International Journal of Information Technology

, Volume 10, Issue 3, pp 379–390 | Cite as

An improved generalized DNA computing model to simulate logic functions and combinational circuits

  • Kuntala Boruah
  • Jiten Chandra Dutta
Original Research


In this paper a reusable, generalized, parallel DNA computing model is presented to evaluate any logic function at molecular level. The gate strands designed by this algorithm act both as logic operator and sensor to detect the output. Though this model could be employed to simulate vast range of logic functions but for simplicity of explanation theoretical simulation results of DNA based NAND, NOR, half-adder, full-adder and four-bit carry ripple adder are demonstrated to validate this model. The proposed model relies on the induced hairpin formation property of naphthyridine dimer in a G–G mismatched DNA oligo strand which is integrated with a generalized gate design algorithm. Contribution of this work lies in the inclusion of features like single design strategy for any logic function, uniformity in representation of logic 0 and 1 throughout the simulation process and is cost and implementation effective with parallel processing capacity.


DNA DNA computing DNA hairpin Logic gate NAND NOR Full-adder Four-bit carry ripple adder 



The authors acknowledge Tezpur University for providing necessary facilities.

Compliance with ethical standards

Conflict of interest

The authors have no conflicts of interest to disclose.


  1. 1.
    Feynman R (1960) There’s plenty of room at the bottom. Eng Sci 23(5):22–36Google Scholar
  2. 2.
    Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 266(5187):1021–1024CrossRefGoogle Scholar
  3. 3.
    Ogihara M, Ray A (1998) DNA-based self-propagating algorithm for solving bounded-fan-in Boolean circuit. In: Proceedings of the third conference on genetic programming. Morgan Kaufman Publisher, San Francisco, p 725–730Google Scholar
  4. 4.
    Ogihara M, Ray A (1999) Simulating Boolean circuits on a DNA computers. Algorithmica 25:239–250MathSciNetCrossRefzbMATHGoogle Scholar
  5. 5.
    Amos M, Dunne P (1997) DNAsimulation of Boolean circuits. Technical report CTAC-97009. Department of Computer Science, University of LiverpoolGoogle Scholar
  6. 6.
    Erk K (1999) Simulating Boolean circuits by finite splicing. In: Proceedings of the congress on evolutionary computation, vol 2. IEEE Press, New York, p 1279–1285Google Scholar
  7. 7.
    Mulawka JJ, Wasiewicz P, Plucienniczak A (1999) Another logical molecular NAND gate system. In: Proceedings of the seventh international conference on microelectronics for neural, fuzzy and bio-inspired systems. Granada, Spain, p 340–346Google Scholar
  8. 8.
    Liu W, Shi X, Zhang S, Liu X, Xu J (2004) A new DNA computing model for the NAND gate based on induced hairpin formation. BioSystems 77:87–92CrossRefGoogle Scholar
  9. 9.
    Liu W, Zhu X, Wang X, Yin Z, Wang S (2008) Simulating the XOR gates based on the induced hairpin formation. Curr Nanosci 4(1):108–110CrossRefGoogle Scholar
  10. 10.
    Smith E, Kyo M, Kumasawa H, Nakatani K, Saito I, Corn RM (2002) Chemically induced hairpin formation in DNA monolayers. J Am Chem Soc 124:6810–6811CrossRefGoogle Scholar
  11. 11.
    Ahrabian H, Ganjtabesh M, Nowzari-Dalini A (2005) DNA algorithm for an unbounded fan-in Boolean circuit. BioSystems 82:52–60CrossRefzbMATHGoogle Scholar
  12. 12.
    Kadkhoda M, Pouyan AA (2006) A DNA-based simulation model for bounded fan-in Boolean circuits. In: Proceedings of the 10th WSEAS international conference on Computers. World Scientific and Engineering Academy and Society (WSEAS)Google Scholar
  13. 13.
    Shapiro E, Gil B (2007) Biotechnology: logic goes in vitro. Nat Nanotechnol 2:84–85CrossRefGoogle Scholar
  14. 14.
    Frezza BM, Cockroft SL, Ghadiri MR (2007) Modular multi-level circuits from immobilized DNA-based logic gate. J Am Chem Soc 129:14875CrossRefGoogle Scholar
  15. 15.
    Zoraida BSE, Arock M, Ronald BSM, Ponalagusamy R (2009) A novel generalized design methodology and realization of Boolean operations using DNA. BioSystems 97:146–153CrossRefGoogle Scholar
  16. 16.
    Park KS, Jung C, Park HG (2010) “Illusionary” polymerase activity triggered by metal ions: use for molecular logic-gate operations. Angew Chem Int Ed 49:9757–9760CrossRefGoogle Scholar
  17. 17.
    Goel A, Morteza I (2011) A renewable, modular, and time-responsive DNA circuit. Nat Comput 10:467–485MathSciNetCrossRefzbMATHGoogle Scholar
  18. 18.
    Genot AJ, Bath J, Turberfield AJ (2011) Reversible logic circuits made of DNA. J Am Chem Soc 133:20080–20083CrossRefGoogle Scholar
  19. 19.
    Li W, Yang Y, Yan H, Liu Y (2013) Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement. Nano Lett 13:2980–2988CrossRefGoogle Scholar
  20. 20.
    Li W, Zhang F, Yan H, Liu Y (2016) DNA based arithmetic function: a half adder based on DNA strand displacement. Nanoscale 8:3775–3784CrossRefGoogle Scholar
  21. 21.
    Boruah K, Deka R,Dutta JC (2018) A model to demonstrate the universality of DNA-NAND gate. In: Advances in electronics, communication and computing. Springer, Singapore, p 67–76Google Scholar
  22. 22.
    Boruah K, Deka R, Dutta JC (2017) Algorithm to simulate a chemically induced DNA logic gate and Boolean circuit. Curr Trends Biotechnol Pharm 11(2):160–166Google Scholar

Copyright information

© Bharati Vidyapeeth's Institute of Computer Applications and Management 2018

Authors and Affiliations

  1. 1.Electronics and Communication Engg.Tezpur UniversityTezpurIndia

Personalised recommendations