Computers with DNA? Brock team working to help make it happen

A Brock University research team has created a tool that can potentially be used in a future computer that will be made out of DNA.

Chemist Feng Li and graduate student Xiaolong Yang, formal postdoctoral fellow Yanan Tang and undergraduate student Sarah Traynor have devised a strategy that “helps simplify the design of DNA circuits that may eventually be used in a DNA computer,” says Li.

The team’s research was recently featured in the Journal of the American Chemical Society.

Scientists are researching ways of using DNA to replace chips, electrical circuits and other materials found within a computer.

“Because we’re at baby steps now, it’s not something like what we know as a computer yet,” says Li. “What we have now, if you can imagine, is something more like a calculator where you can use DNA to solve mathematical questions.”

DNA computers can also be used to store information.

“Living creatures use DNA to store basic genetic information, so in principle, you can save anything into DNA,” he says. “For example, there are researchers who coded an entire book into DNA sequences. It’s different from hardware; you only need a tiny amount of DNA to store an entire book.”

DNA, or deoxyribonucleic acid, is a molecule that contains information from genes that regulates all living organisms’ growth, development, functions and reproduction.

When someone types on the keyboard of a conventional computer, the machine generates binary codes, which consist of a series of 0s and 1s that represent each letter, symbol and anything else is entered into a computer. For example, ‘01100001’ represents the letter ‘a.’

The codes, in turn, translate what is entered into the computer into the form of text, graphics or other things we see on the computer screen. Binary codes are used in various methods of encoding data in computing and telecommunications. They are currently produced and transmitted by silicon-based technologies.

Scientists discovered that DNA is able to generate binary codes just like computers do. And it does not require electricity or materials such as silicon, aluminum and cobalt to do so.

“Chemicals generate their own energy,” explains Li. “DNA mimics the electrical currents in the current computer.

“There are many people who are interested in developing DNA for use in information technology,” says Li. “The big idea is to use DNA as a computing component to construct a molecular computer. It’s not the electricity-based computer we use now, but rather the fundamental units are molecules of DNA.”

What we ‘input’ into a DNA computer are not letters typed on a keyboard but strands of DNA that have been altered to produce a certain result.

Inside the computer are more DNA strands, which ‘read’ and interpret the incoming DNA.

“The physical structures of the DNA molecules are re-arranged; these new structures will give you a series of 0s and 1s,” says Li.

And that’s where Li and his team’s research comes in.

The team developed a method — called the ‘allosteric DNA toehold (A-toehold) strategy’ — in which DNA molecules can be manipulated using the principle of allostery, which has been used widely for regulating enzyme activities by nature.

This is done within the context of a process called “toehold exchange,” in which an input DNA strand binds to a sticky end, or ‘toehold,’ on another DNA molecule.

Li explains that the toehold exchange method streamlines the design of DNA circuits.

“If you want to use DNA to replace a computer, you also need to somehow manipulate those DNA strands the way you want,” explains Li. “You need rules to manipulate those DNA.

“There are existing rules you can use to manipulate DNA, but what we’re trying to do is to simplify this process by providing alternative rules. If you simplify the design, you save DNA molecules, you save money.”

How the output of the DNA computer — a screen displaying text, graphics and video in our current conventional computers — will be displayed for the average user is still unknown in the long run, says Li.

Li and his team’s research, “Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold,” was published recently in the Journal of the American Chemical Society.

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