Schlinkmann K.M.,University of Zürich |
Honegger A.,University of Zürich |
Tureci E.,University of Zürich |
Robison K.E.,Codon Devices |
And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012
The structural features determining efficient biosynthesis, stability in the membrane and, after solubilization, in detergents are not well understood for integral membrane proteins such as G protein-coupled receptors (GPCRs). Starting from the rat neurotensin receptor 1, a class A GPCR, we generated a separate library comprising all 64 codons for eachamino acid position. By combining a previously developed FACS-based selection system for functional expression [Sarkar C, et al. (2009) Proc Natl Acad Sci USA 105:14808-14813] with ultradeep 454 sequencing, we determined the amino acid preference in every position and identified several positions in the natural sequence that restrict functional expression. A strong accumulation of shifts, i.e., a residue preference different from wild type, is detected for helix 1, suggesting a key role in receptor biosynthesis. Furthermore, under selective pressure we observe a shift of the most conserved residues of the N-terminal helices. This unique data set allows us to compare the in vitro evolution of a GPCR to the natural evolution of the GPCR family and to observe how selective pressure shapes the sequence space covered by functional molecules. Under the applied selective pressure, several positions shift away from the wild-type sequence, and these improve the biophysical properties.Wediscuss possible structural reasons for conserved and shifted residues.
Lippow S.M.,Codon Devices |
Moon T.S.,Massachusetts Institute of Technology |
Moon T.S.,University of California at San Francisco |
Basu S.,Codon Devices |
And 7 more authors.
Chemistry and Biology | Year: 2010
Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways. © 2010 Elsevier Ltd. All right reserved.
Blake W.J.,Codon Devices |
Blake W.J.,Greenlight Biosciences |
Chapman B.A.,Codon Devices |
Zindal A.,Codon Devices |
And 4 more authors.
Nucleic Acids Research | Year: 2010
The engineering of biological components has been facilitated by de novo synthesis of gene-length DNA. Biological engineering at the level of pathways and genomes, however, requires a scalable and cost-effective assembly of DNA molecules that are longer than ~10 kb, and this remains a challenge. Here we present the development of pairwise selection assembly (PSA), a process that involves hierarchical construction of long-length DNA through the use of a standard set of components and operations. In PSA, activation tags at the termini of assembly sub-fragments are reused throughout the assembly process to activate vector-encoded selectable markers. Marker activation enables stringent selection for a correctly assembled product in vivo, often obviating the need for clonal isolation. Importantly, construction via PSA is sequence-independent, and does not require primary sequence modification (e.g. the addition or removal of restriction sites). The utility of PSA is demonstrated in the construction of a completely synthetic 91-kb chromosome arm from Saccharomyces cerevisiae. © The Author(s) 2010. Published by Oxford University Press.
News Article | July 14, 2009
Oscient Pharmaceuticals has apparently run short on options to keep its struggling drug business afloat. The Waltham, MA-based biotech firm (NASDAQ:OSCI) and its subsidiary Guardian II Acquisition Corporation have each filed for Chapter 11 bankruptcy protection and Oscient has landed a buyer for one of its two marketed products, Oscient announced late yesterday. The company says it has struck an agreement to sell its assets associated with the antibiotic drug gemifloxacin mesylate (Factive), to a subsidiary of Cary, NC-based Cornerstone Therapeutics (NASDAQ:CRTX) for more than $5 million. Yet it’s expected that there will be a competitive auction for the Factive assets in bankruptcy court before the deal is sealed. The antibiotic, which treats forms of bronchitis and pneumonia, accounted for only $16.5 million of Oscient’s $86.8 million in 2008 revenue. The firm is also seeking a buyer for its top-selling drug, fenofibrate (Antara), which is prescribed for patients with above-normal cholesterol and triglyceride levels. Oscient appears to be the latest victim of a lousy environment for unprofitable life sciences companies searching for funds to stay alive. Other local examples include Waltham, MA-based drug developer Dynogen Pharmaceuticals, which filed for bankruptcy early this year, and synthetic DNA maker Codon Devices, which reportedly shuttered its operations in Cambridge, MA, this spring. The cash shortage has also prompted Lexington, MA-based Epix Pharmaceuticals (NASDAQ:EPIX) to sell off assets and seek other alternatives to stay afloat. Oscient, which plans to continue operations while in bankruptcy, has racked up $183.3 million in debts and has assets valued at $174 million, according to its bankruptcy filing. The filing says that the company owes $46 million to U.S. Bank National Association, of Boston, $7.8 million to funds associated with Dallas-based investment firm Maverick Capital, $6.6 million to BB Bioventures in South San Francisco, and $5.5 million to medical products giant Abbott Labs, headquartered in Abbott Park, IL, to name its four largest creditors listed in the bankruptcy filing. The bankruptcy filing is the latest measure Oscient has taken to keep its business intact. The company cut about 100 of its some 300 workers in February to save money, and last month it said it planned to slash another 180 jobs, including its entire 150-person sales force. Still, the company said last month that it only had enough cash to operate into the third quarter of 2009. Also, the Nasdaq plans to de-list Oscient’s common stock later this month for the company’s failure to pay fees to meet its listing obligations, according to the company.
News Article | August 14, 2007
“The heart of Codon’s approach is the state-of-the-art BioFAB™ design and production platform. The BioFAB platform combines advanced informatics with proprietary algorithms, sophisticated high-capacity automation, and an arsenal of chemical and biochemical protocols that collectively represent the most advanced genetic construction platform in the world. Furthermore, our sequence verification technology ensures delivery of perfect genetic constructs. “Our BioFAB platform utilizes numerous and overlapping patented and patent-pending technologies related to low-cost oligonucleotide production, world-class fidelity optimization, and efficient assembly.” Using our revolutionary BioFAB™ technology platform, Codon Devices designs and constructs genetic sequences quickly and inexpensively. More cost-effective than classical cloning techniques or gene synthesis services, our Constructed Clones enable you to rapidly utilize genetic information in a whole new way to accelerate your experiments, reduce costs, and explore new avenues of research. With industry-leading capacity, delivery in as few in ten days, and the lowest price available, Codon Devices’ Custom Constructed Clones offer many benefits never before possible including: Lower Cost – Constructed Clones can be more cost-effective than traditional cloning techniques or gene synthesis services. Now you can make broad usage of de novo-synthesized genes to improve your productivity and focus on more value-added activities. Ready-to-Use, with Perfect Specificity – Send us the sequence you require and we will deliver 100% sequence-verified Custom Constructed Clones. (((Flexibility – Short or long constructs; simple or complex sequences; from less than 1kb to more than 10kb; the BioFAB™ enables construction of a wide variety of sequences. GC-rich, repeat and homopolymer-containing sequences can also be reliably synthesized. Constructs containing multiple genes, or even entire pathways, are now possible. Reliable Delivery – With delivery in as few as ten days, you can better plan your experiments. Not sure how long it may take to clone a gene? Worried that you may need to repeat the cloning process several times? Let Codon Devices synthesize the gene for you and have it delivered quickly and reliably. Confidentiality Guaranteed – We treat your sequences with utmost confidentiality and will rapidly execute a Confidentiality Agreement upon your request…. Go Back to Top. Skip To: Start of Article.
News Article | July 13, 2010
Franco Cerrina, a Boston University engineering professor, was found dead in a lab at BU’s Photonics Center on Monday morning, the university reported yesterday. He was 62. Colin Riley, a BU spokesman, said in an e-mail this morning that the cause of death is not yet known. Police are not treating Cerrina’s death as a criminal matter, according to BU. Cerrina joined the faculty of BU in 2008 after spending 24 years on the faculty at the University of Wisconsin-Madison. He co-founded five companies, including NimbleGen Systems, Genetic Assemblies (merged with Codon Devices in 2006), Codon Devices, Biolitho, and Gen9, according to Nanowerk News. NimbleGen, a Madison, WI-based provider of DNA microarray technology, was sold to Basel, Switzerland-based Roche in 2007 for $272.5 million.
PubMed | Codon Devices
Type: Journal Article | Journal: Chemistry & biology | Year: 2010
Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.