Multifragment DNA Assembly of Biochemical Pathways via Automated Ligase Cycling Reaction.

The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designed and assembled into suitable expression vectors. The design of these pathways is crucial for balancing the pathway for efficient in vivo activity. This can be achieved through optimization of the pathway regulation by altering transcription and translation rates. The possible permutations of a multigene pathway create a vast design space which is intractable to explore using traditional time-consuming and laborious pathway assembly methods. The advent of multifragment DNA assembly technologies has enabled simultaneous, multiplexed pathway construction allowing an increased capability to sample the design space. Furthermore, the implementation of laboratory automation allows error-reduced, high-throughput (HTP) construction of pathways. In this chapter, we present a workflow that combines automated in silico design of DNA parts followed by pathway assembly using the ligase cycling reaction on robotics platforms, to allow multiplexed assembly of plasmid-borne gene pathways with high efficiency. Details and considerations in designing DNA parts for expression bacterial chassis are discussed followed by laboratory protocols for HTP pathway assembly and screening using robotics platforms. This workflow is employed in the SYNBIOCHEM Synthetic Biology Research Center, providing the capability to assemble over 96 plasmids simultaneously, with over 40% of clones from each assembly harboring the correctly assembled plasmids. This workflow is easy to modify for use in other laboratories and will help to accelerate synthetic biology projects with diverse applications.

Optimizing protein stability in vivo.

Identifying mutations that stabilize proteins is challenging because most substitutions are destabilizing. In addition to being of immense practical utility, the ability to evolve protein stability in vivo may indicate how evolution has formed today's protein sequences. Here we describe a genetic selection that directly links the in vivo stability of proteins to antibiotic resistance. It allows the identification of stabilizing mutations within proteins. The large majority of mutants selected for improved antibiotic resistance are stabilized both thermodynamically and kinetically, indicating that similar principles govern stability in vivo and in vitro. The approach requires no prior structural or functional knowledge and allows selection for stability without a need to maintain function. Mutations that enhance thermodynamic stability of the protein Im7 map overwhelmingly to surface residues involved in binding to colicin E7, showing how the evolutionary pressures that drive Im7-E7 complex formation have compromised the stability of the isolated Im7 protein.

Remarkably slow rotation about a single bond between an sp(3)-hybridised carbon atom and an aromatic ring without ortho substituents.

Look, no ortho substituents! A series of polycycles were prepared by using a three-component Joullié-Ugi reaction. The rate of rotation about the bond between a highly hindered bridgehead and a phenyl ring with no ortho substituents was measured, and was highly dependent on the substitution. Rotamer half-lives of up to 21 h at 298 K were observed (see figure). Rotamers resulting from this restricted rotation were isolated for the first time.A series of polycycles was prepared by using a three-component Joullié-Ugi reaction. The rate of rotation about the bond between a highly hindered bridgehead and a phenyl ring with no ortho substituents was measured by using, in general, variable-temperature HPLC. The rate of rotation was highly dependent on substitution and rotamer half-lives of up to 21 h at 298 K were observed. Insights into the effect of substitution on the rate of rotation were gleaned through electronic structure calculations on closely related derivatives. Rotamers resulting from restricted rotation about a bond between an sp(3)-hybridised carbon atom and a phenyl ring with no ortho substituents were isolated for the first time, and the equilibration of the separated rotamers was followed by using analytical HPLC. It was demonstrated, for the first time, that a highly hindered environment for the sp(3)-hybridised atom is sufficient for slow bond rotation about a single bond between sp(3)- and sp(2)-hybridised carbon atoms.

Synthesis of a library of stereo- and regiochemically diverse aminoglycoside derivatives.

A library of forty modified aminoglycosides was prepared in which the configuration and regiochemistry of two or three rings was widely varied. The library was based around three core ring systems: the 2-deoxystreptamine ring system found in the natural products, and both enantiomers of (1R*,2R*,4R*,5R*)-2,5-diamino-cyclohexane-1,4-diol and (1R*,3R*,4R*,6R*)-4,6-diaminocyclohexane-1,3-diol. In each case, the core was modified by glycosylation with one or two sugar rings. The absolute configuration of the sugar substituents (d or l), the configuration of the anomeric centres (alpha or beta), and the regiochemical arrangement of the amine(s) were varied.