Abstract
With silicon-based microelectronic technology pushed to its limit, scientists hunt to exploit biomolecules to power the bio-computer as substitutes. As a typical biomolecule, DNA now has been employed as a tool to create computing systems because of its superior parallel computing ability and outstanding data storage capability. However, the key challenges in this area lie in the human intervention during the computation process and the lack of platforms for central processor. DNA nanotechnology has created hundreds of complex and hierarchical DNA nanostructures with highly controllable motions by exploiting the unparalleled self-recognition properties of DNA molecule. These DNA nanostructures can provide platforms for central processor and reduce the human intervention during the computation process, which can offer unprecedented opportunities for biocomputing. In this review, recent advances in DNA nanotechnology are briefly summarized and the newly emerging concept of biocomputing with DNA nanostructures is introduced.
Similar content being viewed by others
References
Reif J. H., Science, 2002, 296(5567), 478
Feynman R. P., J. Microelectromech. Syst., 1992, 1(1), 60
Scerri E. R., Interface Focus, 2012, 2(1), 20
Benenson Y., Gil B., Ben-Dor U., Adar R., Shapiro E., Nature, 2004, 429(6990), 423
Seelig G., Soloveichik D., Zhang D. Y., Winfree E., Science, 2006, 314(5805), 1585
Douglas S. M., Bachelet I., Church G. M., Science, 2012, 335(6070), 831
Srinivas N., Ouldridge T. E., Sulc P., Schaeffer J. M., Yurke B., Louis A. A., Doye J. P. K., Winfree E., Nucleic Acids Res., 2013, 41(22), 10641
Vedral V., Plenio M. B., Progress in Quantum Electronics, 1998, 22(1), 1
Gao F., Niu H., Zhao H., Bioimaging, 1997, 5(2), 51
Liu Q. H., Wang L. M., Frutos A. G., Condon A. E., Corn R. M., Smith L. M., Nature, 2000, 403(6766), 175
Braich R. S., Chelyapov N., Johnson C., Rothemund P. W. K., Adleman L., Science, 2002, 296(5567), 499
He Y., Ye T., Su M., Zhang C., Ribbe A. E., Jiang W., Mao C. D., Nature, 2008, 452(7184), 198
Seeman N. C., J. Theor. Biol., 1982, 99(2), 237
Fu T. J., Seeman N. C., Biochemistry, 1993, 32(13), 3211
Winfree E., Liu F. R., Wenzler L. A., Seeman N. C., Nature, 1998, 394(6693), 539
Yan H., Zhang X. P., Shen Z. Y., Seeman N. C., Nature, 2002, 415(6867), 62
Kuzuya A., Wang R. S., Sha R. J., Seeman N. C., Nano Lett., 2007, 7(6), 1757
Wang Y. L., Mueller J. E., Kemper B., Seeman N. C., Biochemistry, 1991, 30(23), 5667
Ma R. I., Kallenbach N. R., Sheardy R. D., Petrillo M. L., Seeman N. C., Nucleic Acids Res., 1986, 14(24), 9745
LaBean T. H., Yan H., Kopatsch J., Liu F., Winfree E., Reif J. H., Seeman N. C., J. Am. Chem. Soc., 2000, 122(9), 1848
Shen Z. Y., Yan H., Wang T., Seeman N. C., J. Am. Chem. Soc., 2004, 126(6), 1666
Mao C. D., Sun W. Q., Seeman N. C., J. Am. Chem. Soc., 1999, 121(23), 5437
Ding B. Q., Sha R. J., Seeman N. C., J. Am. Chem. Soc., 2004, 126(33), 10230
Mao C. D., Sun W. Q., Seeman N. C., J. Am. Chem. Soc., 1999, 121(23), 5437
Liu D., Wang M. S., Deng Z. X., Walulu R., Mao C. D., J. Am. Chem. Soc., 2004, 126(8), 2324
He Y., Tian Y., Ribbe A. E., Mao C. D., J. Am. Chem. Soc., 2006, 128(50), 15978
Pistol C., Dwyer C., Nanotechnology, 2007, 18(12), 125305
Lund K., Liu Y., Yan H., Organic & Biomolecular Chemistry, 2006, 4(18), 3402
Park S. H., Finkelstein G., LaBean T. H., J. Am. Chem. Soc., 2008, 130(1), 40
Lund K., Liu Y., Lindsay S., Yan H., J. Am. Chem. Soc., 2005, 127(50), 17606
Park S. H., Pistol C., Ahn S. J., Reif J. H., Lebeck A. R., Dwyer C., LaBean T. H., Angew. Chem. Int. Ed., 2006, 45(5), 735
Mathieu F., Liao S. P., Kopatscht J., Wang T., Mao C. D., Seeman N. C., Nano Lett., 2005, 5(4), 661
Park S. H., Barish R., Li H. Y., Reif J. H., Finkelstein G., Yan H., LaBean T. H., Nano Lett., 2005, 5(4), 693
Ke Y. G., Liu Y., Zhang J. P., Yan H., J. Am. Chem. Soc., 2006, 128(13), 4414
Zhang C., Su M., He Y., Zhao X., Fang P. A., Ribbe A. E., Jiang W., Mao C. D., P. Natl. Acad. Sci. USA, 2008, 105(31), 10665
Zhang C., Ko S. H., Su M., Leng Y. J., Ribbe A. E., Jiang W., Mao C. D., J. Am. Chem. Soc., 2009, 131(4), 1413
Ke Y. G., Ong L. L., Shih W. M., Yin P., Science, 2012, 338(6111), 1177
Yin P., Hariadi R. F., Sahu S., Choi H. M. T., Park S. H., LaBean T. H., Reif J. H., Science, 2008, 321(5890), 824
Wei B., Dai M. J., Yin P., Nature, 2012, 485(7400), 623
Rothemund P. W. K., Nature, 2006, 440(7082), 297
Andersen E. S., Dong M. D., Nielsen M. M., Jahn K., Lind-Thomsen A., Mamdouh W., Gothelf K. V., Besenbacher F., Kjems J., ACS Nano, 2008, 2(6), 1213
Qian L. L., Wang Y., Zhang Z., Zhao J., Pan D., Zhang Y., Liu Q., Fan C. H., Hu J., He L., Chin. Sci. Bull., 2006, 51(24), 2973
Veneziano R., Ratanalert S., Zhang K. M., Zhang F., Yan H., Chiu W., Bathe M., Science, 2016, 352(6293), 4388
Han D. R., Pal S., Yang Y., Jiang S. X., Nangreave J., Liu Y., Yan H., Science, 2013, 339(6126), 1412
Han D. R., Pal S., Liu Y., Yan H., Nat. Nanotechnol., 2010, 5(10), 712
Ke Y. G., Sharma J., Liu M. H., Jahn K., Liu Y., Yan H., Nano Lett., 2009, 9(6), 2445
Dietz H., Douglas S. M., Shih W. M., Science, 2009, 325(5941), 725
Han D. R., Pal S., Nangreave J., Deng Z. T., Liu Y., Yan H., Science, 2011, 332(6027), 342
Gerling T., Wagenbauer K. F., Neuner A. M., Dietz H., Science, 2015, 347(6229), 1446
Modi S., Swetha M. G., Goswami D., Gupta G. D., Mayor S., Krishnan Y., Nat. Nanotechnol., 2009, 4(5), 325
Saha S., Prakash V., Halder S., Chakraborty K., Krishnan Y., Nat. Nanotechnol., 2015, 10(7), 645
Liu D. S., Balasubramanian S., Angew. Chem. Int. Ed., 2003, 42(46), 5734
Li S. P., Jiang Q., Liu S. L., Zhang Y. L., Tian Y. H., Song C., Wang J., Zou Y. G., Anderson G. J., Han J. Y., Chang Y., Liu Y., Zhang C., Chen L., Zhou G. B., Nie G. J., Yan H., Ding B. Q., Zhao Y. L., Nat. Biotechnol., 2018, 36(3), 258
Joshua D. B., Klavins E., Nano Lett., 2007, 7(9), 2574
Yin P., Yan H., Daniell X. G., Turberfield A. J., Reif J. H., Angew. Chem. Int. Ed., 2004, 43(37), 4906
Liu M. H., Fu J. L., Hejesen C., Yang Y. H., Woodbury N. W., Gothelf K., Liu Y., Yan H., Nat. Commun., 2013, 4, 2127
Turek V. A., Chikkaraddy R., Cormier S., Stockham B., Ding T., Keyser U. F., Baumberg J. J., Adv. Funct. Mater., 2018, 28(25), 1706410
Kopperger E., List J., Madhira S., Rothfischer F., Lamb D. C., Simmel F. C., Science, 2018, 359, 296
Kuzyk A., Yang Y. Y., Duan X. Y., Stoll S., Govorov A. O., Sugiyama H., Endo M., Liu N., Nat. Commun., 2016, 7, 10591
Hernandez A. S., Misiunas K., Thacker V. V., Hemmig E. A., Keyser U. F., Nano Lett., 2014, 14(3), 1270
Kang H. Z., Liu H. P., Phillips J. A., Cao Z. H., Kim Y. M., Chen Y., Yang Z. Y., Li J. W., Tan W. H., Nano Lett., 2009, 9(7), 2690
Liu H. J., Xu Y., Li F. Y., Yang Y., Wang W. X., Song Y. L., Liu D. S., Angew. Chem. Int. Ed., 2007, 46(14), 2515
Mao C. D., Sun W. Q., Shen Z. Y., Seeman N. C., Nature, 1999, 397(6715), 144
Kay E. R., Leigh D. A., Zerbetto F., Angew. Chem. Int. Ed., 2007, 46(1/2), 72
Bath J., Turberfield A. J., Nat. Nanotechnol., 2007, 2(5), 275
Yurke B., Turberfield A. J., Mills A. P., Simmel F. C., Neumann J. L., Nature, 2000, 406(6796), 605
Simmel F. C., Yurke B., Appl. Phys. Lett., 2002, 80(5), 883
Tian Y., Mao C. D., J. Am. Chem. Soc., 2004, 126(37), 11410
Engelen W., Meijer L. H., Somers B., de Greef T. F., Merkx M., Nat. Commun., 2017, 8, 14473
Shin J. S., Pierce N. A., J. Am. Chem. Soc., 2004, 126(35), 10834
Gu H. Z., Chao J., Xiao S. J., Seeman N. C., Nature, 2010, 465(7295), 202
Kosuri P., Altheimer B. D., Dai M., Yin P., Zhuang X., Nature, 2019, 572(7767), 136
Zhang C., Ma L. N., Dong Y. F., Yang J., Xu J., Chin. Sci. Bull., 2013, 58(1), 32
Li W., Yang Y., Yan H., Liu Y., Nano Lett., 2013, 13(6), 2980
Zadegan R. M., Jepsen M. D. E., Hildebrandt L. L., Birkedal V., Kjems J., Small, 2015, 11(15), 1811
Yang J., Wu R. F., Li Y. F., Wang Z. Y., Pan L. Q., Zhang Q., Lu Z. H., Zhang C., Nucleic Acids Res., 2018, 46(16), 8532
Chen J., Pan J., Chen S., Chemical Science, 2018, 9(2), 300
McCulloch W. S., Pitts W. H., Bull. Math. Biol., 1943, 52(1/2), 99
Qian L. L., Winfree E., Science, 2011, 332(6034), 1196
Qian L. L., Winfree E., Bruck J., Nature, 2011, 475(7356), 368
Cherry K. M., Qian L. L., Nature, 2018, 559(7714), 370
Elbaz J., Lioubashevski O., Wang F., Remacle F., Levine R. D., Willner I., Nat. Nanotechnol., 2010, 5(6), 417
Song T. Q., Garg S., Mokhtar R., Bui H., Reif J., ACS Synthetic Biology, 2016, 5(8), 898
Song T. Q., Eshra A., Shah S., Bui H., Fu D., Yang M., Mokhtar R., Reif J., Nat. Nanotechnol., 2019, 14(11), 1075
Liu H. J., Wang J. B., Song S. P., Fan C. H., Gothelf K. V., Nat. Commun., 2015, 6, 10089
Winfree E., J. Biomol. Struct. Dyn., 2000, 17(Suppl. 1), 263
Mao C. D., LaBean T. H., Reif J. H., Seeman N. C., Nature, 2000, 407(6807), 493
Yan H., LaBean T. H., Feng L. P., Reif J. H., P. Natl. Acad. Sci. USA, 2003, 100(14), 8103
Rothemund P. W. K., Papadakis N., Winfree E., PLoS Biol., 2004, 2(12), 2041
Winfree E., Bekbolatov R., DNA Computing, Madison, 2004, 126
Fujibayashi K, Murata S., DNA Computing, Milan, 2005, 113
Tikhomirov G., Petersen P., Qian L. L., Nature, 2017, 552(7683), 67
Brun Y., Theoretical Computer Science, 2007, 378(1), 17
Tikhomirov G., Petersen P., Qian L. L., Nat. Nanotechnol., 2017, 12(3), 251
Woods D., Doty D., Myhrvold C., Hui J., Zhou F., Yin P., Winfree E., Nature, 2019, 567(7748), 366
Liu Q. H., Frutos A. G., Thiel A. J., Corn R. M., Smith L. M., J. Comput. Biol., 1998, 5(2), 269
Boemo M. A., Lucas A. E., Turberfield A. J., Cardelli L., ACS Synthetic Biology, 2016, 5(8), 878
Chatterjee G., Dalchau N., Muscat R. A., Phillips A., Seelig G., Nat. Nanotechnol., 2017, 12(9), 920
Cha T. G., Pan J., Chen H. R., Salgado J., Li X., Mao C. D., Choi J. H., Nat. Nanotechnol., 2014, 9(1), 39
Wickham S. F. J., Bath J., Katsuda Y., Endo M., Hidaka K., Sugiyama H., Turberfield A. J., Nat. Nanotechnol., 2012, 7(3), 169
Douglas S. M., Bachelet I., Church G. M., Science, 2012, 335(6070), 831
Thubagere A. J., Li W., Johnson R. F., Chen Z., Doroudi S., Lee Y. L., Izatt G., Wittman S., Srinivas N., Woods D., Winfree E., Qian L. L., Science, 2017, 357(6356), 6558
Chao J., Wang J. B., Wang F., Ouyang X. Y., Kopperger E., Liu H. J., Li Q., Shi J. Y., Wang L. H., Hu J., Wang L. H., Huang W., Simmel F. C., Fan C. H., Nature Mater., 2019, 18(3), 273
Author information
Authors and Affiliations
Corresponding author
Additional information
Supported by the National Natural Science Foundation of China(Nos.21922408 and 61771253) and the Natural Science Foundation of Jiangsu Province for Distinguished Young Scholars, China(No.BK20190038).
Rights and permissions
About this article
Cite this article
Yin, J., Wang, J., Niu, R. et al. DNA Nanotechnology-based Biocomputing. Chem. Res. Chin. Univ. 36, 219–226 (2020). https://doi.org/10.1007/s40242-020-9086-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s40242-020-9086-5