Limits...
In silico design and in vivo implementation of yeast gene Boolean gates.

Marchisio MA - J Biol Eng (2014)

Bottom Line: Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required.Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits.As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland. marchisio@hit.edu.cn.

ABSTRACT
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

No MeSH data available.


Related in: MedlinePlus

AND gates (N-IMPLY) responsive to β-estradiol. A) tet AND NOT(estr) gives the better performance in term of signal separation and 1-factor. B) IPTG AND NOT(estr) shows the best 1 to 0 gain among the AND gates in our library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC3926364&req=5

Figure 4: AND gates (N-IMPLY) responsive to β-estradiol. A) tet AND NOT(estr) gives the better performance in term of signal separation and 1-factor. B) IPTG AND NOT(estr) shows the best 1 to 0 gain among the AND gates in our library.

Mentions: Overall, the best performance was obtained with the two "tet AND NOT(estr)" gates (to be precise, this Boolean gate is referred to as N-IMPLY in electronics). In particular, the design with the lex operator close to the TATA box (AND lexOp-tetOp) gives a better σ (see Figure4A) whereas no significative difference between the two configurations is registered regarding φ and ρ. The AND lexOp-tetOp configuration, however, shows also that TetR is rather inefficient in repressing transcription when it binds in proximity of the TSS. In contrast, when the tet operator is placed close to the TATA box (AND tetOp-lexOp), TetR action is stronger and the difference among the three 0 output fluorescence levels is reduced.


In silico design and in vivo implementation of yeast gene Boolean gates.

Marchisio MA - J Biol Eng (2014)

AND gates (N-IMPLY) responsive to β-estradiol. A) tet AND NOT(estr) gives the better performance in term of signal separation and 1-factor. B) IPTG AND NOT(estr) shows the best 1 to 0 gain among the AND gates in our library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3926364&req=5

Figure 4: AND gates (N-IMPLY) responsive to β-estradiol. A) tet AND NOT(estr) gives the better performance in term of signal separation and 1-factor. B) IPTG AND NOT(estr) shows the best 1 to 0 gain among the AND gates in our library.
Mentions: Overall, the best performance was obtained with the two "tet AND NOT(estr)" gates (to be precise, this Boolean gate is referred to as N-IMPLY in electronics). In particular, the design with the lex operator close to the TATA box (AND lexOp-tetOp) gives a better σ (see Figure4A) whereas no significative difference between the two configurations is registered regarding φ and ρ. The AND lexOp-tetOp configuration, however, shows also that TetR is rather inefficient in repressing transcription when it binds in proximity of the TSS. In contrast, when the tet operator is placed close to the TATA box (AND tetOp-lexOp), TetR action is stronger and the difference among the three 0 output fluorescence levels is reduced.

Bottom Line: Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required.Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits.As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland. marchisio@hit.edu.cn.

ABSTRACT
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

No MeSH data available.


Related in: MedlinePlus