title: Synthetic recombinase-based state machines in living cells.
abstract: State machines underlie the sophisticated functionality behind human-made and natural computing systems that perform order-dependent information processing. We developed a recombinase-based framework for building state machines in living cells by leveraging chemically controlled DNA excision and inversion operations to encode states in DNA sequences. This strategy enables convenient readout of states (by sequencing and/or polymerase chain reaction) as well as complex regulation of gene expression. We validated our framework by engineering state machines in Escherichia coli that used one, two, or three chemical inputs to control up to 16 DNA states. These state machines were capable of recording the temporal order of all inputs and performing multi-input, multi-output control of gene expression. We also developed a computational tool for the automated design of gene regulation programs using recombinase-based state machines. Our scalable framework should enable new strategies for recording and studying how combinational and temporal events regulate complex cell functions and for programming sophisticated cell behaviors.
authors.affiliation: Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Biophysics Program, Harvard University, Boston, MA 02115, USA.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Roquet
authors.affiliation: Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Ava P
authors.initials: AP
authors.lastname: Soleimany
authors.affiliation: Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Biochemistry Program, Wellesley College, Wellesley, MA 02481, USA.
authors.forename: Alyssa C
authors.initials: AC
authors.lastname: Ferris
authors.affiliation: Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Aaronson
authors.affiliation: Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Biophysics Program, Harvard University, Boston, MA 02115, USA. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. timlu@mit.edu.
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D002477:Cells / Q000737:chemistry*; D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology; D005786:Gene Expression Regulation; D005818:Genetic Engineering; D045522:Recombinases / Q000737:chemistry* / Q000235:genetics; D058615:Synthetic Biology
chemical_list: D045522:Recombinases; D004247:DNA