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Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

Ham TS, Lee SK, Keasling JD, Arkin AP - PLoS ONE (2008)

Bottom Line: This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of California, Berkeley, California, United States of America.

ABSTRACT

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.

Methodology/principal findings: 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/significance: 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.

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Related in: MedlinePlus

Plasmids used in the study.A) Plasmid maps for constructs containing the invertases and the memory switch. B) Detail of structure of the double inversion switch annotated with the primers used to diagnose state as described in the text. The Supplementary Information S1 contains the complete annotated sequence of the switch.
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pone-0002815-g002: Plasmids used in the study.A) Plasmid maps for constructs containing the invertases and the memory switch. B) Detail of structure of the double inversion switch annotated with the primers used to diagnose state as described in the text. The Supplementary Information S1 contains the complete annotated sequence of the switch.

Mentions: The target DNA regions were harbored on a separate plasmid. The switch region was synthesized de-novo and cloned into pPROBE-gfp. The red fluorescence gene was cloned in last. The fluorescent proteins GFP and RFP are placed to the left and right of the device respectively. The resulting plasmid is multicopy, meaning that there are many copies of our device in the cell such that the state of the device could possibly be different for each copy of the plasmid. Since Hin and FimB are reversible enzymes, each cell will harbor a mixture of states of the device as described below. The plasmids for the input and DNA response elements of the device are shown in Figure 2A.


Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

Ham TS, Lee SK, Keasling JD, Arkin AP - PLoS ONE (2008)

Plasmids used in the study.A) Plasmid maps for constructs containing the invertases and the memory switch. B) Detail of structure of the double inversion switch annotated with the primers used to diagnose state as described in the text. The Supplementary Information S1 contains the complete annotated sequence of the switch.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2481393&req=5

pone-0002815-g002: Plasmids used in the study.A) Plasmid maps for constructs containing the invertases and the memory switch. B) Detail of structure of the double inversion switch annotated with the primers used to diagnose state as described in the text. The Supplementary Information S1 contains the complete annotated sequence of the switch.
Mentions: The target DNA regions were harbored on a separate plasmid. The switch region was synthesized de-novo and cloned into pPROBE-gfp. The red fluorescence gene was cloned in last. The fluorescent proteins GFP and RFP are placed to the left and right of the device respectively. The resulting plasmid is multicopy, meaning that there are many copies of our device in the cell such that the state of the device could possibly be different for each copy of the plasmid. Since Hin and FimB are reversible enzymes, each cell will harbor a mixture of states of the device as described below. The plasmids for the input and DNA response elements of the device are shown in Figure 2A.

Bottom Line: This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of California, Berkeley, California, United States of America.

ABSTRACT

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.

Methodology/principal findings: 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/significance: 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.

Show MeSH
Related in: MedlinePlus