Skip to main content
SpringerLink
Log in

A renewable, modular, and time-responsive DNA circuit

  • Published:
Natural Computing Aims and scope Submit manuscript

Abstract

In this article, we introduce a new design for DNA logic gates based on enzymatic restriction of DNA strands. We present a construction for a set of one and two-input logic gates and argue that our construction can be generalized to implement any Boolean operation. A key feature of our design is its time-responsiveness, in the presence of appropriate fuels our circuit can operate continuously and generate a time-dependent output in response to a time-dependent input. Moreover, modulo connectivity information, the strand design and circuit design phases are decoupled.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Notes

  1. Laplace transform is a one-to-one mapping when defined on a set of well-behaved functions.

References

  • Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024

    Article  Google Scholar 

  • Bayer TS, Smolke CD (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 23:337–343

    Article  Google Scholar 

  • Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429(6990):423–429

    Article  Google Scholar 

  • Chen H, Anindya D, Goel A (2008) Towards programmable molecular machines. In: Proceedings of the 5th conference on foundation of nanoscience, Snowbird, Utah, pp 137–139

  • Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841–847

    Article  Google Scholar 

  • Macdonald J, Li Y, Sutovic M, Lederman H, Pendri K, Lu W, Andrews BL, Stefanovic D, Stojanovic MN (2006) Medium scale integration of molecular logic gates in an automaton. Nano Lett 6(11):2598–2603

    Article  Google Scholar 

  • Qian L, Winfree E (2008) A simple DNA gate motif for synthesizing large-scale circuits. In: Proceedings of the 14th international meeting on DNA based computers. Springer, Prague, Czech Republic

  • Reif JH, LaBean TH (2009) DNA nanotechnology and its biological applications. In: Bio-inspired and nanoscale integrated computing, Wiley, Hoboken, NJ, pp 349–375

  • Rothemund P (1996) A DNA and restriction enzyme implementation of turing machines. In: DNA based computers: proceedings of a DIMACS workshop, April 4, 1995, Princeton University, American Mathematical Society

  • Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314(5805):1585

    Google Scholar 

  • Sherman WB, Seeman NC (2004) A precisely controlled DNA bipedal walking device. Nano Lett 4:1203–1207

    Article  Google Scholar 

  • Shin J-S, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126:10834–10835

    Article  Google Scholar 

  • Soloveichik D, Cook M, Winfree E, Bruck J (2008) Computation with finite stochastic chemical reaction networks. Nat Comput 7(4):615–633

    Article  MathSciNet  MATH  Google Scholar 

  • Stojanovic MN, Mitchell TE, Stefanovic D (2002) Deoxyribozyme-based logic gates. J Am Chem Soc 124(14):3555–3561

    Article  Google Scholar 

  • Win MN, Smolke CD (2007) From the cover: a modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci USA 104(36):14283–14288

    Article  Google Scholar 

  • Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322(5900):456–460

    Article  Google Scholar 

  • Yin P, Turberfield AJ, Sahu S, Reif JH (2004a) Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion. In: Proceedings of the 10th international meeting on DNA computing, Springer, Berlin, pp 344–356

  • Yin P, Yan H, Daniell XG, Turberfield AJ, Reif JH (2004b) A unidirectional DNA walker moving autonomously along a linear track. Angew Chem Int Ed 43:4906–4911

    Article  Google Scholar 

  • Yin P, Sahu S, Turberfield AJ, Reif JH (2006) Design of autonomous DNA cellular automata. Lect Notes Comput Sci 3892:399–416

    Article  Google Scholar 

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

    Article  Google Scholar 

Download references

Acknowledgment

The authors would like to acknowledge the anonymous reviewer of this paper whose comments were instrumental in improving the presentation of our work.

Author information

Authors and Affiliations

  1. Departments of Management Science and Engineering and (by courtesy) Computer Science, Stanford University, Stanford, CA, USA

    Ashish Goel

  2. Departments of Electrical Engineering, Stanford University, Stanford, CA, USA

    Morteza Ibrahimi

Authors
  1. Ashish Goel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Morteza Ibrahimi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ashish Goel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Goel, A., Ibrahimi, M. A renewable, modular, and time-responsive DNA circuit. Nat Comput 10, 467–485 (2011). https://doi.org/10.1007/s11047-010-9237-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11047-010-9237-6

Keywords

Search

Navigation