DNA Computer Uses Billions of Molecules in a Tiny Water Droplet to Perform Calculations

Scientists have built a reusable DNA-powered computer that performs calculations using billions—or even trillions—of molecules contained in a tiny water droplet.

Called the Scaffolded DNA Computer (SDC), the system uses the laws of physics and thermodynamics to solve problems. Rather than forcing a fixed sequence of processing steps, it allows DNA molecules to interact and settle into an energetically favorable state that represents the answer.

How the DNA computer works

SDCs are made from short DNA strands that interact with longer DNA scaffolds. Researchers place the strands in a small amount of salted water, then heat and cool the mixture.

As the DNA strands interact, they assemble according to programmed rules. Their arrangement determines which molecules can attach to one another or to different positions on the scaffold. By designing these rules, researchers can program the system to perform specific calculations.

The process resembles a molecular puzzle. Each DNA strand acts like a small puzzle piece, and the way the pieces fit together determines the result.

Thermodynamics turns molecular interactions into computation

The DNA strands compete with one another as they bind to the scaffold. Collisions and binding events allow the molecules to explore different configurations. Eventually, the system settles into an energetically favorable state, and that final structure encodes the answer.

“The clever part is that the binding process is competitive,” study co-author Damien Woods, a professor of computer science at Maynooth University in Ireland, told Live Science. “The DNA molecules compete with each other to choose a winner, and that winner successfully binds to the scaffold.”

Unlike conventional computers, which use energy to carry out a sequence of processing steps, the DNA computer relies on molecules relaxing toward equilibrium. This could eventually enable more energy-efficient forms of biological or molecular computing, although practical applications remain speculative.

What can the Scaffolded DNA Computer calculate?

Researchers tested the SDC on 10 programs involving 100-bit calculations. In one example, the system calculated 10 + 3 in about 30 seconds.

Across the experiment, the researchers demonstrated more than 700 calculations, including:

• Addition
• Multiplication by three
• Division by two
• Eight-bit parity detection, a common type of error correction in computing

Small calculations could be completed in less than a minute. That is slow compared with a silicon computer, which can perform such calculations almost instantly, but it is faster than many earlier DNA-based computers.

More demanding calculations involving numbers from about 11 million to 34 million took as long as 14 hours.

A reusable molecular computer

One important feature of the SDC is that it can be reused. Many earlier molecular computers were designed for one-time experiments, while the SDC can perform calculations repeatedly using the same molecular components.

Three of the programs were successfully rerun up to 24 times. When the researchers repeated the experiment about a year and a half after the original tests, the system had partially dried out. However, adding water allowed the team to run the calculations again.

“Many previous molecular computers relied on specially prepared components or molecular fuels to propel the system forward or drive carefully timed reactions,” study co-author Abir Eshra, an assistant professor of computer science at Maynooth University, told Live Science. “Instead, our DNA computer works by throwing molecules together and letting them relax toward equilibrium.”

Could DNA computers store data or work inside living cells?

The researchers say DNA-based systems could eventually contribute to molecular-scale technologies, energy-efficient computation and DNA data storage. They may also have uses in biological environments or smart materials, although these possibilities have not yet been demonstrated by the SDC.

DNA-based data storage is especially promising because DNA molecules can have built-in natural error correction. However, the researchers said much more work is needed, including designing improved DNA scaffolds, developing better ways to read the results and investigating potential storage applications.

For now, the research primarily demonstrates that thermodynamics can be used to perform useful calculations with interacting molecules. The system is programmable and reusable, but it is not intended to replace conventional electronic computers.