Company News
Synthetic Bio
Analysis and Functional BioDesign of Synthetic genes
Sept 2019

Dear customers,

ATG:biosynthetic Bioinformatics team is always YOUR reliable and trustworthy partner for all issues in Comparative Explorative Genomics - for Genomic Data Mining.

Precise genomic data are leading especially to high functional level molecular BioDesigns, Molecular Engineering of Synthetic Genes and Clusters thereof in Constructional and Artificial Applications of Synthetic Biology.

Based on Synthetic Genes ATG is specialized in planning and realization of bioproduction processes from proof of principle up to the requirements of pilot scales.

Design & Analysis - "codon harmonization" of Synthetic Genes

Core-CDS variants consisting of optimized sequences targting varying codon bias in accordance with the expression host's preferences but showing similar estimated velocity profile shapes can be useful library building blocks for new experimental designs. Provided that other important sequence requirements are considered simultanously in the couse of bioinformatic strategies related to related to "Codon Harmonization" gene function can be influenced towards desired traits. By harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host, Heterologous Protein Expression can be enhanced Fig1.

Fig1.(A)Possible strategy related to "codon harmonization": Signals 1-3 are obtained using different but correlated codon scores based on data-analysis of the native producer. The red line reflects the estimated local translation velocity in the expression host. Velocity indices can be tRNA, codon-bias or codon-enrichment based, preferably combined and crosschecked with insights from mechanistic modeling, or strictly defined according to the customers proposal and specialized knowledge. In the shown example CAI-scores were used and suspected to be problematic codons were avoided. (B,C)Variants of the translation initiation site and in the case of bacterial operons also the translational coupling regions of adjacent orfs should be parametrized and controlled accordingly. The general idea is: When slowing down translational speed, then lower the translation rate according to the pattern in the native host (similar to "codon harmonization") without risking translational arrest, no-go-decay or ribosomal drop-off. (D)Simultaneous control of the synonymous codon frequency distribution following preferences of the eukaryotic expression host for the bacterial NRPS sequence depicted in (A). Codon usage cluster analyses, more detailed tRNA-adaptation analyses and evolutionary-distance based investigations that connect synonymous codon conservation, pausing signals and predicted protein structure have been used to decipher translational regulation (E-G). Data-mining the often highly conserved relative protein expression levels or translational efficiencies of orthologous genes, for which reliable measurements have been performed in the community, is also a promising method to gain insights and estimations.

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Newsletter Archive

Find our past newsletter as PDFs here.

CodoNews#97 (Sept 15):

Analyses and Functional BioDesign of Synthetic Genes

CodoNews#96 (May 24):

NEW! tANCHOR out of Membrane – Mammalian protein display system: Translocate IT – Expose IT

CodoNews #70 (Feb 15):

flexTEC Vectors: Most Flexible Modular Solutions for Multi-Protein Expression - by Use of synthetic genes
CodoNews #69 (Feb 05): Bioinformatics for Semi - Predictive Functional in silico designs of Synthetic Genes and Clusters become more and more reality
CodoNews #68 (Jan 05): Knowlegde Based Deterministic Biodesign Just try Biomorphs and PhysioVars

CodoNews #63 (Jul 24):

flexTEC:a most flexible modular solution for multi-protein expression - by use ofsynthetic genes
CodoNews #62 (Jul 03): Synthetic Gene Sequences-Modulation - Optimization - Function
CodoNews #61 (Jun 25): DNA assembly technology for to integrate your synthetic genes into functionally orchestrated constructions Service in first place:
CodoNews #60 (Jun 12): Service in first place: Synthetic Genes, constructions and all complex calculations around functional modulation and gene improvements
CodoNews #59 (May 28): New Technologies like Synthetic Genes for Solving Emerging Problems
CodoNews #58 (May 22): Computation for Synthetic Biology Projects – Bioinformatics Consulting Service
CodoNews #57 (May 07): Gene Synthesis and Optimization: more than just toying with codon usage
CodoNews #56 (Apr 30): Comparative genomics and synthetic genes are synergistic in improving DNA mediating RNA and protein gene product function by design.
CodoNews #55 (Apr 23): Synthetic genes, clusters, gene assemblies and multi-genic constructs:
CodoNews #54 (Apr 16): Pre-Assembled, Modular, and Optimized Multi-Gene Constructs
CodoNews #53 (Apr 03): FlexTEC- Vectors: the ATG - modular construction systems for multiple synthetic gene expression.
CodoNews #51 (Mar 27): Functional arrangements of Synthetic Genes is our business.
CodoNews #50 (Mar 18): Combinatorial BioDesign starts with FlexTEC- combinatorial vectors.
CodoNews #49 (Jan 29): MultiLabel ideally combines Synthetic Genes with Mammalian Cells: your top-notch solution for multi-protein expression!
CodoNews #48 (Jan 22): flexBacTurbo: your premier solution for multi-protein expression in insect cells!

CodoNews #47 (Jan 12): Iterative Multi-Gene Expression Optimization by use of Synthetic Genes
CodoNews #46 (Jan 02): Computation for Synthetic Biology Projects – Bioinformatics Consulting Service
CodoNews #45 (Dec 14): FlexTEC - pA0 -basic vector
CodoNews #44 (Nov 07): ATG: BioInformatics and BioDesign - Services
CodoNews #43 (Oct 24): Introducing flEXColi - the multi-protein expression system for E.coli
CodoNews #42 (Oct 10): Protein assemblies and multi-protein expression tools
CodoNews #41 (Oct 02): ACDC-SC design: constructive and functional multi-gene expression designs
CodoNews #40 (Sep 19): Looking to integrate synthetic biology into your research & development?
CodoNews #39 (Sep 02): Meet ATG at ...
CodoNews #38 (Aug 27): PepID: a research tool for immunology and molecular biology research

CodoNews #37 (August 15):MultiLabel: your top-notch solution for multi-protein expression in mammalian cells!
CodoNews #36 (August 8): flexBacTurbo: baculo expression system
CodoNews #35 (July 25): L and XL plasmid preps
CodoNews #34 (July 18): Toggle Tec and ACDC-SC design
CodoNews #33 (June 27): Computational Biology Solutions
CodoNews #32 (June 20): PepID
CodoNews #31 (June 11): Multi-Gene Assemblies
CodoNews #30 (May 29): Gene Synthesis and Gene Optimization
CodoNews #29 (May 22): MultiLabel: multi-gene expression in mammalian cells
CodoNews #28 (May 15): ATG's new website
CodoNews #27: PepID: rational peptide library design and expression
CodoNews #26: ACDC-SD Design and Toggle