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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.

Show MeSH
Culture PCR results for the response to the different input sequences.{FimB}, {HinB}, {FimB, HinB} and {HinB, FimB}. Each lane probes for the existence of a state or states, as shown in the legend. Because of the possible arrangements of DNA, lanes E and F could result in either short or long PCR products, indicating states {1, 3}, and {2, 4} respectively. See Figure 2 for relative location of the primers. No State 5 was observed when Hin and FimB were simultaneously expressed.
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pone-0002815-g003: Culture PCR results for the response to the different input sequences.{FimB}, {HinB}, {FimB, HinB} and {HinB, FimB}. Each lane probes for the existence of a state or states, as shown in the legend. Because of the possible arrangements of DNA, lanes E and F could result in either short or long PCR products, indicating states {1, 3}, and {2, 4} respectively. See Figure 2 for relative location of the primers. No State 5 was observed when Hin and FimB were simultaneously expressed.

Mentions: Figure 3 shows the results of our experiments. In these experiments cells were grown in LB at 37°C and exposed to either arabinose or tetracycline. The hin mirrored pair was replaced with hixC, a variant inversion sequence which allows inversion in both directions without impediment [13], as the hin mirrored pair behaved unpredictably due to its native mirrored-pair like structure (data not shown). HixC, however, does have a side effect of resulting in a higher rate of self-excision of the DNA when in a directly repeated orientation.


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)

Culture PCR results for the response to the different input sequences.{FimB}, {HinB}, {FimB, HinB} and {HinB, FimB}. Each lane probes for the existence of a state or states, as shown in the legend. Because of the possible arrangements of DNA, lanes E and F could result in either short or long PCR products, indicating states {1, 3}, and {2, 4} respectively. See Figure 2 for relative location of the primers. No State 5 was observed when Hin and FimB were simultaneously expressed.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0002815-g003: Culture PCR results for the response to the different input sequences.{FimB}, {HinB}, {FimB, HinB} and {HinB, FimB}. Each lane probes for the existence of a state or states, as shown in the legend. Because of the possible arrangements of DNA, lanes E and F could result in either short or long PCR products, indicating states {1, 3}, and {2, 4} respectively. See Figure 2 for relative location of the primers. No State 5 was observed when Hin and FimB were simultaneously expressed.
Mentions: Figure 3 shows the results of our experiments. In these experiments cells were grown in LB at 37°C and exposed to either arabinose or tetracycline. The hin mirrored pair was replaced with hixC, a variant inversion sequence which allows inversion in both directions without impediment [13], as the hin mirrored pair behaved unpredictably due to its native mirrored-pair like structure (data not shown). HixC, however, does have a side effect of resulting in a higher rate of self-excision of the DNA when in a directly repeated orientation.

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