Abstract
Engineering DNA logic systems is considered as one of the most promising strategies for next-generation molecular computers. Owing to the inherent features of DNA, such as low cost, easy synthesis, and controllable hybridization, various DNA logic devices with different functions have been developed in the recent decade. Besides, a variety of logic-programmed biological applications are also explored, which initiates a new chapter for DNA logic computing. Although this field has gained rapid developments, a systematical review that could not only elaborate the logic principles of diverse DNA logic devices but also outline recent representative works is urgently needed. In this review, we first elaborate the general classification and logical principle of diverse DNA logic devices, in which the operating strategy of these devices and representative examples are selectively presented. Then, we review state-of-the-art advancements in DNA computing based on different non-canonical DNA-nanostructures during the past decade, in which some classical works are summarized. After that, the innovative applications of DNA computing to logic-controlled bioanalysis, cell imaging, and drug load/delivery are selectively presented. Finally, we analyze current obstacles and suggest appropriate prospects for this area.
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References
Shapiro E, Gil B. Nat Nanotech, 2007, 2: 84–85
de Silva AP, Uchiyama S. Nat Nanotech, 2009, 2: 399–410
de Silva PA, Gunaratne NHQ, McCoy CP. Nature, 1993, 364: 42–44
Andréasson J, Pischel U. Chem Soc Rev, 2010, 39: 174–188
Andréasson J, Pischel U. Chem Soc Rev, 2015, 44: 1053–1069
Erbas-Cakmak S, Kolemen S, Sedgwick AC, Gunnlaugsson T, James TD, Yoon J, Akkaya EU. Chem Soc Rev, 2018, 47: 2228–2248
Mailloux S, Guz N, Zakharchenko A, Minko S, Katz E. J Phys Chem B, 2014, 118: 6775–6784
Adleman LM. Science, 1994, 266: 1021–1024
Jones MR, Seeman NC, Mirkin CA. Science, 2015, 347: 1260901
Ma DL, He HZ, Chan DSH, Leung CH. Chem Sci, 2013, 4: 3366–3380
Xia F, Zuo X, Yang R, White RJ, Xiao Y, Kang D, Gong X, Lubin AA, Vallée-Bélisle A, Yuen JD, Hsu BYB, Plaxco KW. J Am Chem Soc, 2010, 132: 8557–8559
Ding B, Seeman NC. Science, 2006, 314: 1583–1585
Cherry KM, Qian L. Nature, 2018, 559: 370–376
Seelig G, Soloveichik D, Zhang DY, Winfree E. Science, 2006, 314: 1585–1588
Tang Q, Lai W, Wang P, Xiong X, Xiao M, Li L, Fan C, Pei H. Angew Chem Int Ed, 2021, 60: 15013–15019
Feng L, Lyu Z, Offenhäusser A, Mayer D. Angew Chem Int Ed, 2015, 54: 7693–7697
Breaker RR, Joyce GF. Chem Biol, 1994, 1: 223–229
Elbaz J, Lioubashevski O, Wang F, Remacle F, Levine RD, Willner I. Nat Nanotech, 2010, 5: 417–422
Orbach R, Remacle F, Levine RD, Willner I. Chem Sci, 2014, 5: 1074–1081
Harding BI, Pollak NM, Stefanovic D, Macdonald J. Nano Lett, 2019, 19: 7655–7661
Fan D, Wang E, Dong S. Chem Sci, 2017, 8: 1888–1895
Zhu J, Zhang L, Li T, Dong S, Wang E. Adv Mater, 2013, 25: 2440–2444
Fan D, Wang E, Dong S. Mater Horiz, 2017, 4: 924–931
Fan D, Wang J, Wang E, Dong S. Chem Sci, 2019, 10: 7290–7298
Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Chem Commun, 2016, 52: 179–182
D Huang, C Yang, Y Yao, J Li, C Guo, J Chen, Y Zhang, S Yang, Q Yang, Y Tang. Chem-Eur J, 2019, 25: 6996–7003
Du Y, Peng P, Li T. Chem Commun, 2018, 54: 6132–6135
Du Y, Peng P, Li T. ACS Nano, 2019, 13: 5778–5784
Li H, Guo S, Liu Q, Qin L, Dong S, Liu Y, Wang E. Adv Sci, 2015, 2: 1500054
Gao W, Zhang L, Zhang YM, Liang RP, Qiu JD. J Phys Chem C, 2014, 118: 14410–14417
Yin J, Wang J, Niu R, Ren S, Wang D, Chao J. Chem Res Chin Univ, 2020, 36: 219–226
Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ. Nat Nanotech, 2008, 3: 93–96
Zhou Z, Fan D, Willner I. ACS Nano, 2020, 14: 5046–5052
Arugula MA, Bocharova V, Halámek J, Pita M, Katz E. J Phys Chem B, 2010, 114: 5222–5226
Wu C, Wang K, Fan D, Zhou C, Liu Y, Wang E. Chem Commun, 2015, 51: 15940–15943
Fan D, Zhu J, Liu Y, Wang E, Dong S. Nanoscale, 2016, 8: 3834–3840
Andréasson J, Pischel U, Straight SD, Moore TA, Moore AL, Gust D. J Am Chem Soc, 2011, 133: 11641–11648
Bälter M, Li S, Nilsson JR, Andréasson J, Pischel U. J Am Chem Soc, 2013, 135: 10230–10233
Fan D, Wang K, Zhu J, Xia Y, Han Y, Liu Y, Wang E. Chem Sci, 2015, 6: 1973–1978
Fan D, Wang E, Dong S. Nano Res, 2017, 10: 2560–2569
Wang K, Ren J, Fan D, Liu Y, Wang E. Chem Commun, 2014, 50: 14390–14393
Orbach R, Wang F, Lioubashevski O, Levine RD, Remacle F, Willner I. Chem Sci, 2014, 5: 3381–3387
Margulies D, Melman G, Shanzer A. J Am Chem Soc, 2006, 128: 4865–4871
Chen J, Zhou S, Wen J. Angew Chem Int Ed, 2014, 54: 446–450
Pei H, Liang L, Yao G, Li J, Huang Q, Fan C. Angew Chem Int Ed, 2012, 51: 9020–9024
Lin Q, Wang A, Liu S, Li J, Wang J, Quan K, Yang X, Huang J, Wang K. Chem Commun, 2020, 56: 5303–5306
Rothemund PWK. Nature, 2006, 440: 297–302
Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM. Nature, 2009, 459: 414–418
Dietz H, Douglas SM, Shih WM. Science, 2009, 325: 725–730
Douglas SM, Bachelet I, Church GM. Science, 2012, 335: 831–834
Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G. Nat Nanotech, 2017, 12: 920–927
Fan D, Zhu J, Zhai Q, Wang E, Dong S. Chem Commun, 2016, 52: 3766–3769
Han D, Zhu Z, Wu C, Peng L, Zhou L, Gulbakan B, Zhu G, Williams KR, Tan W. J Am Chem Soc, 2012, 134: 20797–20804
Zhang S, Li KB, Shi W, Zhang J, Han DM, Xu JJ. Nanoscale, 2019, 11: 5048–5057
Woods D, Doty D, Myhrvold C, Hui J, Zhou F, Yin P, Winfree E. Nature, 2019, 567: 366–372
Chen S, Xu Z, Yang W, Lin X, Li J, Li J, Yang H. Angew Chem Int Ed, 2019, 58: 18186–18190
Chang X, Zhang C, Lv C, Sun Y, Zhang M, Zhao Y, Yang L, Han D, Tan W. J Am Chem Soc, 2019, 141: 12738–12743
Qu X, Wang S, Ge Z, Wang J, Yao G, Li J, Zuo X, Shi J, Song S, Wang L, Li L, Pei H, Fan C. J Am Chem Soc, 2017, 139: 10176–10179
Liao WC, Willner I. Adv Funct Mater, 2017, 27: 1702732
Chen WH, Luo GF, Sohn YS, Nechushtai R, Willner I. Adv Funct Mater, 2019, 29: 1805341
Chen WH, Yu X, Cecconello A, Sohn YS, Nechushtai R, Willner I. Chem Sci, 2017, 8: 5769–5780
Peng R, Zheng X, Lyu Y, Xu L, Zhang X, Ke G, Liu Q, You C, Huan S, Tan W. J Am Chem Soc, 2018, 140: 9793–9796
Zhang C, Zhao Y, Xu X, Xu R, Li H, Teng X, Du Y, Miao Y, Lin HC, Han D. Nat Nanotechnol, 2020, 15: 709–715
Wang J, Fan D, Jiang C, Lu L. Nano Today, 2021, 36: 101034
Li Z, Wang J, Chen Q, Ai K, Lu L. Sci China Chem, 2021, 64: 1389–1400
Yang L, Zhao Y, Xu X, Xu K, Zhang M, Huang K, Kang H, Lin HC, Yang Y, Han D. Angew Chem Int Ed, 2020, 59: 17697–17704
Gao Q, Zhao Y, Xu K, Zhang C, Ma Q, Qi L, Chao D, Zheng T, Yang L, Miao Y, Han D. Angew Chem Int Ed, 2020, 59: 23564–23568
Miao P, Tang Y. ACS Cent Sci, 2021, 7: 1036–1044
Zhu Z, Zhai Y, Li Z, Zhu P, Mao S, Zhu C, Du D, Belfiore LA, Tang J, Lin Y. Mater Today, 2019, 30: 52–79
Wang J, Li Z, Wang Y, Wei C, Ai K, Lu L. Mater Horiz, 2019, 6: 1517–1525
Wang J, Ai K, Lu L. J Mater Chem A, 2019, 7: 16850–16858
Fan D, Wang J, Wang E, Dong S. Adv Sci, 2020, 7: 2001766
Wang S, Sun J, Zhao J, Lu S, Yang X. Anal Chem, 2018, 90: 3437–3442
Acknowledgements
This work was supported by the National Natural Science Foundation of China (21427811, 21675151). Dr. D. Fan thanks the starting support from Ocean University of China.
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Fan, D., Wang, J., Han, J. et al. Engineering DNA logic systems with non-canonical DNA-nanostructures: basic principles, recent developments and bio-applications. Sci. China Chem. 65, 284–297 (2022). https://doi.org/10.1007/s11426-021-1131-1
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DOI: https://doi.org/10.1007/s11426-021-1131-1