Japanese scientists are applying logic to the protein that causes jellyfish to fluoresce green.

Takahiko Nojima, and colleagues at the University of Tokyo, have created a system that uses protein synthesis to report on the success of four different biochemical logic gates. Analogous to computer logic gates, biochemical logic gates are used to direct simple biological functions.  

The system consists of two parts: a logic gate that amplifies the DNA that codes for the protein and a report gate where the protein is expressed. In the first part a polymerase enzyme amplifies the DNA of interest - the template DNA - in a process called the polymerase chain reaction (PCR). Two pieces of complementary DNA called primers are required to start the PCR, and these act as the input signals for the gate. The amplified DNA contains not only a code for the protein but also sequences that recognise the 'machinery' in the report gate. As this enters the report gate the protein is expressed and the output measured by the green fluorescence coming from the protein.

The team successfully designed and constructed different primers and templates so that AND, OR, NOT and AND-NOT operations could be executed, with all four gates reporting successfully and fluorescing as expected.

Many DNA-based logic systems suffer from false positive signals, says Nojima. In our system, by adding the protein expression step, this possibility is cut off, he explains. This is because only a completely correct piece of DNA will express the protein, giving a fluorescent output. Nojima says he believes this definite on/off fluorescent signal is the most exciting aspect of his work.

A P de Silva, an expert in molecular logic at Queen's University, Belfast, UK, says that this work is valuable because it brings the important technique of PCR into the fold of biological versions of molecular logic.

Nojima says his group is now aiming 'to install the PCR-based logic gate into a microfluidic device.'

Frances Galvin