Synthetic biology in the context of Control engineering

Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.

Synthesis of the first complete gene, a yeast tRNA, was demonstrated by Har Gobind Khorana and coworkers in 1972. Synthesis of the first peptide- and protein-coding genes was performed in the laboratories of Herbert Boyer and Alexander Markham, respectively. More recently, artificial gene synthesis methods have been developed that will allow the assembly of entire chromosomes and genomes. The first synthetic yeast chromosome was synthesised in 2014, and entire functional bacterial chromosomes have also been synthesised. In addition, artificial gene synthesis could in the future make use of novel nucleobase pairs (unnatural base pairs).

An artificial cell, synthetic cell or minimal cell is an engineered particle that mimics one or many functions of a biological cell. Often, artificial cells are biological or polymeric membranes which enclose biologically active materials. As such, liposomes, polymersomes, nanoparticles, microcapsules and a number of other particles can qualify as artificial cells.

The terms "artificial cell" and "synthetic cell" are used in a variety of different fields and can have different meanings, as it is also reflected in the different sections of this article. Some stricter definitions are based on the assumption that the term "cell" directly relates to biological cells and that these structures therefore have to be alive (or part of a living organism) and, further, that the term "artificial" implies that these structures are artificially built from the bottom-up, i.e. from basic components. As such, in the area of synthetic biology, an artificial cell can be understood as a completely synthetically made cell that can capture energy, maintain ion gradients, contain macromolecules as well as store information and have the ability to replicate. This kind of artificial cell has not yet been made.

Cellular agriculture is the production of agricultural products from cell cultures using a combination of biotechnology, tissue engineering, molecular biology, and synthetic biology to create and design new methods of producing proteins, fats, and tissues that would otherwise come from traditional agriculture. Most of the industry is focused on animal products such as meat, milk, and eggs, produced in cell culture, an alternative to raising and slaughtering farmed livestock which is associated with substantial global problems regarding its environmental impact (e.g. of meat production), animal welfare, food security and human health. Cellular agriculture is a field of the biobased economy. The most well known cellular agriculture concept is cultured meat.

Playing God refers to assuming powers of decision, intervention, or control metaphorically reserved to God. Acts described as playing God may include, for example, deciding who should live or die in a situation where not everyone can be saved, the use and development of biotechnologies such as synthetic biology, and in vitro fertilisation. Usually the expression is used pejoratively and to criticize or argue against the supposedly God-like actions.

The concept of biological computation proposes that living organisms perform computations, and that as such, abstract ideas of information and computation may be key to understanding biology. As a field, biological computation can include the study of the systems biology computations performed by biota, the design of algorithms inspired by the computational methods of bio-data, the design and engineering of manufactured computational devices using synthetic biology and computer methods for biological data, Computational Biology. This extenuates DNA Computation, Evolutionary Computation, Autonomic Computation, Morphological Computation, Morphogenetic Computation, Amorphous Computation, and Hyperdimensional Computation.

According to Dominique Chu, Mikhail Prokopenko, and J. Christian J. Ray, "the most important class of natural computers can be found in biological systems that perform computation on multiple levels. From molecular and cellular information processing networks to ecologies, economies and brains, life computes. Despite ubiquitous agreement on this fact going back as far as von Neumann automata and McCulloch–Pitts neural nets, we so far lack principles to understand rigorously how computation is done in living, or active, matter".

In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain (namely DNA or RNA). Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (with regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. Endonucleases differ from exonucleases, which cleave the ends of recognition sequences instead of the middle (endo) portion. Some enzymes known as "exo-endonucleases", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like. Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity.

Restriction enzymes are endonucleases from eubacteria and archaea that recognize a specific DNA sequence. The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site. Typically, a restriction site will be a palindromic sequence about four to six nucleotides long. Most restriction endonucleases cleave the DNA strand unevenly, leaving complementary single-stranded ends. These ends can reconnect through hybridization and are termed "sticky ends". Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. The DNA fragments cleaved by the same endonuclease can be joined regardless of the origin of the DNA. Such DNA is called recombinant DNA; DNA formed by the joining of genes into new combinations. Restriction endonucleases (restriction enzymes) are divided into three categories, Type I, Type II, and Type III, according to their mechanism of action. These enzymes are often used in genetic engineering to make recombinant DNA for introduction into bacterial, plant, or animal cells, as well as in synthetic biology. One of the more famous endonucleases is Cas9.

A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering various sub-cellular structures like the nucleus. They are used to study the fundamental properties of biological membranes in a simplified and well-controlled environment, and increasingly in bottom-up synthetic biology for the construction of artificial cells. A model bilayer can be made with either synthetic or natural lipids. The simplest model systems contain only a single pure synthetic lipid. More physiologically relevant model bilayers can be made with mixtures of several synthetic or natural lipids.

There are many different types of model bilayers, each having experimental advantages and disadvantages. The first system developed was the black lipid membrane or "painted" bilayer, which allows simple electrical characterization of bilayers but is short-lived and can be difficult to work with. Supported bilayers are anchored to a solid substrate, increasing stability and allowing the use of characterization tools not possible in bulk solution. These advantages come at the cost of unwanted substrate interactions which can denature membrane proteins.