Novel Process for Synthesizing DNA could lead to better Gene Therapies

Postdoc Jinsen Chen, left, and chemistry professor Shiyue Fang in the lab where Fang’s group discovered a new way to synthesize DNA. Credit: Michigan Tech

Michigan Technological University scientists have developed a process that could lead to stickier and better gene therapy drugs. The drugs, called antisense DNA, are made from short, single strands of synthetic DNA. They work by blocking cells from making harmful proteins, which can cause maladies ranging from cancer to Ebola to HIV-AIDS. Only a couple of these synthetic DNA drugs are on the market, but a number are in clinical trials, including a potential treatment for ALS.

Disease organisms can inject harmful proteins into our bodies, and so can mutations in our own genetic material. Essentially, when all goes well, mRNA molecules produce the good proteins essential to life. But when mutations occur, messenger RNA can go rogue and start making proteins that make us sick.

By use of 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) as a protecting group and linker for oligodeoxynucleotide (ODN) synthesis, deprotection and cleavage are achieved under non-nucleophilic oxidative conditions. The nucleophile-sensitive thioester and α-chloroacetyl groups are conveniently incorporated into ODN sequences. The technology could be universally useful for electrophilic ODN synthesis.

Drugs made from synthetic DNA are tailored to grab onto these mutant messenger RNA molecules, binding to them and preventing them from churning out toxic proteins. However synthetic DNA sometimes it loosens its grip, setting the messenger RNA free to resume its dirty work. Scientists know how to make synthetic DNA stickier. One way is to tack on some functional groups of atoms with a partial positive charge, called electrophiles. The electrophiles react with nucleophiles – groups in the RNA with a partial negative charge. This forms a powerful covalent bond, locking the RNA up for good.

Unfortunately, the conventional process for making synthetic DNA involves a final bath in ammonia which washes away the chemical groups used to assemble synthetic DNA, called linkers and protecting groups – and also neutralizes electrophiles. And other processes are expensive, unreliable and can involve toxic materials. But now in synthesizing DNA, Fang’s group uses different chemicals to make linkers and protecting groups. These chemicals wash away easily in a relatively harmless solution that doesn’t destroy electrophiles.

The new process has other advantages: it’s cheap and safe. Plus, it gives a new tool to microbiologists and biochemists, who could use the technique to develop synthetic DNA with a whole array of new properties. http://www.mtu.edu/news/stories/2016/august/sticking-rogue-rna.html