Construction of multilayered gene circuits using de-novo-designed synthetic transcriptional regulators in cell-free systems

Brophy JA, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014;11(5):508–20.

Article  Google Scholar 

Guo S, Xu Z, Lin L, Guo Y, Li J, Lu C, et al. Using CIVT-SELEX to select aptamers as genetic parts to regulate gene circuits in a cell-free system. Int J Mol Sci. 2023;24(3):2833.

Article  Google Scholar 

Guo S, Wang M, Xu W, Zou F, Lin J, Peng Q, et al. Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system. Phytochemistry. 2022;193:113007.

Article  Google Scholar 

Slomovic S, Pardee K, Collins JJ. Synthetic biology devices for in vitro and in vivo diagnostics. Proc Natl Acad Sci U S A. 2015;112(47):14429-35.

Xiao J, Guo S, Shi X. Metabolic engineering of Escherichia coli for the production of (R)-α-lipoic acid. Biotechnol Lett. 2023;45(2):273–86.

Article  Google Scholar 

Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000;403(6767):335–8.

Article  Google Scholar 

Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000;403(6767):339–42.

Article  Google Scholar 

Tamsir A, Tabor JJ, Voigt CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature. 2011;469(7329):212–15.

Article  Google Scholar 

Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science. 2011;332(6034):1196–201.

Article  Google Scholar 

Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell. 2003;113(5):597–607.

Article  Google Scholar 

Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P. Complex cellular logic computation using ribocomputing devices. Nature. 2017;548(7665):117–21.

Article  Google Scholar 

Subsoontorn P, Kim J, Winfree E. Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch. ACS Synth Biol. 2012;1(8):299–316.

Article  Google Scholar 

Kim J, White KS, Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol. 2006;2(1):68.

Article  Google Scholar 

Guo S, Murray RM. Construction of incoherent feedforward loop circuits in a cell-free system and in cells. ACS Synth Biol. 2019;8(3):606–10.

Article  Google Scholar 

Guo S, Lin J, Lin L, Xu W, Guo Y, Xu Z, et al. Selecting small molecule DNA aptamers with significant conformational changes for constructing transcriptional switches and biosensors. Sci China Chem. 2023;66(5):1529–36.

Article  Google Scholar 

Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, et al. Burden-driven feedback control of gene expression. Nat Methods. 2018;15(5):387–93.

Article  Google Scholar 

Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb). 2016;8(4):456–64.

Article  Google Scholar 

Cao M, Sun Q, Zhang X, Ma Y, Wang J. Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system. Biosens Bioelectron. 2021;182:113173.

Article  Google Scholar 

Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, et al. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell. 2016;165(5):1255–66.

Article  Google Scholar 

Chappell J, Takahashi MK, Meyer S, Loughrey D, Watters KE, Lucks J. The centrality of RNA for engineering gene expression. Biotechnol J. 2013;8(12):1379–95.

Article  Google Scholar 

Carothers JM, Goler JA, Juminaga D, Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science. 2011;334(6063):1716–19.

Article  Google Scholar 

Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, et al. NUPACK: Analysis and design of nucleic acid systems. J Comput Chem. 2011;32(1):170–73.

Article  Google Scholar 

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, et al. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A. 2011;108(27):11063-68.

Tan Z, Fu Y, Sharma G, Mathews DH. TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic Acids Res. 2017;45(20):11570–81.

Article  Google Scholar 

Bellaousov S, Reuter JS, Seetin MG, Mathews DH, RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 2013;41(W1):W471–4.

Chappell J, Takahashi MK, Lucks JB. Creating small transcription activating RNAs. Nat Chem Biol. 2015;11(3):214–20.

Article  Google Scholar 

Hong S, Kim J, Kim J. Multilevel gene regulation using switchable transcription terminator and toehold switch in Escherichia coli. Appl Sci. 2021;11(10):4532.

Article  Google Scholar 

Chappell J, Westbrook A, Verosloff M, Lucks JB. Computational design of small transcription activating RNAs for versatile and dynamic gene regulation. Nat Commun. 2017;8:1051.

Article  Google Scholar 

Yarnell WS, Roberts JW. Mechanism of intrinsic transcription termination and antitermination. Science. 1999;284(5414):611–5.

Article  Google Scholar 

Valeri JA, Collins KM, Ramesh P, Alcantar MA, Lepe BA, Lu TK, et al. Sequence-to-function deep learning frameworks for engineered riboregulators. Nat Commun. 2020;11:5058.

Article  Google Scholar 

Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999;288(5):911–40.

Article  Google Scholar 

Fornace ME, Porubsky NJ, Pierce NA. A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synth Biol. 2020;9(10):2665–78.

Article  Google Scholar 

Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Constrained multistate sequence design for nucleic acid reaction pathway engineering. J Am Chem Soc. 2017;139(8):3134–44.

Article  Google Scholar 

Chen Y-J, Liu P, Nielsen AA, Brophy JA, Clancy K, Peterson T, et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods. 2013;10(7):659–64.

Article  Google Scholar 

Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A fluorescent split aptamer for visualizing RNA–RNA assembly in vivo. ACS Synth Biol. 2017;6(9):1710–21.

Article  Google Scholar 

Angenent-Mari NM, Garruss AS, Soenksen LR, Church G, Collins JJ. A deep learning approach to programmable RNA switches. Nat Commun. 2020;11:5057.

Article  Google Scholar 

Cella F, Wroblewska L, Weiss R, Siciliano V. Engineering protein-protein devices for multilayered regulation of mRNA translation using orthogonal proteases in mammalian cells. Nat Commun. 2018;9:4392.

Article  Google Scholar 

Anderson JC, Voigt CA, Arkin AP. Environmental signal integration by a modular AND gate. Mol Syst Biol. 2007;3(1):133.

Article  Google Scholar 

Ellis T, Wang X, Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol. 2009;27(5):465–71.

Article  Google Scholar 

Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 2014;111(13):4838–43.

Article  Google Scholar 

Zhang S, Voigt CA. Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design. Nucleic Acids Res. 2018;46(20):11115–25.

Google Scholar 

Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol. 2018;14(8):e1006170.

Article  Google Scholar 

Ceroni F, Algar R, Stan G-B, Ellis T. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods. 2015;12(5):415–18.

Article  Google Scholar 

Hong S, Jeong D, Ryan J, Foo M, Tang X, Kim J. Design and evaluation of synthetic RNA-based incoherent feed-forward loop circuits. Biomolecules. 2021;11(8):1182.

Article  Google Scholar 

van der Linden AJ, Pieters PA, Bartelds MW, Nathalia BL, Yin P, Huck WT, et al. DNA input classification by a riboregulator-based cell-free perceptron. ACS Synth Biol. 2022;11(4):1510–20.

Article  Google Scholar 

Kim J, Quijano JF, Kim J, Yeung E, Murray RM. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Biotechnol J. 2022;17(3):2000449.

Article  Google Scholar 

Specht DA, Cortes LB, Lambert G. Overcoming leak sensitivity in CRISPRi circuits using antisense RNA sequestration and regulatory feedback. ACS Synth Biol. 2022;11(9):2927–37.

Article  Google Scholar 

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–83.

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