Schultz, D., Wolynes, P. G., Jacob, E. B. & Onuchic, J. N. Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc. Natl Acad. Sci. USA 106, 21027–21034 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Oppenheim, A. B., Kobiler, O., Stavans, J., Court, D. L. & Adhya, S. Switches in bacteriophage lambda development. Annu. Rev. Genet. 39, 409–429 (2005).

CAS  PubMed  Article  Google Scholar 

Peter, I. S. & Davidson, E. H. Assessing regulatory information in developmental gene regulatory networks. Proc. Natl Acad. Sci. USA 114, 5862 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Alon, U. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450–461 (2007).

CAS  PubMed  Article  Google Scholar 

van Esch, J. H., Klajn, R. & Otto, S. Chemical systems out of equilibrium. Chem. Soc. Rev. 46, 5474–5475 (2017).

PubMed  Article  Google Scholar 

van Roekel, H. W. H. et al. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach. Chem. Soc. Rev. 44, 7465–7483 (2015).

PubMed  Article  Google Scholar 

Ferrell, J. E.Jr & Ha, S. H. Ultrasensitivity part III: cascades, bistable switches, and oscillators. Trends Biochem. Sci. 39, 612–618 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

McAdams Harley, H. & Shapiro, L. Circuit simulation of genetic networks. Science 269, 650–656 (1995).

Article  Google Scholar 

Ackermann, J., Wlotzka, B. & McCaskill, J. S. In vitro DNA-based predator–prey system with oscillatory kinetics. Bull. Math. Biol. 60, 329–354 (1998).

CAS  Article  Google Scholar 

Montagne, K., Plasson, R., Sakai, Y., Fujii, T. & Rondelez, Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011).

PubMed  PubMed Central  Article  Google Scholar 

Semenov, S. N. et al. Rational design of functional and tunable oscillating enzymatic networks. Nat. Chem. 7, 160–165 (2015).

CAS  PubMed  Article  Google Scholar 

Kim, J. & Winfree, E. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7, 465 (2011).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Montagne, K., Gines, G., Fujii, T. & Rondelez, Y. Boosting functionality of synthetic DNA circuits with tailored deactivation. Nat. Commun. 7, 13474 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Padirac, A., Fujii, T. & Rondelez, Y. Bottom-up construction of in vitro switchable memories. Proc. Natl Acad. Sci. USA 109, E3212–E3220 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Helwig, B., van Sluijs, B., Pogodaev, A. A., Postma, S. G. J. & Huck, W. T. S. Bottom-up construction of an adaptive enzymatic reaction network. Angew. Chem. Int. Ed. 57, 14065–14069 (2018).

CAS  Article  Google Scholar 

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

CAS  PubMed  Article  Google Scholar 

Postma, S. G. J., te Brinke, D., Vialshin, I. N., Wong, A. S. Y. & Huck, W. T. S. A trypsin-based bistable switch. Tetrahedron 73, 4896–4900 (2017).

CAS  Article  Google Scholar 

Genot, A. J. et al. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nat. Chem. 8, 760 (2016).

CAS  PubMed  Article  Google Scholar 

Kim, J., White, K. S. & Winfree, E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2, 68 (2006).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Kim, J., Khetarpal, I., Sen, S. & Murray, R. M. Synthetic circuit for exact adaptation and fold-change detection. Nucleic Acids Res. 42, 6078–6089 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Zadorin, A. S. et al. Synthesis and materialization of a reaction–diffusion French flag pattern. Nat. Chem. 9, 990 (2017).

CAS  PubMed  Article  Google Scholar 

Gines, G. et al. Microscopic agents programmed by DNA circuits. Nat. Nanotechnol. 12, 351 (2017).

CAS  PubMed  Article  Google Scholar 

Dupin, A. & Simmel, F. C. Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat. Chem. 11, 32–39 (2019).

CAS  PubMed  Article  Google Scholar 

Green, L. N. et al. Autonomous dynamic control of DNA nanostructure self-assembly. Nat. Chem. 11, 510–520 (2019).

CAS  PubMed  Article  Google Scholar 

Franco, E. et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl Acad. Sci. USA 108, E784–E793 (2011).

CAS  PubMed  PubMed Central  Google Scholar 

Meijer, L. H. H. et al. Hierarchical control of enzymatic actuators using DNA-based switchable memories. Nat. Commun. 8, 1117 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Schaffter, S. W. & Schulman, R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat. Chem. 11, 829–838 (2019).

CAS  PubMed  Article  Google Scholar 

Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011).

CAS  PubMed  Article  Google Scholar 

Song, T. et al. Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase. Nat. Nanotechnol. 14, 1075–1081 (2019).

CAS  PubMed  Article  Google Scholar 

Kishi, J. Y., Schaus, T. E., Gopalkrishnan, N., Xuan, F. & Yin, P. Programmable autonomous synthesis of single-stranded DNA. Nat. Chem. 10, 155–164 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Shah, S. et al. Using strand displacing polymerase to program chemical reaction networks. J. Am. Chem. Soc. 142, 9587–9593 (2020).

CAS  PubMed  Google Scholar 

Chen, Z. et al. De novo design of protein logic gates. Science 368, 78 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Franco, E., Giordano, G., Forsberg, P.-O. & Murray, R. M. Negative autoregulation matches production and demand in synthetic transcriptional networks. ACS Synth. Biol. 3, 589–599 (2014).

CAS  PubMed  Article  Google Scholar 

Kim, J., Hopfield, J. & Winfree, E. in Advances in Neural Information Processing Systems 17 (eds Saul, L. K., Weiss, Y. & Bottou, L.) 681–688 (MIT Press, 2005).

Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).

CAS  PubMed  Article  Google Scholar 

Dabby, N. Synthetic Molecular Machines for Active Self-assembly: Prototype Algorithms, Designs, and Experimental Study. PhD thesis, California Institute of Technology (2013).

Groves, B. et al. Computing in mammalian cells with nucleic acid strand exchange. Nat. Nanotechnol. 11, 287–294 (2016).

CAS  PubMed  Article  Google Scholar 

Isambert, H. The jerky and knotty dynamics of RNA. Methods 49, 189–196 (2009).

CAS  PubMed  Article  Google Scholar 

Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009).

CAS  PubMed  Article  Google Scholar 

Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA 100, 11980–11985 (2003).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Krupp, G. RNA synthesis: strategies for the use of bacteriophage RNA polymerases. Gene 72, 75–89 (1988).

CAS  PubMed  Article  Google Scholar 

Lapham, J. & Crothers, D. M. RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA 2, 289–296 (1996).

CAS  PubMed  PubMed Central