DNA logic programming: Fromconcept to construction

Yi Zhang , Ning Hu , Jiajie Xu , Zhen Wang

VIEW ›› 2024, Vol. 5 ›› Issue (1) : 20230062

PDF
VIEW ›› 2024, Vol. 5 ›› Issue (1) : 20230062 DOI: 10.1002/VIW.20230062
REVIEW

DNA logic programming: Fromconcept to construction

Author information +
History +
PDF

Abstract

DNA programming, which is based on the principle of base complementary pairing and Boolean operations, exhibits organizational structures and algorithms similar to those observed in machine language. Consequently, the practical implementation of DNA logic programming can be achieved through the utilization of programming techniques, enabling the discrimination and output generation. In recent years, DNA programming has witnessed a convergence with disciplines, such as life sciences, medicine, and other interdisciplinary areas, thereby giving rise to an advanced research system that yields valuable insights. This development has paved the way for multidisciplinary cutting-edge research. Furthermore, the successful transition from conceptualization to the practical implementation of DNA programming has been accomplished. This review summarizes the recent advances in DNA logic programming within the biomedical fields, specifically emphasizing the conceptualization and execution of DNA logic programming constructs. The benefits and obstacles associated with the adoption of DNA programming in cutting-edge research areas are also highlighted.

Keywords

biological storage / circuit / gene edition / logic programming

Cite this article

Download citation ▾
Yi Zhang, Ning Hu, Jiajie Xu, Zhen Wang. DNA logic programming: Fromconcept to construction. VIEW, 2024, 5(1): 20230062 DOI:10.1002/VIW.20230062

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

A. Sgro, P. Blancafort, Nucleic. Acids. Res. 2020, 48, 12453.

[2]

J. Larouche, C. A. Aguilar, Trends Biotechnol. 2019, 37, 604.

[3]

P. Miao, Y. Tang, B. Wang, F. Meng, Anal. Chem. 2016, 88, 7567.

[4]

Y. Peng, W. Zhou, R. Yuan, Y. Xiang, Sensors Actuators B Chem. 2018, 264, 202.

[5]

J. Fortin, D. E. Rogge, C. Fellner, D. Flotzinger, J. Grond, K. Lerche, B. Saugel, Nat. Commun. 2021, 12, 1387.

[6]

P. Miggiels, B. Wouters, G. J. P. van Westen, A.-C. Dubbelman, T. Hankemeier, TrAC Trends Anal. Chem. 2019, 120, 115323.

[7]

C. Ronco, R. Bellomo, Crit. Care 2022, 26, 135.

[8]

N. P. Pai, A. Karellis, J. Kim, T. Peter, Lancet HIV 2020, 7, e574.

[9]

J. Li, Q. Wang, Y. Han, L. Jiang, S. Lu, B. Wang, W. Qian, M. Zhu, H. Huang, P. Qian, J. Hematol. Oncol. 2023, 16, 65.

[10]

J. Ouyang, A. Xie, J. Zhou, R. Liu, L. Wang, H. Liu, N. Kong, W. Tao, Chem. Soc. Rev. 2022, 51, 4996.

[11]

J. V Rau, R. De Santis, G. Ciofani, Bioact. Mater 2017, 2, 119.

[12]

N. C. Seeman, H. F. Sleiman, Nat. Rev. Mater. 2017, 3, 17068.

[13]

D. Wu, J. Zhou, M. N. Creyer, W. Yim, Z. Chen, P. B. Messersmith, J. V. Jokerst, Chem. Soc. Rev. 2021, 50, 4432.

[14]

A. Ebrahimi, H. Ravan, S. Khajouei, TrAC Trends Anal. Chem. 2019, 114, 126.

[15]

Q. Hu, H. Li, L. Wang, H. Gu, C. Fan, Chem. Rev. 2019, 119, 6459.

[16]

S. Kotani, W. L. Hughes, J. Am. Chem. Soc. 2017, 139, 6363.

[17]

V. Kumar, S. Palazzolo, S. Bayda, G. Corona, G. Toffoli, F. Rizzolio, Theranostics 2016, 6, 710.

[18]

F. Li, J. Li, B. Dong, F. Wang, C. Fan, X. Zuo, Chem. Soc. Rev. 2021, 50, 5650.

[19]

L. M. Adleman, Science 1994, 266, 1021.

[20]

M. N. Stojanovic, T. E. Mitchell, D. Stefanovic, J.Am. Chem. Soc. 2002, 124, 3555.

[21]

A. Okamoto, K. Tanaka, I. Saito, J. Am. Chem. Soc. 2004, 126, 9458.

[22]

S. Bi, Y. Yan, S. Hao, S. Zhang, Angew. Chemie. Int. Ed. 2010, 49, 4438.

[23]

S. Chen, Z. Xu, W. Yang, X. Lin, J. Li, J. Li, H. Yang, Angew. Chemie. Int. Ed. 2019, 58, 18186.

[24]

J. Dong, M. Wang, Y. Zhou, C. Zhou, Q. Wang, Angew. Chemie. Int. Ed. 2020, 59, 15038.

[25]

A. Lake, S. Shang, D. M. Kolpashchikov, Angew. Chemie. Int. Ed. 2010, 49, 4459.

[26]

J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, D. Endy, Science 2013, 340, 599.

[27]

R. Liu, Y. Han, F. Sun, G. Khatri, J. Kwon, C. Nickle, L. Wang, C.-K. Wang, D. Thompson, Z.-L. Li, C. A. Nijhuis, E. del Barco, Adv. Mater. 2022, 34, 2202135.

[28]

G. Seelig, D. Soloveichik, D. Y. Zhang, E. Winfree, Science 2006, 314, 1585.

[29]

A. A. K Nielsen, B. S. Der, J. Shin, P. Vaidyanathan, V. Paralanov, E. A. Strychalski, D. Ross, D. Densmore, C. A. Voigt, Science 2016, 352, aac7341.

[30]

R. Peng, X. Zheng, Y. Lyu, L. Xu, X. Zhang, G. Ke, Q. Liu, C. You, S. Huan, W. Tan, J. Am. Chem. Soc. 2018, 140, 9793.

[31]

H. Wang, J. Zheng, Y. Sun, T. Li, Biosens. Bioelectron. 2018, 117, 729.

[32]

B. M. G Janssen, M. van Rosmalen, L. van Beek, M. Merkx, Angew. Chemie. Int. Ed. 2015, 54, 2530.

[33]

M. Chen, C. Wang, Z. Ding, H. Wang, Y. Wang, Z. Liu, ACSCent. Sci. 2022, 8, 837.

[34]

Y. Du, P. Peng, T. Li, ACS Nano 2019, 13, 5778.

[35]

Y. Guo, J. Ren, E. Wang, Nano Today 2022, 44, 101476.

[36]

M. You, G. Zhu, T. Chen, M. J. Donovan, W. Tan, J. Am. Chem. Soc. 2015, 137, 667.

[37]

Y. L. Vishweshwaraiah, J. Chen, V. R. Chirasani, E. D. Tabdanov, N. V Dokholyan, Nat. Commun. 2021, 12, 6615.

[38]

H. Pei, L. Liang, G. Yao, J. Li, Q. Huang, C. Fan, Angew. Chemie. Int. Ed. 2012, 51, 9020.

[39]

T. Tian, T. Zhang, S. Shi, Y. Gao, X. Cai, Y. Lin, Nat. Protoc. 2023, 18, 1028.

[40]

R. M. Zadegan, M. D. E. Jepsen, L. L. Hildebrandt, V. Birkedal, J. Kjems, Small 2015, 11, 1811.

[41]

C. Zhou, H. Geng, P. Wang, C. Guo, Small 2019, 15, 1903489.

[42]

A. A. Tregubov, P. I. Nikitin, M. P. Nikitin, Chem. Rev. 2018, 118, 10294.

[43]

H. Lv, N. Xie, M. Li, M. Dong, C. Sun, Q. Zhang, L. Zhao, J. Li, X. Zuo, H. Chen, F. Wang, C. Fan, Nature 2023, 622, 292.

[44]

B. Shlyahovsky, Y. Li, O. Lioubashevski, J. Elbaz, I. Willner, ACS Nano 2009, 3, 1831.

[45]

D. Hartmann, R. Chowdhry, J. M. Smith, M. J. Booth, J. Am. Chem. Soc. 2023, 145, 9471.

[46]

M. Massey, I. L. Medintz, M. G. Ancona, W. R. Algar, ACS Sensors 2017, 2, 1205.

[47]

A. D’Urso, A. Mammana, M. Balaz, A. E. Holmes, N. Berova, R. Lauceri, R. Purrello, J. Am. Chem. Soc. 2009, 131, 2046.

[48]

D. Miyoshi, M. Inoue, N. Sugimoto, Angew. Chemie. Int. Ed. 2006, 45, 7716.

[49]

L. Wang, S. Tang, L. Li, K. Jin, X. Xie, Y. Chen, K. Cai, J. Zhang, Adv. Sens. Res. 2023, 2, 2200062.

[50]

Y. Yang, Q. Huang, Z. Xiao, M. Liu, Y. Zhu, Q. Chen, Y. Li, K. Ai, Mater Today Bio. 2022, 13, 100218.

[51]

K. Morihiro, N. Ankenbruck, B. Lukasak, A. Deiters, J. Am. Chem. Soc. 2017, 139, 13909.

[52]

D. Y. Tam, Z. Dai, M. S. Chan, L. S. Liu, M. C. Cheung, F. Bolze, C. Tin, P. K. Lo, Angew. Chemie. Int. Ed. 2016, 55, 164.

[53]

X. Song, C. Yang, R. Yuan, Y. Xiang, Biosens. Bioelectron 2022, 202, 114000.

[54]

K. E. Bujold, A. Lacroix, H. F. Sleiman, Chem. 2018, 4, 495.

[55]

M. Xiao, W. Lai, T. Man, B. Chang, L. Li, A. R. Chandrasekaran, H. Pei, Chem. Rev. 2019, 119, 11631.

[56]

W. Deng, J. Y. Xu, H. Peng, C. Z. Huang, X. C. Le, H. Zhang, Biosens. Bioelectron. 2022, 217, 114704.

[57]

E. A. Pumford, J. Lu, I. Spaczai, M. E. Prasetyo, E. M. Zheng, H. Zhang, D. T. Kamei, Biosens. Bioelectron 2020, 170, 112674.

[58]

Z. Huang, L. Qiu, T. Zhang, W. Tan, Matter 2021, 4, 461.

[59]

L. Chen, W. Chen, G. Liu, J. Li, C. Lu, J. Li, W. Tan, H. Yang, Chem. Soc. Rev. 2021, 50, 12551.

[60]

C. Zhu, F. Zhang, H. Li, Z. Chen, M. Yan, L. Li, F. Qu, TrAC Trends Anal. Chem. 2023, 158, 116775.

[61]

H. Chen, Z. Yan, S. Wu, F. Li, Colloids Surfaces B Biointerfaces 2021, 205, 111902.

[62]

D. X. Wang, J. Wang, Y. X. Wang, Y. C. Du, Y. Huang, A. N. Tang, Y. X. Cui, D. M. Kong, Chem. Sci. 2021, 12, 7602.

[63]

M. Cao, X. Xiong, Y. Zhu, M. Xiao, L. Li, H. Pei, TrAC Trends Anal. Chem. 2023, 159, 116911.

[64]

S. Yue, Z. Qiao, X. Wang, S. Bi, Chem. Eng. J. 2022, 446, 136838.

[65]

Z. Yang, N. Wang, H. Wen, R. Cui, J. Yu, S. Yang, T. Qu, X. Wang, S. He, J. Qi, J. Wang, Q. Ye, Y. Liu, Sensors Actuators B Chem. 2019, 298, 126901.

[66]

S. J. Smith, C. R. Nemr, S. O. Kelley, J. Am. Chem. Soc. 2017, 139, 1020.

[67]

A. Bertschi, P. Wang, S. Galvan, A. P. Teixeira, M. Fussenegger, Nat. Chem. Biol. 2023, 19, 767.

[68]

F. Deng, J. Pan, Z. Liu, L. Zeng, J. Chen, Biosens. Bioelectron. 2023, 223, 115025.

[69]

X. Huang, E. Kon, X. Han, X. Zhang, N. Kong, M. J. Mitchell, D. Peer, W. Tao, Nat. Nanotechnol. 2022, 17, 1027.

[70]

T. Masubuchi, M. Endo, R. Iizuka, A. Iguchi, D. H. Yoon, T. Sekiguchi, H. Qi, R. Iinuma, Y. Miyazono, S. Shoji, T. Funatsu, H. Sugiyama, Y. Harada, T. Ueda, H. Tadakuma, Nat. Nanotechnol. 2018, 13, 933.

[71]

S. Matsuura, H. Ono, S. Kawasaki, Y. Kuang, Y. Fujita, H. Saito, Nat. Commun. 2018, 9, 4847.

[72]

M. W. Gander, J. D. Vrana, W. E. Voje, J. M. Carothers, E. Klavins, Nat. Commun. 2017, 8, 15459.

[73]

L. Oesinghaus, F. C. Simmel, Nat. Commun. 2019, 10, 2092.

[74]

Y. Hao, J. Li, Q. Li, L. Zhang, J. Shi, X. Zhang, A. Aldalbahi, L. Wang, C. Fan, F. Wang, Angew. Chemie. Int. Ed. 2020, 59, 20612.

[75]

W. Zhou, L. Hu, L. Ying, Z. Zhao, P. K. Chu, X.-F. Yu, Nat. Commun. 2018, 9, 5012.

[76]

F. Deng, J. Pan, M. Chen, Z. Liu, J. Chen, C. Liu, Sci. Total Environ. 2023, 881, 163465.

[77]

M. J. Mitchell, M. M. Billingsley, R. M. Haley, M. E. Wechsler, N. A. Peppas, R. Langer, Nat. Rev. Drug Discov. 2021, 20, 101.

[78]

Q. Liu, H.-B. Cheng, R. Ma, M. Yu, Y. Huang, L. Li, J. Zhao, Nano Today 2023, 48, 101747.

[79]

M. Lu, H. Xing, A. Zheng, Y. Huang, X.-J. Liang, Acc. Chem. Res. 2023, 56, 224.

[80]

M. Li, G. Yang, Y. Zheng, J. Lv, W. Zhou, H. Zhang, F. You, C. Wu, H. Yang, Y. Liu, J. Nanobiotechnology 2023, 21, 186.

[81]

Z. Liu, Z. Feng, M. Chen, J. Zhan, R. Wu, Y. Shi, Y. Xue, R. Liu, J.-J. Zhu, J. Zhang, Chem. Sci. 2023, 14, 4102.

[82]

N. Xie, M. Li, Y. Wang, H. Lv, J. Shi, J. Li, Q. Li, F. Wang, C. Fan, J. Am. Chem. Soc. 2022, 144, 9479.

[83]

Z. Weng, H. Yu, W. Luo, Y. Guo, Q. Liu, L. Zhang, Z. Zhang, T. Wang, L. Dai, X. Zhou, X. Han, L. Wang, J. Li, Y. Yang, G. Xie, ACS Nano 2022, 16, 3135.

[84]

X. Wang, Z. Mao, R. Chen, S. Li, S. Ren, J. Liang, Z. Gao, Biosens. Bioelectron. 2022, 211, 114336.

[85]

Q. Jiang, S. Yue, K. Yu, T. Tian, J. Zhang, H. Chu, Z. Cui, S. Bi, J Nanobiotechnology 2021, 19, 288.

[86]

P. Miao, X. Ma, L. Xie, Y. Tang, X. Sun, Z. Wen, Z. Wang, Nano Energy 2022, 92, 106781.

[87]

F. Pu, J. Ren, X. Qu, Adv. Mater. 2014, 26, 5742.

[88]

F. Yin, F. Wang, C. Fan, X. Zuo, Q. Li, VIEW 2021, 2, 20200038.

[89]

X. Tang, C. Feng, Q. Pan, F. Sun, X. Zhu, TrAC Trends Anal. Chem. 2021, 145, 116456.

[90]

L. Li, X. Chen, C. Cui, X. Pan, X. Li, H. S. Yazd, Q. Wu, L. Qiu, J. Li, W. Tan, J. Am. Chem. Soc. 2019, 141, 17174.

[91]

W. Ma, Y. Yang, J. Zhu, W. Jia, T. Zhang, Z. Liu, X. Chen, Y. Lin, Adv. Mater. 2022, 34, 2109609.

[92]

J. Chen, S. Fu, C. Zhang, H. Liu, X. Su, Small 2022, 18, 2108008.

[93]

J. Yang, R. Wu, Y. Li, Z. Wang, L. Pan, Q. Zhang, Z. Lu, C. Zhang, Nucleic. Acids. Res. 2018, 46, 8532.

[94]

H. Su, J. Xu, Q. Wang, F. Wang, X. Zhou, Nat. Commun. 2019, 10, 5390.

[95]

J. Liu, C. Zhang, J. Song, Q. Zhang, R. Zhang, M. Zhang, D. Han, W. Tan, Adv. Sci. 2023, 10, 2206343.

[96]

A. Doricchi, C. M. Platnich, A. Gimpel, F. Horn, M. Earle, G. Lanzavecchia, A. L. Cortajarena, L. M. Liz-Marzán, N. Liu, R. Heckel, R. N. Grass, R. Krahne, U. F. Keyser, D. Garoli, ACS Nano 2022, 16, 17552.

[97]

Y. Hao, Q. Li, C. Fan, F. Wang, Small Struct. 2021, 2, 2000046.

[98]

S. Wang, X. Mao, F. Wang, X. Zuo, C. Fan, Adv.Mater. 2024, 34, 2309840.

[99]

L. Ceze, J. Nivala, K. Strauss, Nat. Rev. Genet. 2019, 20, 456.

[100]

B. Cao, X. Zhang, J. Wu, B. Wang, Q. Zhang, X. Wei, IEEE Trans. Nanobioscience 2021, 20, 212.

[101]

K. Z. Abram, Z. Udaondo, Microb. Biotechnol. 2023, 16, 1709.

[102]

C. K. Lim, S. Nirantar, W. S. Yew, C. L. Poh, Trends Biotechnol. 2021, 39, 990.

[103]

X. Chen, S. M. Argandona, F. Melle, N. Rampal, D. Fairen-Jimenez, Chem. 2023. https://doi.org/10.1016/j.chempr.2023.09.016

[104]

Y. Dong, F. Sun, Z. Ping, Q. Ouyang, L. Qian, Natl. Sci. Rev. 2020, 7, 1092.

[105]

L. Anavy, I. Vaknin, O. Atar, R. Amit, Z. Yakhini, Nat. Biotechnol. 2019, 37, 1229.

[106]

J. P. L Cox, Trends Biotechnol. 2001, 19, 247.

RIGHTS & PERMISSIONS

2023 The Authors. View published by Shanghai Fuji Technology Consulting Co., Ltd, authorized by Professional Community of Experimental Medicine, National Association of Health Industry and Enterprise Management (PCEM) and John Wiley & Sons Australia, Ltd.

AI Summary AI Mindmap
PDF

168

Accesses

0

Citation

Detail

Sections
Recommended

AI思维导图

/