De Novo DNA

De Novo DNA is a design software and services company focused on engineering genetic systems and organisms. Their web-based platform provides researchers and synthetic biologists with powerful computational tools to predict, control, design, and optimize gene expression, metabolic pathways, and protein libraries across a wide range of organisms and applications.

With over 10,000 registered researchers, more than 850,000 designed genetic systems, and applications spanning 1,200+ use cases, De Novo DNA serves a broad scientific community including academic institutions, biotech companies, and research laboratories working in synthetic biology, metabolic engineering, biologics development, and beyond.

Core Software Tools

• Promoter Calculator: Calculates transcription rates across genetic systems, identifies cryptic promoters and mis-annotated coding sequences, and enables the design of synthetic promoters with desired expression levels.
• RBS Calculator: Predicts and controls translation rates and mRNA decay rates, and designs ribosome binding sites (RBS) to achieve targeted protein expression levels.
• RBS Library Calculator: Enables systematic variation and optimization of enzyme expression levels across metabolic pathways, supporting the identification of rate-limiting steps and maximization of organism productivity.
• Operon Calculator: Supports the design and optimization of multi-gene operons, allowing researchers to redirect metabolic fluxes and maximize production titers.

Massively Parallel Protein Libraries

• De Novo DNA offers a protein library service supporting between 10 and 10,000 proteins at approximately $100 per cloned expression plasmid.
• Supports any amino acid sequence of up to 900 amino acids in length.
• Designed for applications including bioprospecting, biologics development, and enzyme engineering.

Published Research Applications

• Researchers at MIT used the RBS Library Calculator to vary expression of enzymes in the nif gene cluster, maximizing nitrogen fixation rates in Rhizobium sp. IRBG74 and identifying design rules for engineered operons (Ryu et al., Nature Microbiology, 2020).
• Researchers at MIT applied the RBS Calculator to optimize a genetic circuit in engineered L. lactis probiotic bacteria capable of detecting and suppressing cholera infection in vivo (Mao et al., Science Translational Medicine, 2018).
• Researchers at the University of Manchester used the RBS Library Calculator combined with machine learning to optimize expression of ten enzymes for limonene production in E. coli, boosting production titers by over 60% while screening less than 3% of the combinatorial library (Jervis et al., ACS Synthetic Biology, 2018).
• Researchers at the University of Illinois at Urbana-Champaign applied the RBS Library Calculator with Bayesian optimization and automated strain construction via iBioFab to overproduce lycopene in E. coli (HamediRad et al., Nature Communications, 2019).
• Researchers at Washington University used the RBS Calculator to optimize enzyme expression for limonene production in the cyanobacterium Synechococcus 2973, finding that high Limonene Synthase and intermediate GPPS expression levels maximized titers (Lin et al., Metabolic Engineering Communications, 2021).
• Researchers at MIT used the RBS Calculator to optimize 12 inducible transcription factors, creating a "Marionette" E. coli strain capable of tunable control of 12 proteins via small molecule inducers (Meyer et al., Nature Chemical Biology, 2019).
• Researchers at Columbia University applied the RBS Calculator to engineer a CRISPR-based genetic circuit that records temporal biological signals as physical genomic modifications, functioning as a biological tape recorder (Sheth et al., Science, 2017).
• Researchers at the Joint BioEnergy Institute used the RBS Calculator to optimize enzyme expression for overproduction of three types of C5 alcohols in E. coli, achieving 70% of the maximum possible production titer while reducing toxic byproduct formation (George et al., Scientific Reports, 2015).
• Researchers at MIT applied the RBS Library Calculator to systematically vary expression of 16 enzymes in the nif gene cluster, identifying optimal expression levels and design rules to maximize nitrogenase activity (Smanski et al., 2014).

Team

• Howard Salis, Ph.D. — Chemical engineer, synthetic biologist, software developer, entrepreneur, and professor, serving as the scientific and technical foundation of the company.
• Anna Chan-Salis — Research scientist with expertise in molecular biology, biochemistry, genomics, and next-generation sequencing.

De Novo DNA's platform bridges computational design and experimental synthetic biology, providing researchers with the tools needed to rationally engineer organisms for applications in medicine, agriculture, bioenergy, and industrial biotechnology.