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DNA synthesis

DNA synthesis

The process of linking together nucleotide bases adenine (A), thymine (T), cytosine (C) and guanine (G) to form a DNA molecule. DNA synthesis occurs in the cell during DNA replication. Synthetic DNA synthesis, also called gene synthesis, is the chemical synthesis of single stranded DNA oligonucleotides which are assembled into DNA.

Engineering of biological systems has increased the demand for custom synthetic DNA sequences especially in cases where there is no available organism from which to obtain DNA, but sequence data is available. Unlike the cost of sequencing DNA which has dropped majorly over time, the cost of gene synthesis which is tied to the cost of oligonucleotide synthesis had not decreased appreciably as of 2017.

Synthetic oligonucleotides, also called oligos, are synthesized using phosphoramidite chemistry methods on either traditional column-based synthesizer or microarray-based synthesizers. Individual phosphoramidite monomers of A, G, C and T are combined to form oligonucleotides of 60-100 nucleotide (nt) length. These single-stranded oligonucleotides are assembled into double-stranded DNA called synthons of 200-2000 base pairs (bp) in length. Once sequences are verified, synthons are assembled together to form larger synthetic DNA constructs.

Oligonucleotides, DNA and RNA are also synthesized for use as PCR primers and as hybridization probes. Making use of the complementary base pairing, which makes each of the two strands of DNA stick together, hybridization probes can be used to stick to, label or extract out DNA or RNA of interest.

DNA and oligonucleotide synthesis companies

Agilent Technologies and Twist Bioscience Corp. both use phosphoramidite chemistry and inkjet-based processes. Agilent uses a process called SurePrint to make arrays of 244 thousand DNA oligos with lengths of up to 230 nt on glass slides. Twist synthesizes DNA oligo arrays on silicon chips with 10 thousand microwells and they can be subsequently assembled into genes.

GenScript acquired CustomArray, Inc in 2017. CustomArray uses electrochemical detritylation and chips with thousands of electrodes to synthesize arrays of 90 thousand oligos of 200 nt length.

Roche NimbleGen Inc. uses a photolithographic process to process an array using a method developed at University of Wisconsin called the Maskless Array Synthesis (MAS). LC Sciences, LLC also uses a photolithographic process but they use a digital micromirror device to control spots on the array that are exposed to light.

Evonetix Ltd spun out of Cambridge Consultants uses an array chip with micro-heaters on each spot and wax-like material is added to protect spots where the micro-heater is not activated.

Synthomics, Inc. have a parallel oligo synthesizer called a “Green Machine” which uses fluidic processes. SGI-DNA uses fluidics automation to synthesize genes by a method called Gibson assembly. Other DNA synthesis companies using fluidic processes are The Genome Foundry Ltd, MacConnel Research Corporation and Kilobaser (Briefcase Biotec GmbH). Kilobaser is developing a tabletop DNA synthesizer for making primers or short DNA oligos.

As opposed to chemical synthesis, enzymatic synthesis of DNA uses enzymes, like in the natural synthesis of DNA inside cells. Companies using enzymatic synthesis are DNA Script, Molecular Assemblies Inc., Nuclera Nucleics Ltd. and Ansa Biotechnologies, Inc.

Companies that use column based phosphoramidite synthesis include IDT, GenScript USA, Inc., Thermo Fisher Scientific Inc., Blue Heron, Eurofins Genomics and ATUM (previously DNA2.0).

Other DNA synthesis companies include Base6 Bio, LabGenius, Iridia, Inc. (formerly Dodo Omnidata, Inc.)

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