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Heat-rechargeable computation in DNA logic circuits and neural networks

  • Yurke, B., Turberfield, A. J., Mills Jr, A. P., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Yan, H., Zhang, X., Shen, Z. & Seeman, N. C. A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Turberfield, A. J. et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Simmel, F. C. DNA nanotechnology out of equilibrium. in Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman (eds Jonoska, N. & Winfree, E.) 17–29 (Springer, 2023).


    Google Scholar
     

  • Dirks, R. M. & Pierce, N. A. Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci. USA 101, 15275–15278 (2004).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bois, J. S. Analysis of Interacting Nucleic Acids in Dilute Solutions (California Institute of Technology, 2006).


    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).

    Article 
    PubMed 
    PubMed Central 

    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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schaffter, S. W. et al. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nat. Chem. 14, 1224–1232 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Okumura, S. et al. Nonlinear decision-making with enzymatic neural networks. Nature 610, 496–501 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Simpson, Z. B., Tsai, T. L., Nguyen, N., Chen, X. & Ellington, A. D. Modelling amorphous computations with transcription networks. J. R. Soc. Interface 6, S523–S533 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic Acids Res. 38, 4182–4197 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lv, H. et al. DNA-based programmable gate arrays for general-purpose DNA computing. Nature 622, 292–300 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Cherry, K. M. & Qian, L. Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks. Nature 559, 370–376 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Xiong, X. et al. Molecular convolutional neural networks with DNA regulatory circuits. Nat. Mach. Intell. 4, 625–635 (2022).

    Article 

    Google Scholar
     

  • Genot, A. J., Bath, J. & Turberfield, A. J. Reversible logic circuits made of DNA. J. Am. Chem. Soc. 133, 20080–20083 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, B., Chalk, C., Doty, D. & Soloveichik, D. Molecular computation at equilibrium via programmable entropy. Preprint at bioRxiv 10.1101/2024.09.13.612990v1 (2024).

  • Vasić, M., Soloveichik, D. & Khurshid, S. CRN++: molecular programming language. Nat. Comput. 19, 391–407 (2020).

    Article 
    MathSciNet 

    Google Scholar
     

  • Lakin, M. R. & Stefanovic, D. Supervised learning in adaptive DNA strand displacement networks. ACS Synth. Biol. 5, 885–897 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • DelRosso, N. V., Hews, S., Spector, L. & Derr, N. D. A molecular circuit regenerator to implement iterative strand displacement operations. Angew. Chem. Int. Ed. Engl. 56, 4443–4446 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Scalise, D., Dutta, N. & Schulman, R. DNA strand buffers. J. Am. Chem. Soc. 140, 12069–12076 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Garg, S. et al. Renewable time-responsive DNA circuits. Small 14, 1801470 (2018).

    Article 

    Google Scholar
     

  • Eshra, A., Shah, S., Song, T. & Reif, J. Renewable DNA hairpin-based logic circuits. IEEE Trans. Nanotechnol. 18, 252–259 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Hahn, J. & Shih, W. M. Thermal cycling of DNA devices via associative strand displacement. Nucleic Acids Res. 47, 10968–10975 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lakin, M. R., Youssef, S., Cardelli, L. & Phillips, A. Abstractions for DNA circuit design. J. R. Soc. Interface 9, 470–486 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Lauback, S. et al. Real-time magnetic actuation of DNA nanodevices via modular integration with stiff micro-levers. Nat. Commun. 9, 1446 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kopperger, E. et al. A self-assembled nanoscale robotic arm controlled by electric fields. Science 359, 296–301 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Liang, X., Nishioka, H., Takenaka, N. & Asanuma, H. A DNA nanomachine powered by light irradiation. ChemBioChem 9, 702–705 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Song, X., Eshra, A., Dwyer, C. & Reif, J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv. 7, 28130–28144 (2017).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Doty, D., Rogers, T. A., Soloveichik, D., Thachuk, C. & Woods, D. Thermodynamic binding networks. In Proc. DNA Computing and Molecular Programming: 23rd International Conference (eds Brijder, R., Qian, L.) 249–266 (Springer, 2017).

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

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Takinoue, M. & Suyama, A. Hairpin-DNA memory using molecular addressing. Small 2, 1244–1247 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Viasnoff, V., Meller, A. & Isambert, H. DNA nanomechanical switches under folding kinetics control. Nano Lett. 6, 101–104 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Machinek, R. R., Ouldridge, T. E., Haley, N. E., Bath, J. & Turberfield, A. J. Programmable energy landscapes for kinetic control of DNA strand displacement. Nat. Commun. 5, 5324 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Haley, N. E. et al. Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement. Nat. Commun. 11, 2562 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, H.-L., Doty, D., Reeves, W. & Soloveichik, D. Rate-independent computation in continuous chemical reaction networks. J. ACM 70, 1–61 (2023).

    MathSciNet 
    CAS 

    Google Scholar
     

  • Kim, J., Hopfield, J. & Winfree, E. Neural network computation by in vitro transcriptional circuits. In Advances in Neural Information Processing Systems 17 (NIPS 2004) (eds Saul, L. K., et al.) 681–688 (MIT Press, 2004).

  • Genot, A. J., Fujii, T. & Rondelez, Y. Scaling down DNA circuits with competitive neural networks. J. R. Soc. Interface 10, 20130212 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, D. Y. Cooperative hybridization of oligonucleotides. J. Am. Chem. Soc. 133, 1077–1086 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lothaire, M. Algebraic Combinatorics on Words, Vol. 90 (Cambridge Univ. Press, 2002).

    Book 
    MATH 

    Google Scholar
     

  • Yin, P., Choi, H. M., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318–322 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, X., Briggs, N., McLain, J. R. & Ellington, A. D. Stacking nonenzymatic circuits for high signal gain. Proc. Natl Acad. Sci. USA 110, 5386–5391 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Simmel, F. C., Yurke, B. & Singh, H. R. Principles and applications of nucleic acid strand displacement reactions. Chem. Rev. 119, 6326–6369 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martin, W., Baross, J., Kelley, D. & Russell, M. J. Hydrothermal vents and the origin of life. Nat. Rev. Microbiol. 6, 805–814 (2008).

    Article 
    CAS 
    PubMed 

    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 (2018).

    Article 
    CAS 
    PubMed 

    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).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Thubagere, A. J. et al. Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components. Nat. Commun. 8, 14373 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouldridge, T. E., Šulc, P., Romano, F., Doye, J. P. & Louis, A. A. DNA hybridization kinetics: zippering, internal displacement and sequence dependence. Nucleic Acids Res. 41, 8886–8895 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Srinivas, N. et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 41, 10641–10658 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • SantaLucia Jr, J., & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).

    Article 
    PubMed 

    Google Scholar
     

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