Artificial gene synthesis, or 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.
Gene synthesis has multiple advantages including, it is used generate mutated, recombinant and completely novel DNA sequences without use of template. A wide variety of types of sequences can be produced which aid in research applications. Moreover,along with DNA sequences, RNA& oligos containing modified bases, chimeric DNA-RNA backbones can also be synthesized. In the era of gene synthesis, 2003 was the milestone as, thefirst synthesis of an entire viral genome, that of phiX174 bacteriophage is successfully completed.
Synthesizing DNA is a growing business as companies order custom-made genes so they can produce biologic drugs, industrial enzymes or useful chemicals in vats of microbes. Researchers purchase synthetic genes to insert into plants or animals or try out new CRISPR-based disease therapies.
Some scientists have even proposed storing information in DNA, much like digital data is stored today in computer hard drives, since a gram of DNA could theoretically store the equivalent of 50 million DVDs and should be stable for centuries. However, that would mean synthesizing immensely larger quantities of DNA strands than those used in the biotech industry today.
All of these applications require that the synthesis process faithfully produces the desired sequence of nucleotides or bases – the building blocks of DNA – in each of millions or even billions of copies of DNA molecules.
Artificial gene synthesis
Gene synthesis also refers as the artificial gene synthesis. Gene synthesis is described as the group of methods involves into the synthetic biology to construct and assemble gene from nucleotides.
Unlike DNA synthesis in living cells, gene synthesis does not require template DNA. Gene synthesis involves two key steps, among them, the first step is solid phase DNA synthesis also known as ‘DNA printing’ that produces oligonucleotide fragments which 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.
The next step then involves connecting oligonucleotide fragments using multiple DNA assembly methods. Since gene synthesis does not need template DNA, this make possible to synthesis a completely synthetic DNA molecules with no limits on the nucleotide sequence or size.
The first efforts to write DNA began in the 1980s using a phosphoramidite chemistry process, which is still the industry mainstay. This DNA synthesis technology was a tremendous breakthrough, giving scientists incredible opportunities to create genetic probes, study cell behavior and develop new generations of diagnostics, vaccines and therapies.
However, in the process of overcoming one barrier, phosphoramidite chemistry created others. The process must take place under tight environmental control, relies on toxic reagents and solvents and generates large amounts of hazardous waste.
If a research lab or core facility wants to bring DNA synthesis in-house, they must wrestle with lab environmental conditions; bringing in highly trained, dedicated chemists; safety protocols associated with handling hazardous chemicals; and proper waste disposal. These conditions make it impractical, and too great a burden, for most labs. The result? Limited access to synthetic DNA via third-party oligo services.
Current DNA synthesis, which dates from 1981 and uses techniques from organic chemistry labs, is limited to directly producing so-called oligonucleotides about 200 bases long, because inevitable errors in the process lead to a low yield of correct sequences as the length increases. To assemble even a small gene, scientists have to synthesize it piecemeal, in segments about 200 bases long, and then stitch them together. This is time consuming, often requires multiple attempts and sometimes fails completely.
In addition, when ordered from synthesis companies like Twist Biosciences Inc. and Integrated DNA Technologies (IDT), the turnaround time for one small gene around 1,500 bases long can be two weeks at a cost of $300, limiting the number of genetic tweaks researchers can afford to try and the speed with which they can experiment.
These delays add up, prolonging early-stage diagnostic or therapeutic development by weeks or months. In-house DNA printing resources are the best means to remove this bottleneck and provide obvious efficiencies, reducing time lags and potential time-to-market costs.
Enzymatic DNA synthesis (EDS)
In 2018, Scientists at the UC Berkeley and Lawrence Berkeley National Laboratory invented a new way to synthesize DNA that promises to be easier and faster, does not require the use of toxic chemicals and is potentially more accurate. The new technique relies on a DNA-synthesizing enzyme found in cells of the immune system that naturally has the ability to add nucleotides to an existing DNA molecule in water, where DNA is most stable. The technique promises improved precision, which could allow synthesis of DNA strands 10 times longer, or several thousand bases long – the size of a medium-sized gene.
Cell’s do not typically synthesize DNA from scratch; they mostly copy it with the help of a lot of different polymerase enzymes that build on DNA templates already in the cell. In the 1960s, however, scientists found an unusual polymerase that doesn’t rely on an existing DNA template, but randomly adds nucleotides to genes that make antibodies for use in the immune system. Called terminal deoxynucleotidyl transferase (TdT), the enzyme creates random variation in these genes so that the resulting antibody proteins are better able to target never-before-seen invaders.
TdT works equally well adding all four DNA nucleotides, does not have side-reactions that could screw up the resulting molecule, and is very fast, extending DNA by about 200 bases per minute if you let it free-wheel, Sebastian Palluk a doctoral student at the Technische Universität Darmstadt in Germany and a visiting student at Berkeley Lab said. Numerous labs over the years tried to harness this enzyme to synthesize desired DNA sequences, but the enzyme was hard to control.
Arlow’s idea was to securely tether an unblocked nucleotide to TdT, so that after the nucleotide is added to a growing DNA molecule, the enzyme remains attached and itself protects the end of the chain from further additions. After the DNA molecule has been extended, they cut the linking tether to release the enzyme and re-expose the end for the next addition.
Recently, commercialized benchtop synthesizers that incorporate enzymatic DNA synthesis (EDS) technologies, mimicking the same DNA-building processes used in cells, have overcome many of phosphoramidite chemistry’s barriers. There are several companies, with different business models, working on commercializing products using enzymatic synthesis technology.
Based in biology, EDS does not require toxic reagents. With minimal training, even inexperienced lab staff can set up a synthesis run in around 15 minutes to produce custom oligos within a few hours. Enzymatic synthesis produces quality DNA like phosphoramidite chemistry, but uses a simpler process, relying on enzymes that do not produce hazardous organic waste.
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)
DNA Synthesis Market
Gene Synthesis Market is valued at USD 3.14 Billion in 2018 and expected to reach USD 17.5 Billion by 2025 with the CAGR of 27.9% over the forecast period.
Some of the Gene Synthesis Companies are Thermo Genewiz, Eurofins Scientific, Quintara Biosciences, ATD Bio Ltd.,Fisher Scientific, Inc., OriGene Technologies, Inc., Bioneer Corporation, Atum, Integrated DNA Technologies, Inc., BioCat GmbH, GenScript, Eurogentec,
Twist Bioscience, LGC Biosearch Technologies, Eton Bioscience, Inc., Bio Basic Inc., SBS Genetech Co., Ltd., Merck KGaA and others.
French Biotech Raises $200 Million Series C for DNA Printing Platform in Jan 2022. The proceeds will enable DNA Script to advance the first EDS-powered benchtop DNA printer, the SYNTAX Platform, and accelerate the commercialization of the enzymatic DNA-printing platform.
DNA Script’s technology holds a promise to transform research processes across multiple industries where synthetic biology is involved by offering to print longer DNA sequences than before and deliver them within a matter of hours.
The SYNTAX System empowers scientists by allowing rapid, on-site DNA production. It accelerates lab workflows and helps scientists find answers faster as on-demand printing allows labs to iterate without waiting days or weeks to receive genetic material from third-party service providers.