Cellular “Computers” Gain a Hard Drive

DNA-based memory can record multiple inputs from engineered gene circuits

In previous synthetic-biology attempts, data storage has been laborious to create. Credit: Thinkstock

A new DNA-based recorder allows bioengineers to create cell cultures that detect information in their environment and store it for later use. Such 'designer' cells might in the future be used to monitor water quality in a village, or measure the amount of sugar a person eats. The technique is described this week inScience.

Insynthetic biology, genes are engineered to regulate each other's expression in such a way that they can perform logic operations similar to those in computer circuits. Memory storage has long been considered one of the key components needed to fulfil the promise of this technology.

Building gene circuits requires not only computation and logic, but a way to store that information, says bioengineer Timothy Lu of the Massachusetts Institute of Technology in Cambridge. DNA provides a very stable form of memory and will allow us to do more complex computing tasks.

In previous synthetic-biology attempts, data storage has been laborious to create. It also recorded only the presence or absence of one particular sensory input, and could be used only for limited applications. In the latest paper, Lu and his colleague Fahim Farzadfard describe how they can record many types of data simultaneously, and can register the accumulation of the input over time, like a cars odometer counts kilometers. The stored information can then be read out by sequencing the DNA. They dub their method SCRIBE, for Synthetic Cellular Recorders Integrating Biological Events.

Its a nice addition to the toolbox, which could complement other memory-storage techniques, says Jrme Bonnet, a bioengineer at the Centre for Structural Biochemistry in Montpellier, France, who was not involved in the research. Theres room for different types of memory in synthetic biology as in computing you have the hard drive and the RAM.

Living memory The team's work on SCRIBE began three years ago as an attempt to improve gene editing, in which cells are coaxed to incorporate new information into their genomes. One seemingly straightforward approach involves using single-stranded DNA molecules.

Bacterial genomes, like human genomes, are made up of double-stranded DNA molecules. But when single-stranded DNA is floating around in the cell, it is possible to stimulate the bacterium to insert it into its genome, using an enzyme from a virus. However, most bacteria do not readily manufacture a significant number of single-stranded DNAs.

Farzadfard and Lu found a 1984 paper on a soil bacterium that contained hundreds of copies of single-stranded DNA. This DNA was manufactured by a freely floating strucure made of double-stranded DNA, called a retron.

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Cellular "Computers" Gain a Hard Drive