Synthetic genomics

Overview

Synthetic genomics is unlike genetic modification in the sense that it does not use naturally occurring genes in its life forms. It may make use of custom designed base pair series, though in a more expanded and presently unrealized sense synthetic genomics could utilize genetic codes that are not composed of the two base pairs of DNA that are currently used by life.

The development of synthetic genomics is related to certain recent technical abilities and technologies in the field of genetics. The ability to construct long base pair chains cheaply and accurately on a large scale has allowed researchers to perform experiments on genomes that do not exist in nature. Coupled with the developments in protein folding models and decreasing computational costs the field of synthetic genomics is beginning to enter a productive stage of vitality.

Recombinant DNA technology

Soon after the discovery of restriction endonucleases and ligases, the field of genetics began using these molecular tools to assemble artificial sequences from smaller fragments of synthetic or naturally occurring DNA. The advantage in using the recombinatory approach as opposed to continual DNA synthesis stems from the inverse relationship that exists between synthetic DNA length and percent purity of that synthetic length. In other words, as you synthesize longer sequences, the number of error-containing clones increases due to the inherent error rates of current technologies. Although recombinant DNA technology is more commonly used in the construction of fusion proteins and plasmids, several techniques with larger capacities have emerged, allowing for the construction of entire genomes.

Polymerase cycling assembly

Gibson assembly method

A T5 exonuclease performs a chew-back reaction at the terminal segments, working in the 5' to 3' direction, thereby producing complementary overhangs. The overhangs hybridize to each other, a Phusion DNA polymerase fills in any missing nucleotides and the nicks are sealed with a ligase. However, the genomes capable of being synthesized using this method alone is limited because as DNA cassettes increase in length, they require propagation in vitro in order to continue hybridizing; accordingly, Gibson assembly is often used in conjunction with transformation-associated recombination (see below) to synthesize genomes several hundred kilobases in size.

Transformation-associated recombination

Full genomes and viable organisms

Researchers were able to create a synthetic organism for the first time in 2010. This breakthrough was undertaken by Synthetic Genomics, Inc., which continues to specialize in the research and commercialization of custom designed genomes. This "Mycoplasma laboratorium" (Synthia) project consists of a 600 kbp genome (resembling that of Mycoplasma mycoides, save the insertion of a few watermarks) via the Gibson Assembly method and Transformation Associated Recombination. It was inserted into a DNA-free shell of Mycoplasma capricolum to produce a living, dividing bacterium. This line has since been further minimized and improved.

In May 2019, a full E. coli genome modified to only use 61 out of 64 possible codons called Syn61 was synthesized. It was assembled by bacterial conjugation resulting in a lineage of living, dividing bacteria.

In April 2019, scientists at ETH Zurich modified a Caulobacter crescentus genome using computer algorithms to map out the entire genome's structure optimising it for stability, function, and ease of synthesis. They call the result "Caulobacter ethensis 2.0", but although full DNA genomic molecules were produced, they did not succeed in creating a living, dividing bacterial cell containing this genome. If they end up succeeding in creating a viable version in the future, it would prove to be a major step in customizing the genomes of microorganisms in fields such as medicine, energy and environmental science. A 2021 paper analyzes the differences in gene transcription between the natural genome and the synthetic version, suggesting ways to make a synthetic genome work. Many supposedly neutral mutations introduced by the computer turned out to change previously unknown regulatory systems.

In 2025, researchers reported that they had created a new "Syn57" strain of E. coli, which removes the use of 7 out of 64 codons completely.

Unnatural base pair (UBP)

Main article: Base pair#Unnatural base pair (UBP)

An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. In 2012, a group of American scientists led by Floyd E. Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed, and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into E. coli bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.

The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.

References

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