American Journal of Nanomaterials
ISSN (Print): 2372-3114 ISSN (Online): 2372-3122 Website: Editor-in-chief: Apply for this position
Open Access
Journal Browser
American Journal of Nanomaterials. 2017, 5(2), 51-58
DOI: 10.12691/ajn-5-2-2
Open AccessReview Article

Encoding Information in DNA: From Basic Structure to Nanoelectronics

Mohammed Enamul Hoque1, and Nordiana Rajaee1

1Department of Electrical & Electronic Engineering, University Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia

Pub. Date: August 07, 2017

Cite this paper:
Mohammed Enamul Hoque and Nordiana Rajaee. Encoding Information in DNA: From Basic Structure to Nanoelectronics. American Journal of Nanomaterials. 2017; 5(2):51-58. doi: 10.12691/ajn-5-2-2


DNA (Deoxyribonucleic Acid) computing is a recent computing technique which is also referred as bio molecular computing or molecular computing. DNA computing is a new avenue for solving the computational problem manipulating the distinct nanoscopic molecule and nowadays the approaches of DNA computing are being employed to resolve combinatorial problems utilizing the advantages of parallelism and high-density storage characteristics of DNA. Besides DNA is considered as the most feasible substance to shape the most nanoscopic materials, manufacture distinct nanomechanical devices and formulating large-scale nanostructures due to its expedient structural features and molecular recognition properties. A concise discussion regarding the splendid advances in constructing nanoelectronics employing DNA computing paradigm and challenges of DNA computing is focused in this paper.

DNA computing NP-complete problems DNA self-assembly DNA computer nano devices DNA as storage applications

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


Figure of 1


[1]  Abbasy, M.R. & Shanmugam, B. (2011). Enabling data Hiding for Resource Sharing in Cloud Computing Environments Based on DNA Sequences. (385-390), 2011 IEEE World Congress on Services. Services (SERVICES), 2011 IEEE World Congress on.
[2]  Adleman, L.M. (1994). Molecular computation of solutions to combinatorial problems. Science, (266) 1021-24.
[3]  Aldaye, F., Palmer, A. & Sleiman, H. (2008). Assembling Materials with DNA as the Guide. SCIENCE 321(2008), 1795-1799.
[4]  Amos, M. (2008). DNA computing, Invited Article for the Encyclopedia of Complexity and System Science, Springer.
[5]  Bakar, R.A., Watada,J. & Pedrycz,W. (2008). DNA approaches to solve clustering problem based on mutual order. Biosystem 91(2008)1-12.
[6]  Batley, J. & Edwards, D. (2009). Genome sequence data: management, storage, and visualization. Bio Techniques 46 (5), 333-335.
[7]  Benenson, Y., Adar,R., Paz-Elizur, T., Livneh, Z. & Shapiro, E. (2003). DNA molecule provides a computing machine with both data and fuel. PNAS 100(5), 2191-2196.
[8]  Bhargava, D. & Arora, D. (2008). Computer researchers harnessing DNA for computing. Proceeding of the 2nd National Conference; INDIAcom-2008, Bharati Vidyapeeth’s Institute of Computer Applications and Management, New Delhi.
[9]  Bonnet,J., Subsoontorn,P. & Endy,D. (2012). Rewritable digital data storage in live cells via engineered control of recombination directionality. PNAS 109 (23), 8884-8889.
[10]  Church, G.M., Gao, Y.S & Kosuri1, S. (2012). Next-generation digital information storage in DNA. Science 337 (6102), 1628.
[11]  Cui, G., Qin, L., Wnag, Y. & Zhang, X. (2008). An encryption scheme using DNA technology. Bio-Inspired Computing Theories and Applications, 2008. BICTA 3rd International conference. 37-42.
[12]  Deaton, R., Murphy, R.C., Garzon,M., Franceschetti, D. R. & Stevens, S. E. (1996). Good encodings for DNA-based solutions to combinatorial problems. ResearchGate. Retrieved from
[13]  Deng, Z. & Mao, C. (2003). DNA-templated fabrication of 1D parallel and 2D crossed metallic nanowire arrays. Nano Letters 3 (11), 1545-1548.
[14]  Dimitrova, N. (2006). The many strands of DNA. In W.Verhaegh, E. Aarts, & J. Korst (Eds.), Intelligent Algorithms in Ambient and Biomedical Computing (pp. 21-35). Dordrecht, The Netherlands: Springer.
[15]  Dittmer, W.U. & Simmel, F.C. (2004). Transcriptional control of DNA-based nanomachines. Nano Letters 4(4), 689-691.
[16]  Dwyer, C., Poulton,J., Taylor,R. & Vicci, L. (2004). DNA self-assembled parallel computer architectures. Nanotechnology15 (2004), 1688-1694.
[17]  Ezziane, Z. (2005). DNA computing: applications and challenges. Nanotechnology, 17 (2006) R27-R39.
[18]  Feynman, R.P. (1961). There’s plenty of room at the bottom. Miniaturization, pages 282-296.
[19]  Georgalis, Dr.E. E. (2016). A new economic era in computer science: DNA vs quantum computing. Journal of Research in Business, Economics and Management, 6(1) 822-834.
[20]  Kari, L. (1997). DNA computing: arrival of biological mathematics. The Mathematical Intelligencer 19(2), 9-22.
[21]  Kari, L. & Landweber, L.F. (1999). Computing with DNA. In S. Misener & S. A. Krawetz (Eds.), Bioinformatics Methods and Protocols ( pp. 413-430). Totowa, NJ: Humana Press.
[22]  Kim, I., Jeng, D.J. & Watada, J. (2006). Redesigning subgroups in a personnel network based on DNA computing. International Journal of Innovative Computing, Information and Control, 2(4), 885-896.
[23]  LaBean, T.H. & Li,. H (2007). Constructing novel materials with DNA. Nanotoday 2(2), 26-35.
[24]  Leier, A., Richter,C., Banzhaf,W. & Rauhe, H. (2000). Cryptography with DNA binary strands. Biosystems 57 (2000), 13-22.
[25]  Li, Z., Chen,Y., Li, X., Kamins, T.I., Nauka, K. & Williams, R.S. (2004). Sequence-specific label-free DNA sensors based on silicon nanowires. Nano Letters 4 (2), 245-247.
[26]  Lipton, R.J. (1995a). Speeding up computation via molecular biology. DNA Based Computers. Retrived from
[27]  Lipton, R.J. (1995b). Using DNA to solve NP-Complete problems. Semantic Scholar. Retrived from
[28]  Liu, D., Park, S.H., Reif, J.H. & LaBean, T.H. (2004). DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. PNAS 101 (3), 717-722.
[29]  Ma, Y., Zhang, J., Zhang, G. & He,H. (2004). Polyaniline nanowires on Si surfaces fabricated with DNA templates. . Journal of the American Chemical Society126 (22), 7097-7101.
[30]  Mbindyo,J.K.N., Reiss,B.D., Martin,B.R., Keating,C.D., Natan,M.J. and Mallouk,T.E. (2001). DNA-directed assembly of gold nanowires on complementary surfaces. Advanced Materials 13 (4), 249-254.
[31]  Monson, C.F. & Woolley, A.T. (2003). DNA-templated construction of copper nanowires. Nano Letters 3 (3), 559-563.
[32]  Nordiana Rajaee, Azham Zulkharnain & Awang Ahmad Sallehin Awang Hussaini.(2016). Basic architecture and applications of DNA computing. Transactions on Science and Technology, 3(1-2), 277-282.
[33]  Park, S.H., Yan. H., Reif, J.H., LaBean,T.H. & Finkelstein, G. (2004). Electronic nanostructures templated on self-assembled DNA scaffolds. Nanotechnology 15 (10), S525-S527.
[34]  Park, S.H., Barish, R., Li,H., Reif, J.H., Finkelstein, G., Yan,H. & LaBean, T.H. (2005). Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires. Nano Letters 5 (4), 693-696.
[35]  Pinheiro, A.V., Han, D., Shih, W.M. & Hao Yan,H.(2011). Challenges and opportunities for structural DNA nanotechnology. Nature Nano Technology 6(2011), 763-772.
[36]  Pray, L. (2008). Discovery of DNA structure and function: Watson and Crick. Nature Education 1 (1), 100.
[37]  Ranalkar, R.H. and Phulpagar, B.D (2014). DNA based cryptography in multi-cloud: security Strategy and analysis. International Journal of Emerging Trends & Technology in Computer Science (IJETTCS) 3(2), 189-192.
[38]  Reif J.H., LaBean T.H. & Seeman N.C. (2001). Challenges and applications for self-assembled DNA nanostructures. In: Condon A., & Rozenberg G. (Eds.), DNA Computing. DNA 2000. Lecture Notes in Computer Science 2054(pp. 173-198).Berlin, Heidelberg: Springer.
[39]  Richtar,J., Merting,M. & Pompe, W. (2001). Construction of highly conductive nanowires on a DNA template. Applied Physics Letters 78 (4), 536-538.
[40]  Sherman, W.B. & Seeman, N.C. (2004). A precisely controlled DNA biped walking device. Nano Letters 4 (7), 1203-1207.
[41]  Shin, J. & Pierce, N.A. (2004a). Rewritable memory by controllable nanopatterning of DNA. Nano Letters 4 (5), 905-909.
[42]  Shin, J. & Pierce, N.A (2004b). A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 129 (35), 10834-10835.
[43]  Siddhant Shrivastava & Rohan Badlani (2014). Data Storage in DNA. International Journal of Electrical Energy 2 (2), 119-124.
[44]  Staden,R. (1980). A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Research 8 (16), 3673-3694.
[45]  Tagore S, Bhattacharya S, Islam MA & Islam ML (2010). DNA computation: applications and perspectives. Journal of Proteomics & Bioinformatics, 3(7) 234-243.
[46]  Tian, T. & Mao,C.(2004). Molecular gears: A pair of DNA circles continuously rolls against each. Journal of the American Chemical Society 126(37), 11410-11411.
[47]  Walsh, F., Balasubramaniam, S., Botvich, D., Suda, T., Nakano, T., Bush, S.F., & Foghlú, M.O. (2009). Hybrid DNA and enzyme based computing for address encoding, link switching and error correction in molecular communication. In: Cheng M. (Eds.). Nano Net 2008. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, 3(pp. 28-38). Berlin, Heidelberg: Springer.
[48]  Walsh, F., Balasubramaniam, S., Botvitch, D. & Donnelly, W. (2010). Synthetic protocols for nano sensor transmitting platforms using enzyme and DNA based computing. Nano Communication Networks 1(2010), 50-62.
[49]  Watada, J. (2008). DNA computing and its application. Computational intelligence: a compendium (pp. 1065-1089). Springer Berlin Heidelberg.
[50]  Watada, J. & Rohani Abu Bakar. (2008). DNA computing and its applications. Eighth International Conference on Intelligent Systems Design and Applications, 2, 288-294.
[51]  Watson, J.D. & Crick F. H. C. (1953). The structure of DNA. Cold Spring Harbor Symposia on Quantitative Biology, 18: 123-131.
[52]  Xia, F., Guo, W., Mao,Y., Hou, X., Xue, J., Xia, H., ……. Jiang, L. (2008). Gating of single synthetic nanopores by proton-driven DNA molecular motors. Journal of the American Chemical Society130 (26), 8345-8350.
[53]  Yachie, N., Sekiyama, K., Sugahara, J., Ohashi, Y. & Tomita, T. (2007). Alignment-based approach for durable data storage into living organisms. Biotechnology Progress 23 (2), 501-505.
[54]  Yan, H., LaBean, T.H., Feng, L. & Reif, J. (2003). Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. PNAS 100(14), 8103-8108.
[55]  Zhang, B.T. & Kim, J.K (2006). DNA hypernetworks for information storage and retrieval. In: Mao C., & Yokomori T. (Eds.), DNA Computing. DNA 2006. Lecture Notes in Computer Science, 4287. (pp. 298-307).Berlin, Heidelberg: Springer.