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Scientists Turn DNA into Hard Drives

05/21/2012
Jesse Jenkins

To record biological events in living cells, synthetic biologist Drew Endy and his team have created the first rewriteable DNA-based memory module.

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When we talk about data storage, it’s usually in terms of bits, hard drives, and servers. But recently researchers have been looking into a new storage device: DNA. The idea is that DNA could record cellular events that trigger aging, cancer, and other developmental processes. So far, however, scientists have only created limited single-write technology.

The RAD module, driven by set-and-reset input signals, modifies a part of DNA within microbes that determines how the one-celled organisms will fluoresce under ultraviolet light. The microbes glow red or green depending upon the orientation of the section of DNA. Source: PNAS





But now researchers from Stanford University have now engineered the first rewriteable DNA-based memory module called the recombinase addressable data (RAD) module, which provides up to one bit of data storage within living cells. The module has the capability to write, erase, and rewrite data to record repetitive events like cell division. In contrast, previous single-write DNA-based data storage systems can only address linear data.

“Think of a CD that you can only write onto once… you fill up space really quickly,” said study author Jerome Bonnet, a post-doc in Drew Endy’s Stanford lab. “But we came up with a way where we can write and rewrite as many times as we want, and we haven’t seen any change in performance.”

To create the module, Bonnet and his co-authors needed to reliably flip a DNA sequence’s genetic orientation between two states repeatedly. In one state, the sequence would express a green fluorescent protein; in the other, a red fluorescent protein. To switch between the two states, the team relied on the synthesis of two proteins: integrase and excisionase. In their system, integrase would invert the DNA sequence; the presence of both proteins would reset the modules to its original orientation.

But these two proteins are highly volatile when placed within the same cell, so many of the initial designs failed. “This kind of stoichiometry inside a living cell is very tricky,” said co-author Pakpoom Subsoontorn, a graduate student at Stanford. “We needed to have precise control over how much we had of each protein to get to the correct state.”

After three years of optimizing the design, the team found the right balance of those two proteins. In a paper published in the Proceedings of the National Academy of Sciences (1), the team described their RAD memory element, which is capable of passive information storage in the absence of heterologous gene expression for more than 100 cell divisions.

Now, while the team is exploring other enzymes to improve the efficiency of their method, their next big target is increase the storage capability of the module to 8 bits, or 1 byte.

“If you want to use this kind of memory to keep track of the events inside a living cell for a study in aging for example, the scale or number of the events that you are tracking is normally 50-200 events. We would need about 8 bits of data storage to record that,” said Subsoontorn.

References

  1. Bonnet J., P. Subsoontorn, and D. Endy. 2012. Rewritable digital data storage in live cells via engineered control of recombination directionality. PNAS [published online May 21, 2012]

Keywords:  synthetic biology