A conventional affinity protein purification system often requires a separate protease to separate the target protein from the affinity tag. This paper describes a unique protein purification system in which the target protein is fused to the C-terminus of a modified protein splicing element (intein). A small affinity tag is inserted in a loop region of the endonuclease domain of the intein to allow affinity purification. Specific mutations at the C-terminal splice junction of the intein allow controllable C-terminal peptide bond cleavage. The cleavage is triggered by addition of thiols such as dithiothreitol or free cysteine, resulting in elution of the target protein while the affinity-tagged intein remains immobilized on the affinity column. This system eliminates the need for a separate protease and allows purification of a target protein without the N-terminal methionine. We have constructed general cloning vectors and demonstrated single-column purification of several proteins. In addition, we discuss several factors that may affect the C-terminal peptide bond cleavage activity.

Synthetic biology relies on the manufacture of large and complex DNA constructs from libraries of genetic parts. Golden Gate and other Type IIS restriction enzymedependent DNA assembly methods enable rapid construction of genes and operons through one-pot, multifragment assembly, with the ordering of parts determined by the ligation of Watson−Crick base-paired overhangs. However, ligation of mismatched overhangs leads to erroneous assembly, and low-efficiency Watson Crick pairings can lead to truncated assemblies. Using sets of empirically vetted, highaccuracy junction pairs avoids this issue but limits the number of parts that can be joined in a single reaction. Here, we report the use of comprehensive end-joining ligation fidelity and bias data to predict high accuracy junction sets for Golden Gate assembly. The ligation profile accurately predicted junction fidelity in ten-fragment Golden Gate assembly reactions and enabled accurate and efficient assembly of a lac cassette from up to 24-fragments in a single reaction.

DNA assembly is an integral part of modern synthetic biology, as intricate genetic engineering projects require robust molecular cloning workflows. Golden Gate assembly is a frequently employed DNA assembly methodology that utilizes a Type IIS restriction enzyme and a DNA ligase to generate recombinant DNA constructs from smaller DNA fragments. However, the utility of this methodology has been limited by a lack of resources to guide experimental design. For example, selection of the DNA sequences at fusion sites between fragments is based on broad assembly guidelines or pre-vetted sets of junctions, rather than being customized for a particular application or cloning project. To facilitate the design of robust assembly reactions, we developed a high-throughput DNA sequencing assay to examine reaction outcomes of Golden Gate assembly with T4 DNA ligase and the most commonly used Type IIS restriction enzymes that generate three-base and four-base overhangs. Next, we incorporated these findings into a suite of webtools that design assembly reactions using the experimental data. These webtools can be used to create customized assemblies from a target DNA sequence or a desired number of fragments. Lastly, we demonstrate how using these tools expands the limits of current assembly systems by carrying out one-pot assemblies of up to 35 DNA fragments. Full implementation of the tools developed here enables direct expansion of existing assembly standards for modular cloning systems (e.g. MoClo) as well as the formation of robust new high-fidelity standards.

The biosynthesis of poly(l-alanylglycine) (poly(AG)) was performed in high cell density cultures of recombinant Escherichia coli. The purity of the material was determined by amino acid analysis, elemental analysis, and 1H NMR spectroscopy. Fed batch fermentation increased the yield of recombinant protein from levels of tens of milligrams per liter (typical of batch fermentation in rich media) to hundreds of milligrams per liter. Poly(AG) comprising 64 diads [(AG)64] was recrystallized from dichloroacetic acid solutions in the form of texture-oriented chain-folded lamellae with a lamellar stack periodicity of 3.2 nm. The crystal structure within the lamellar core is similar in general, but different in detail, to the antiparallel β-sheet structure previously reported for oriented films of poly(AG) and fibers of Bombyx mori silk fibroin (silk II). The structure consists of polar antiparallel (ap) β-sheets, with repetitive folding through γ-turns every eighth amino acid (including the fold), stacking with like surfaces together. The wide-angle X-ray diffraction signals index on an orthorhombic unit cell with a (hydrogen bond direction) = 0.948 nm, b (sheet stacking direction) = 0.922 nm, and c (chain direction) = 0.695 nm. The stacking distance (b-value) is increased by about 3% in comparison with the previously reported structure of poly(AG), owing, we believe, to steric interaction at the lamellar fold surfaces. Random shears of approximately ±a/4 and shears of ±c/2 in the ac plane are required to obtain a good fit between the calculated and measured X-ray structure factors.