Design and construction of a double inversion recombination switch for heritable sequential genetic memory.
BACKGROUND
Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence.


RESULTS
In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch.


CONCLUSIONS
We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable.
Ham
Timothy S
TS
Department of Bioengineering, University of California, Berkeley, California, United States of America.
Lee
Sung K
SK
Keasling
Jay D
JD
Arkin
Adam P
AP
D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics; D007446:Chromosome Inversion; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D005798:Genes, Bacterial; D005818:Genetic Engineering; D005821:Genetic Techniques; D019426:Integrases / Q000235:genetics; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D045522:Recombinases; D011995:Recombination, Genetic
D001426:Bacterial Proteins; D045522:Recombinases; D004247:DNA; D019426:Integrases