Genome engineering

A self-replicating programmable constructor in a kinematic simulation environment

Cellular automata can model the information processing aspects of a self-replicating programmable constructing system (SRPC), but these models do not contain any notion of material parts and are poor at modelling features of a system that depend upon the motion and connectivity of its components. Physical systems with thousands of parts have the disadvantage that they are time consuming to develop. To overcome these limitations, a simulation environment is presented at a level of abstraction that models motion and connectivity. An SRPC which takes a disorganised collection of parts as its input has been implemented in this environment.

Hierarchical gene synthesis using DNA microchip oligonucleotides

High-cost of oligonucleotides is one of the major problems to low-cost gene synthesis. Although DNA oligonucleotides from cleavable DNA microchips has been adopted for the low-cost gene synthesis, construction of DNA molecules larger than 1 kb has been largely hampered due to the difficulties of DNA assembly associated with the negligible quantity of chip oligonucleotides. Here we report a hierarchical method for the synthesis of large genes using oligonucleotides from programmable DNA microchips. Using this hierarchical method, we successfully synthesized 1056 bp Dpo4 and 2325 bp Pfu DNA polymerase genes as models. This hierarchical strategy can be further expanded for the syntheses of multiple large genes in a scalable manner.

Synthetic physiology strategies for adapting tools from nature for genetically targeted control of fast biological processes

The life and operation of cells involve many physiological processes that take place over fast timescales of milliseconds to minutes. Genetically encoded technologies for driving or suppressing specific fast physiological processes in intact cells, perhaps embedded within intact tissues in living organisms, are critical for the ability to understand how these physiological processes contribute to emergent cellular and organismal functions and behaviors. Such "synthetic physiology" tools are often incredibly complex molecular machines, in part because they must operate at high speeds, without causing side effects. We here explore how synthetic physiology molecules can be identified and deployed in cells, and how the physiology of these molecules in cellular contexts can be assessed and optimized. For concreteness, we discuss these methods in the context of the "optogenetic" light-gated ion channels and pumps that we have developed over the past few years as synthetic physiology tools and widely disseminated for use in neuroscience for probing the role of specific brain cell types in neural computations, behaviors, and pathologies. We anticipate that some of the insights revealed here may be of general value for the field of synthetic physiology, as they raise issues that will be of importance for the development and use of high-performance, high-speed, side-effect free physiological control tools in heterologous expression systems.

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

The construction of synthetic biological systems involving millions of nucleotides is limited by the lack of high-quality synthetic DNA. Consequently, the field requires advances in the accuracy and scale of chemical DNA synthesis and in the processing of longer DNA assembled from short fragments. Here we describe a highly parallel and miniaturized method, called megacloning, for obtaining high-quality DNA by using next-generation sequencing (NGS) technology as a preparative tool. We demonstrate our method by processing both chemically synthesized and microarray-derived DNA oligonucleotides with a robotic system for imaging and picking beads directly off of a high-throughput pyrosequencing platform. The method can reduce error rates by a factor of 500 compared to the starting oligonucleotide pool generated by microarray. We use DNA obtained by megacloning to assemble synthetic genes. In principle, millions of DNA fragments can be sequenced, characterized and sorted in a single megacloner run, enabling constructive biology up to the megabase scale.

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

Development of cheap, high-throughput, and reliable gene synthesis methods will broadly stimulate progress in biology and biotechnology1. Currently, the reliance on column-synthesized oligonucleotides as a source of DNA limits further cost reductions in gene synthesis2. Oligonucleotides from DNA microchips can reduce costs by at least an order of magnitude3,4,5, yet efforts to scale their use have been largely unsuccessful due to the high error rates and complexity of the oligonucleotide mixtures. Here we use high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols, and enzymatic error correction to develop a highly parallel gene synthesis platform. We tested our platform by assembling 47 genes, including 42 challenging therapeutic antibody sequences, encoding a total of ~35 kilo-basepairs of DNA. These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding ~2.5 megabases of DNA, which is at least 50 times larger than previously published attempts.

Synthetic toxicology: where engineering meets biology and toxicology

This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production.

Synthetic genomes for synthetic biology

A genome synthesized entirely from scratch has been used to replace the native genome of a living cell, thus creating a new cell. This achievement marks a new frontier in synthetic biology to design and create genomes for organisms with few genetic tools and for applications in areas of energy, health care and the environment.

Classifying DNA assembly protocols for devising cellular architectures

DNA assembly is one of the most fundamental techniques in synthetic biology. Efficient methods can turn traditional DNA cloning into time-saving and higher efficiency practice, which is a foundation to accomplish the dreams of synthetic biologists for devising cellular architectures, reprogramming cellular behaviors, or creating synthetic cells. In this review, typical strategies of DNA assembly are discussed with special emphasis on the assembly of long and multiple DNA fragments into intact plasmids or assembled compositions. Constructively, all reported strategies were categorized into in vivo and in vitro types, and protocols are presented in a functional and practice-oriented way in order to portray the general nature of DNA assembly applications. Significantly, a five-step blueprint is proposed for devising cell architectures that produce valuable chemicals.

Update on designing and building minimal cells

Minimal cells comprise only the genes and biomolecular machinery necessary for basic life. Synthesizing minimal and minimized cells will improve understanding of core biology, enhance development of biotechnology strains of bacteria, and enable evolutionary optimization of natural and unnatural biopolymers. Design and construction of minimal cells is proceeding in two different directions: 'top-down' reduction of bacterial genomes in vivo and 'bottom-up' integration of DNA/RNA/protein/membrane syntheses in vitro. Major progress in the past 5 years has occurred in synthetic genomics, minimization of the Escherichia coli genome, sequencing of minimal bacterial endosymbionts, identification of essential genes, and integration of biochemical systems.

Personal genomes in progress: from the human genome project to the personal genome project

The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007- even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polymorphisms, this has caused a significant rise in interest in correlating genome sequences with comprehensive environmental and trait data (GET). The cost of electronic health records, imaging, and microbial, immunological, and behavioral data are also dropping quickly. Sharing such integrated GET datasets and their interpretations with a diversity of researchers and research subjects highlights the need for informed-consent models capable of addressing novel privacy and other issues, as well as for flexible data-sharing resources that make materials and data available with minimum restrictions on use. This article examines the Personal Genome Project's effort to develop a GET database as a public genomics resource broadly accessible to both researchers and research participants, while pursuing the highest standards in research ethics.

Integration of stable extracellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method

The stable cloning of giant DNA is a necessary process in the production of recombinant/synthetic genomes. Handling DNA molecules in test tubes becomes increasingly difficult as their size increases, particularly above 100 kb. The need to prepare such large DNA molecules in a regular manner has limited giant DNA cloning to certain laboratories. Recently, we found stable plasmid DNA of up to 100 kb in Escherichia coli culture medium during the infection and propagation of lambda phage. The extracellular plasmid DNA (excpDNA) released from lysed E. coli was demonstrably stable enough to be taken up by competent Bacillus subtilis also present in the medium. ExcpDNA transfer, induced by simply mixing E. coli lysate with recipient B. subtilis, required no biochemical purification of the DNA. Here, this simple protocol was used to integrate excpDNA into a B. subtilis genome, designated the ‘BGM vector’. A slightly modified protocol for DNA cloning in BGM is presented for DNA fragments >100 kb. This technique should facilitate giant DNA cloning in the BGM vector and allow its application to other hosts that can undergo natural transformation.

Next-generation synthetic gene networks

Synthetic biology is focused on the rational construction of biological systems based on engineering principles. During the field's first decade of development, significant progress has been made in designing biological parts and assembling them into genetic circuits to achieve basic functionalities. These circuits have been used to construct proof-of-principle systems with promising results in industrial and medical applications. However, advances in synthetic biology have been limited by a lack of interoperable parts, techniques for dynamically probing biological systems and frameworks for the reliable construction and operation of complex, higher-order networks. As these challenges are addressed, synthetic biologists will be able to construct useful next-generation synthetic gene networks with real-world applications in medicine, biotechnology, bioremediation and bioenergy.