DNA Nanotechnology-based Biocomputing

doi:10.1007/s40242-020-9086-5

Abstract

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. How-ever, 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.

Key words: DNA computing, DNA nanotechnology, DNA strand-displacement, Programmable self-assembly, DNA origami

YIN Jue, WANG Junke, NIU Renjie, REN Shaokang, WANG Dexu, CHAO Jie. DNA Nanotechnology-based Biocomputing[J]. Chemical Research in Chinese Universities, 2020, 36(2): 219-226.

References 103

[1]	Reif J. H., Science, 2002, 296(5567), 478
[2]	Feynman R. P., J. Microelectromech. Syst., 1992, 1(1), 60
[3]	Scerri E. R., Interface Focus, 2012, 2(1), 20
[4]	Benenson Y., Gil B., Ben-Dor U., Adar R., ShapiroE., Nature, 2004, 429(6990), 423
[5]	Seelig G., Soloveichik D., Zhang D. Y., Winfree E., Science, 2006, 314(5805), 1585
[6]	Douglas S. M., Bachelet I., Church G. M., Science, 2012, 335(6070), 831
[7]	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
[8]	Vedral V., Plenio M. B., Progress in Quantum Electronics, 1998, 22(1), 1
[9]	Gao F., Niu H., Zhao H., Bioimaging, 1997, 5(2), 51
[10]	Liu Q. H., Wang L. M., Frutos A. G., Condon A. E., Corn R. M., Smith L. M., Nature, 2000, 403(6766), 175
[11]	Braich R. S., Chelyapov N., Johnson C., Rothemund P. W. K., Adleman L., Science, 2002, 296(5567), 499
[12]	He Y., Ye T., Su M., Zhang C., Ribbe A. E., Jiang W., Mao C. D., Nature, 2008, 452(7184), 198
[13]	Seeman N. C., J. Theor. Biol., 1982, 99(2), 237
[14]	Fu T. J., Seeman N. C., Biochemistry, 1993, 32(13), 3211
[15]	Winfree E., Liu F. R., Wenzler L. A., Seeman N. C., Nature, 1998, 394(6693), 539
[16]	Yan H., Zhang X. P., Shen Z. Y., Seeman N. C., Nature, 2002, 415(6867), 62
[17]	Kuzuya A., Wang R. S., Sha R. J., Seeman N. C., Nano Lett., 2007, 7(6), 1757
[18]	Wang Y. L., Mueller J. E., Kemper B., Seeman N. C., Biochemistry, 1991, 30(23), 5667
[19]	Ma R. I., Kallenbach N. R., Sheardy R. D., Petrillo M. L., Seeman N. C., Nucleic Acids Res., 1986, 14(24), 9745
[20]	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
[21]	Shen Z. Y., Yan H., Wang T., Seeman N. C., J. Am. Chem. Soc., 2004, 126(6), 1666
[22]	Mao C. D., Sun W. Q., Seeman N. C., J. Am. Chem. Soc., 1999, 121(23), 5437
[23]	Ding B. Q., Sha R. J., Seeman N. C., J. Am. Chem. Soc., 2004, 126(33), 10230
[24]	Mao C. D, Sun W. Q., Seeman N. C., J. Am. Chem. Soc., 1999, 121(23), 5437
[25]	Liu D., Wang M. S., Deng Z. X., Walulu R., Mao C. D., J. Am. Chem. Soc., 2004, 126(8), 2324
[26]	He Y., Tian Y., Ribbe A. E., Mao C. D., J. Am. Chem. Soc., 2006, 128(50), 15978
[27]	Pistol C., Dwyer C., Nanotechnology, 2007, 18(12), 125305
[28]	Lund K., Liu Y., Yan H., Organic & Biomolecular Chemistry, 2006, 4(18), 3402
[29]	Park S. H., Finkelstein G., LaBean T. H., J. Am. Chem. Soc., 2008, 130(1), 40
[30]	Lund K., Liu Y., Lindsay S., Yan H., J. Am. Chem. Soc., 2005, 127(50), 17606
[31]	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
[32]	Mathieu F., Liao S. P., Kopatscht J., Wang T., Mao C. D., Seeman N. C., Nano Lett., 2005, 5(4), 661
[33]	Park S. H., Barish R., Li H. Y., Reif J. H., Finkelstein G., Yan H., LaBean T. H., Nano Lett., 2005, 5(4), 693
[34]	Ke Y. G., Liu Y., Zhang J. P., Yan H., J. Am. Chem. Soc., 2006, 128(13), 4414
[35]	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
[36]	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
[37]	Ke Y. G., Ong L. L., Shih W. M., Yin P., Science, 2012, 338(6111), 1177
[38]	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
[39]	Wei B., Dai M. J., Yin P., Nature, 2012, 485(7400), 623
[40]	Rothemund P. W. K., Nature, 2006, 440(7082), 297
[41]	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
[42]	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
[43]	Veneziano R., Ratanalert S., Zhang K. M., Zhang F., Yan H., Chiu W., Bathe M., Science, 2016, 352(6293), 4388
[44]	Han D. R., Pal S., Yang Y., Jiang S. X., Nangreave J., Liu Y., Yan H., Science, 2013, 339(6126), 1412
[45]	Han D. R., Pal S., Liu Y., Yan H., Nat. Nanotechnol., 2010, 5(10), 712
[46]	Ke Y. G., Sharma J., Liu M. H., Jahn K., Liu Y., Yan H., Nano Lett., 2009, 9(6), 2445
[47]	Dietz H., Douglas S. M., Shih W. M., Science, 2009, 325(5941), 725
[48]	Han D. R., Pal S., Nangreave J., Deng Z. T., Liu Y., Yan H., Science, 2011, 332(6027), 342
[49]	Gerling T., Wagenbauer K. F., Neuner A. M., Dietz H., Science, 2015, 347(6229), 1446
[50]	Modi S., Swetha M. G., Goswami D., Gupta G. D., Mayor S., Krishnan Y., Nat. Nanotechnol., 2009, 4(5), 325
[51]	Saha S., Prakash V., Halder S., Chakraborty K., Krishnan Y., Nat. Nanotechnol., 2015, 10(7), 645
[52]	Liu D. S., Balasubramanian S., Angew. Chem. Int. Ed., 2003, 42(46), 5734
[53]	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
[54]	Joshua D. B., Klavins E., Nano Lett., 2007, 7(9), 2574
[55]	Yin P., Yan H., Daniell X. G., Turberfield A. J., Reif J. H., Angew. Chem. Int. Ed., 2004, 43(37), 4906
[56]	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
[57]	Turek V. A., Chikkaraddy R., Cormier S., Stockham B., Ding T., Keyser U. F., Baumberg J. J., Adv. Funct. Mater., 2018, 28(25), 1706410
[58]	Kopperger E., List J., Madhira S., Rothfischer F., Lamb D. C., Simmel F. C., Science, 2018, 359, 296
[59]	Kuzyk A., Yang Y. Y., Duan X. Y., Stoll S., Govorov A. O., Sugiyama H., Endo M., Liu N., Nat. Commun., 2016, 7, 10591
[60]	Hernandez A. S., Misiunas K., Thacker V. V., Hemmig E. A., Keyser U. F., Nano Lett., 2014, 14(3), 1270
[61]	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
[62]	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
[63]	Mao C. D., Sun W. Q., Shen Z. Y., Seeman N. C., Nature, 1999, 397(6715), 144
[64]	Kay E. R., Leigh D. A., Zerbetto F., Angew. Chem. Int. Ed., 2007, 46(1/2), 72
[65]	Bath J., Turberfield A. J., Nat. Nanotechnol., 2007, 2(5), 275
[66]	Yurke B., Turberfield A. J., Mills A. P., Simmel F. C., Neumann J. L., Nature, 2000, 406(6796), 605
[67]	Simmel F. C., Yurke B., Appl. Phys. Lett., 2002, 80(5), 883
[68]	Tian Y., Mao C. D., J. Am. Chem. Soc., 2004, 126(37), 11410
[69]	Engelen W., Meijer L. H., Somers B., de Greef T. F., Merkx M., Nat. Commun., 2017, 8, 14473
[70]	Shin J. S., Pierce N. A., J. Am. Chem. Soc., 2004, 126(35), 10834
[71]	Gu H. Z., Chao J., Xiao S. J., Seeman N. C., Nature, 2010, 465(7295), 202
[72]	Kosuri P., Altheimer B. D., Dai M., Yin P., Zhuang X., Nature, 2019, 572(7767), 136
[73]	Zhang C., Ma L. N., Dong Y. F., Yang J., Xu J., Chin. Sci. Bull., 2013, 58(1), 32
[74]	Li W., Yang Y., Yan H., Liu Y., Nano Lett., 2013, 13(6), 2980
[75]	Zadegan R. M., Jepsen M. D. E., Hildebrandt L. L., Birkedal V., Kjems J., Small, 2015, 11(15), 1811
[76]	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
[77]	Chen J., Pan J., Chen S., Chemical Science, 2018, 9(2), 300
[78]	McCulloch W. S., Pitts W. H., Bull. Math. Biol., 1943, 52(1/2), 99
[79]	Qian L. L., Winfree E., Science, 2011, 332(6034), 1196
[80]	Qian L. L., Winfree E., Bruck J., Nature, 2011, 475(7356), 368
[81]	Cherry K. M., Qian L. L., Nature, 2018, 559(7714), 370
[82]	Elbaz J., Lioubashevski O., Wang F., Remacle F., Levine R. D., Willner I., Nat. Nanotechnol., 2010, 5(6), 417
[83]	Song T. Q., Garg S., Mokhtar R., Bui H., Reif J., ACS Synthetic Biology, 2016, 5(8), 898
[84]	Song T. Q., Eshra A., Shah S., Bui H., Fu D., Yang M., Mokhtar R., Reif J., Nat. Nanotechnol., 2019, 14(11),1075
[85]	Liu H. J., Wang J. B., Song S. P., Fan C. H., Gothelf K. V., Nat. Commun., 2015, 6, 10089
[86]	Winfree E., J. Biomol. Struct. Dyn., 2000, 17(Suppl. 1), 263
[87]	Mao C. D., LaBean T. H., Reif J. H., Seeman N. C., Nature, 2000, 407(6807), 493
[88]	Yan H., LaBean T. H., Feng L. P., Reif J. H., P. Natl. Acad. Sci. USA, 2003, 100(14), 8103
[89]	Rothemund P. W. K., Papadakis N., Winfree E., PLoS Biol., 2004, 2(12), 2041
[90]	Winfree E., Bekbolatov R., DNA Computing, Madison, 2004, 126
[91]	Fujibayashi K, Murata S., DNA Computing, Milan, 2005, 113
[92]	Tikhomirov G., Petersen P., Qian L. L., Nature, 2017, 552(7683), 67
[93]	Brun Y., Theoretical Computer Science, 2007, 378(1), 17
[94]	Tikhomirov G., Petersen P., Qian L. L., Nat. Nanotechnol., 2017, 12(3), 251
[95]	Woods D., Doty D., Myhrvold C., Hui J., Zhou F., Yin P., Winfree E., Nature, 2019, 567(7748), 366
[96]	Liu Q. H., Frutos A. G., Thiel A. J., Corn R. M., Smith L. M., J. Comput. Biol., 1998, 5(2), 269
[97]	Boemo M. A., Lucas A. E., Turberfield A. J., Cardelli L., ACS Synthetic Biology, 2016, 5(8), 878
[98]	Chatterjee G., Dalchau N., Muscat R. A., Phillips A., Seelig G., Nat. Nanotechnol., 2017, 12(9), 920
[99]	Cha T. G., Pan J., Chen H. R., Salgado J., Li X., Mao C. D., Choi J. H., Nat. Nanotechnol., 2014, 9(1), 39
[100]	Wickham S. F. J., Bath J., Katsuda Y., Endo M., Hidaka K., Sugiyama H., Turberfield A. J., Nat. Nanotechnol., 2012, 7(3), 169
[101]	Douglas S. M., Bachelet I., Church G. M., Science, 2012, 335(6070), 831
[102]	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
[103]	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