Single-Nucleotide-Resolution Computing and Memory in Living Cells

Fahim Farzadfard; Nava Gharaei; Yasutomi Higashikuni; Giyoung Jung; Jicong Cao; Timothy K Lu

doi:10.1016/j.molcel.2019.07.011

Single-Nucleotide-Resolution Computing and Memory in Living Cells

Mol Cell. 2019 Aug 22;75(4):769-780.e4. doi: 10.1016/j.molcel.2019.07.011.

Authors

Fahim Farzadfard¹, Nava Gharaei², Yasutomi Higashikuni³, Giyoung Jung⁴, Jicong Cao³, Timothy K Lu⁵

Affiliations

¹ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge MA 02139, USA. Electronic address: ffard@mit.edu.
² MCO Graduate Program, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
³ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA.
⁴ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
⁵ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge MA 02139, USA. Electronic address: timlu@mit.edu.

Abstract

The ability to process and store information in living cells is essential for developing next-generation therapeutics and studying biology in situ. However, existing strategies have limited recording capacity and are challenging to scale. To overcome these limitations, we developed DOMINO, a robust and scalable platform for encoding logic and memory in bacterial and eukaryotic cells. Using an efficient single-nucleotide-resolution Read-Write head for DNA manipulation, DOMINO converts the living cells' DNA into an addressable, readable, and writable medium for computation and storage. DOMINO operators enable analog and digital molecular recording for long-term monitoring of signaling dynamics and cellular events. Furthermore, multiple operators can be layered and interconnected to encode order-independent, sequential, and temporal logic, allowing recording and control over the combination, order, and timing of molecular events in cells. We envision that DOMINO will lay the foundation for building robust and sophisticated computation-and-memory gene circuits for numerous biotechnological and biomedical applications.

Keywords: DNA memory; DNA writing; analog and digital recording and computation; base editing; cellular computation; dynamic genome engineering; logic circuits; molecular recording; synthetic gene circuits.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computers, Molecular*
DNA* / chemistry
DNA* / metabolism
HEK293 Cells
Humans

Substances

DNA

Grants and funding

P50 GM098792/GM/NIGMS NIH HHS/United States