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Living cells engineered to be computing and recording devices

August 22, 2019

Cells can be viewed as natural minicomputers that execute programs encoded in their DNA. In a paper appearing August 22 in the journal Molecular Cell, MIT researchers describe a new technology that uses DNA for information processing and storage in living cells.

Using a system called DOMINO (DNA-based Ordered Memory and Iteration Network Operator), the technology can execute cascades of DNA writing events - where one DNA mutation event triggers another - in response to biological signals. This technology enables the deep interrogation of biology and the use of engineered cells as living computing and recording devices that can process, monitor, and store information occurring within cells and/or their environment.

"We need better strategies to unravel how complex biology works, especially in diseases like cancer where multiple biological events can occur to transform normal cell into diseased ones," says senior author Timothy Lu, an electrical engineer and computer scientist at MIT and the Broad Institute. "With this method we are using DNA as a memory tape to permanently record biological events that are occur in disease. This technology can give us deeper insights into what signals go up and down over time to drive disease development."

The team's DOMINO technology builds on established genome-editing CRISPR tools. Instead of cutting the DNA at a specific location, DOMINO uses a base editing approach to overwrite DNA at particular locations.

With DOMINO, we can write DNA to change the information encoded into different positions, and then read out this information on the fly, like a read-write head in a computer hard drive" says first author Fahim Farzadfard, a postdoctoral fellow and former PhD student in Lu's laboratory who developed the DOMINO concept.

"We can also combine and layer multiple DNA reading and writing events together to build various forms of logic, such as 'AND' and 'OR' operations, which can then be used to create more complex memory and computing operations in living cells."

DOMINO is a modular system made of operator units. Each unit is composed of a base editor (a non-cutting variant of Cas9 fused to a cytidine deaminase) and one guide RNA that binds to its complementary sequence on the genome and recruits the base editor to that sequence. Once recruited, the base editor can introduce cytosine (C) to thymine (T) mutations into the vicinity of the gRNA binding site. The guide RNA in DOMINO operator can be designed in a way that it can bind to its target sequence only after a certain mutation is first introduced into that sequence by a previous event. Thus, for the base editor to make a change, a previous mutation must have been made so that the next mutation can be made. If a particular sequence is mutated, then the next step can happen.

If it is not mutated, then the next step cannot happen. That allows a cascade of writing events that is ultimately 'recorded' as unique mutational signatures in the cell's DNA. These signatures can be read out by DNA sequencing to infer information about the history of events or be read out by other DOMINO operators that couple the information into downstream computations. The team also demonstrated that these DNA signatures can be coupled with a fluorescent reporter, so that DNA writing/editing results in higher fluorescence signal. This allows for continuous monitoring of DNA memory without the need to kill cells for sequencing.

Currently, the team has used the technology to record events on the order of hours. But they are hopeful they can improve the temporal resolution and adapt it for recording cellular events that occur on faster timescales. They also plan on expanding DOMINO's application to highly-parallel computing and recording to process and interrogate more complex biological events.

"This type of biocomputing is an exciting new way of getting and processing information," says Lu. "It is part of a longer-term path to take advantage of the natural memory and computing capabilities in cells." Other applications include using cells as sensors and storage vehicles within the body or in the environment, such as a biosensor to record contamination levels in water. "These designer cells can constantly assess their environment and record information that can be read at a later time," says Lu.

"Biological systems can be thought of as conglomerates of information processing and storage systems, with DNA being one of the many possible media that can be used. The ability to read and write DNA and possibly other biological media could bring us closer to be able to study and program biology in a modular systematic fashion," says Farzadfard.
-end-
This work was supported by the National Institutes of Health, the Office of Naval Research, the National Science Foundation, Defense Advanced Research Projects Agency, the MIT Center for Microbiome Informatics and Therapeutics, and NSF Expeditions in Computing Program Award.

Molecular Cell, Farzadfard et al.: "Single-Nucleotide-Resolution Computing and Memory in Living Cells" https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30541-6

Molecular Cell (@MolecularCell), published by Cell Press, is a bimonthly journal that focuses on analyses at the molecular level, with an emphasis on new mechanistic insights. The scope of the journal encompasses all of "traditional" molecular biology as well as studies of the molecular interactions and mechanisms that underlie basic cellular processes. Visit: http://www.cell.com/molecular-cell. To receive Cell Press media alerts, please contact press@cell.com.

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