary Structure

All Life Copies DNA Unambiguously Into Proteins. Archaea May Be The Exception.

Synthetic Biology: Syn57 Represents A New Chapter In The Genetic Code Of Life

Chemists Recreate How RNA Might Have Reproduced For The First Time

Recoding A Genome For Programmable Synthetic Proteins

Study Sheds Light On The Origin Of The Genetic Code

Astrobiology Graduate Conference (AbGradCon26) Update

ExMODE: A Comprehensive Resource For Extremophile Genomic And Functional Exploration

Mass Wasting On Mars

The Hill Sphere Transits of Beta Pictoris c and The Search for Another 1981-like Event

Sample Return Tech: Pre-impact Meteorite Strewn Field Predictions For Imminent Impactors And Meteorite Recovery