By ATG:biosynthetics GmbH
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Bioinformatic-based synthetic gene optimization
ATG:biosynthetic’s core capabilities include high-tech analytical and constructive synthetic bioinformatic-based approaches to highly parallel, multi-parametric design and optimization of single and multi-genic DNA sequences and expressed molecular libraries as well as combinatorial biodesigns.
ATG uses in silico analysis and identification of optimal promoters and enhancers to enhance in vitro experiments for the powerful, fast, effective and intelligent optimization of synthetic genes.
Synthetic gene optimization
Basic gene development consists of extracting a coding sequence, adding a promoter and terminator to it and using the resulting gene construct in expression plasmid. However evolved approaches go much further, applying advanced biocomputational calculations to optimize and streamline the expression constructs.
The bioinformatic approach is particularly necessary where promoters and other control elements from diverse organisms are incorporated into heterologous expression constructs. One example is in metabolic engineering where endogenous genes may be too weakly expressed, too tightly controlled or not exist at all.
ATG has developed in-house expertise and tools for optimization of genes, gene cassettes and entire gene clusters.
ATG’s in silico evolution-mediated artificial genetics platform, EvoMAGIS, can be used for parallel optimization of the various gene and gene cluster parameters including codon use and adaption, restriction site preferences, indices, cryptic splice sites and 5′-mRNA superstructures.
Selected parameters can be weighted over others before the sequence runs through repeated rounds of an evolutionary “tournament” that will return one or several ‘winner’ sequences.
The customer can view pre- and post-comparisons and discuss the results with ATG’s biocomputing specialists.
EvoMAGIS combines synthetic bioinformatics with gene cluster designs for multi-protein expression and minimal molecular function.
ATG has continuously developed the EvoMAGIS GeneIntelligence software, based on years of service and feed-back from customers. In response to their specific requirements, it has optimized constructive aspects, such as the selection and choice for suitable genetic parts and synthesis efficiency and functional aspects, including expression and solubility.
Research has shown that individual genes and gene cassettes in multi-gene operons e.g. biochemical gene clusters and other assemblies can be differentially expressed thus leading to unbalanced expression of the protein products. This makes DNA cluster design and optimization extremely critical to eventual success.
Cluster design is particularly relevant in protein complexes that are sensitive to a specific stoichiometry of their component proteins.
ATG: biosynthetics are leaders in this rapidly evolving field of applied bioinformatics for Synthetic Biology.
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