Scientists create biological nanocomputer

A group of scientists at the Weizmann Institute of Science have used biological molecules to create a tiny computer – a programmable two-state, two-symbol finite automaton – in a test tube.

A group of scientists headed by Professor Ehud Shapiro at the Weizmann Institute of Science has used biological molecules to create a tiny computer – a programmable two-state, two-symbol finite automaton – in a test tube.

This biological nanocomputer is said to be so small that a trillion such computers co-exist and compute in parallel, in an area the size of 1/10 of a millilitre of watery solution held at room temperature.

Collectively, the computers are said to perform a billion operations per second with greater than 99.8% accuracy per operation while requiring less than a billionth of a Watt of power.

The computer’s input, output, and ‘software’ are made up of DNA molecules. For ‘hardware,’ the computer uses two naturally occurring enzymes that manipulate DNA. When mixed together in solution, the software and hardware molecules operate together on the input molecule to create the output molecule, forming a simple mathematical computing machine, known as finite automaton.

This nanocomputer can reportedly be programmed to perform simple tasks by choosing different software molecules to be mixed in solution. It can detect whether, in an input molecule encoding a list made of binary code, all the 0’s precede all the 1’s.

‘The living cell contains incredible molecular machines that manipulate information-encoding molecules such as DNA and RNA in ways that are fundamentally very similar to computation,’ said Professor Shapiro. ‘Since we don’t know how to effectively modify these machines or create new ones just yet, the trick is to find naturally existing machines that, when combined, can be steered to actually compute.’

Shapiro challenged his Ph.D. Student, Yaakov Benenson to find a molecular realisation of one of the simplest mathematical computing machines – a finite automaton that detects whether a list of 0’s and 1’s has an even number of 1’s.

Benenson came up with a solution using DNA molecules and two naturally occurring DNA-manipulating enzymes: Fok-I and Ligase. Operating like a biological editing kit, Fok-I functions as a chemical scissors, cleaving DNA in a specific pattern, whereas the Ligase enzyme seals DNA molecules together.

Shapiro and his team found that the automaton they built could be programmed to perform different tasks by selecting different subsets of the molecules realising the eight possible rules of operation controlling the performance of a two-state, two-symbol finite automaton.

The software molecules, together with two ‘output display’ molecules used to visualise the final result of the computation can be used to create a total of 735 programs.

The nanocomputer is currently too simple to have immediate applications, although it may pave the way to future computers that can operate within the human body with unique biological and pharmaceutical applications.

‘For instance, such a future computer could sense an abnormal biochemical change in the body and decide how to correct it by synthesising and releasing the necessary drug,’ said Professor Zvi Livneh, a DNA expert from the Institute’s Department of Biological Chemistry who collaborated on the project.