Integrating Ligands into Nucleic Acid Systems.
Biosensors
Gene Regulation
Ligand Integration
Nucleic Acid Nanomachines
Journal
Chembiochem : a European journal of chemical biology
ISSN: 1439-7633
Titre abrégé: Chembiochem
Pays: Germany
ID NLM: 100937360
Informations de publication
Date de publication:
15 09 2023
15 09 2023
Historique:
revised:
12
06
2023
received:
11
04
2023
medline:
18
9
2023
pubmed:
4
7
2023
entrez:
4
7
2023
Statut:
ppublish
Résumé
Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.
Identifiants
pubmed: 37401635
doi: 10.1002/cbic.202300292
doi:
Substances chimiques
Nucleic Acids
0
Ligands
0
Proteins
0
Oligonucleotides
0
Types de publication
Review
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e202300292Informations de copyright
© 2023 Wiley-VCH GmbH.
Références
Y. Zhu, J. Wu, Q. Zhou, Biosens. Bioelectron. 2023, 230, 115282;
R. M. Bialy, A. Mainguy, Y. Li, J. D. Brennan, Chem. Soc. Rev. 2022, 51, 9009-9067.
F. C. Simmel, B. Yurke, H. R. Singh, Chem. Rev. 2019, 119, 6326-6369;
D. Y. Zhang, G. Seelig, Nat. Chem. 2011, 3, 103-113;
A. Bertucci, A. Porchetta, E. Del Grosso, T. Patiño, A. Idili, F. Ricci, Angew. Chem. Int. Ed. 2020, 59, 20577-20581;
T. Heyduk, E. Heyduk, Nat. Biotechnol. 2002, 20, 171-176;
J. Liu, Z. Cao, Y. Lu, Chem. Rev. 2009, 109, 1948-1998.
J. D. Munzar, A. Ng, D. Juncker, Chem. Soc. Rev. 2019, 48, 1390-1419;
T. A. Feagin, N. Maganzini, H. T. Soh, ACS Sens. 2018, 3, 1611-1615;
F. Wang, X. Liu, I. Willner, Angew. Chem. Int. Ed. 2015, 54, 1098-1129;
D. K. Agrawal, R. Schulman, Nucleic Acids Res. 2020, 48, 6431-6444.
L. Wu, Y. Wang, X. Xu, Y. Liu, B. Lin, M. Zhang, J. Zhang, S. Wan, C. Yang, W. Tan, Chem. Rev. 2021, 121, 12035-12105;
M. Li, F. Yin, L. Song, X. Mao, F. Li, C. Fan, X. Zuo, Q. Xia, Chem. Rev. 2021, 121, 10469-10558;
H.-M. Meng, H. Liu, H. Kuai, R. Peng, L. Mo, X.-B. Zhang, Chem. Soc. Rev. 2016, 45, 2583-2602.
M. R. Dunn, R. M. Jimenez, J. C. Chaput, Nat. Chem. Rev. 2017, 1, 1-16;
L. Zhao, W. Tan, X. Fang, Aptamers Selected by Cell-SELEX for Theranostics 2015, 352, 1-11.
H. Yu, Z. Chen, Y. Liu, O. Alkhamis, Z. Song, Y. Xiao, Angew. Chem. 2021, 133, 3030-3037;
T. T.-Q. Nguyen, E. R. Kim, M. B. Gu, Biosens. Bioelectron. 2022, 198, 113835;
S. Lin, X. Cheng, J. Zhu, B. Wang, D. Jelinek, Y. Zhao, T.-Y. Wu, A. Horrillo, J. Tan, J. Yeung, Sci. Adv. 2022, 8, eabq4539;
Y. Li, Q. Zhao, Anal. Chem. 2019, 91, 7379-7384;
Z. Zhu, C. Ravelet, S. Perrier, V. r Guieu, E. Fiore, E. Peyrin, Anal. Chem. 2012, 84, 7203-7211;
Q. Zhao, J. Tao, J. S. Uppal, H. Peng, H. Wang, X. C. Le, TrAC Trends Anal. Chem. 2019, 110, 401-409;
H.-K. Walter, J. Bauer, J. Steinmeyer, A. Kuzuya, C. M. Niemeyer, H.-A. Wagenknecht, Nano Lett. 2017, 17, 2467-2472.
H. Ueyama, M. Takagi, S. Takenaka, J. Am. Chem. Soc. 2002, 124, 14286-14287;
M. N. Stojanovic, P. De Prada, D. W. Landry, J. Am. Chem. Soc. 2001, 123, 4928-4931;
C. J. Yang, S. Jockusch, M. Vicens, N. J. Turro, W. Tan, Proc. Nat. Acad. Sci. 2005, 102, 17278-17283.
M. N. Stojanovic, P. de Prada, D. W. Landry, J. Am. Chem. Soc. 2000, 122, 11547-11548;
A. E. Rangel, A. A. Hariri, M. Eisenstein, H. T. Soh, Adv. Mater. 2020, 32, 2003704;
L. Shen, T. Bing, X. Liu, J. Wang, L. Wang, N. Zhang, D. Shangguan, ACS Appl. Mater. Interfaces 2018, 10, 2312-2318.
A. Chen, M. Yan, S. Yang, TrAC Trends Anal. Chem. 2016, 80, 581-593.
R. Nutiu, Y. Li, J. Am. Chem. Soc. 2003, 125, 4771-4778;
R. Nutiu, Y. Li, Angew. Chem. Int. Ed. 2005, 44, 1061-1065;
P. S. Lau, B. K. Coombes, Y. Li, Angew. Chem. 2010, 122, 8110-8114;
Z. Wang, H. Yu, J. Canoura, Y. Liu, O. Alkhamis, F. Fu, Y. Xiao, Nucleic Acids Res. 2018, 46, e81-e81;
B. Li, A. D. Ellington, X. Chen, Nucleic Acids Res. 2011, 39, e110-e110;
R. Nutiu, Y. Li, Angew. Chem. Int. Ed. 2005, 44, 5464-5467;
D. Han, Z. Zhu, C. Wu, L. Peng, L. Zhou, B. Gulbakan, G. Zhu, K. R. Williams, W. Tan, J. Am. Chem. Soc. 2012, 134, 20797-20804;
J. H. Monserud, K. M. Macri, D. K. Schwartz, Angew. Chem. Int. Ed. 2016, 55, 13710-13713;
W. Yoshida, Y. Yokobayashi, Chem. Commun. 2007, 195-197.
M. Wieland, A. Benz, J. Haar, K. Halder, J. S. Hartig, Chem. Commun. 2010, 46, 1866-1868;
B. D. Wilson, A. A. Hariri, I. A. Thompson, M. Eisenstein, H. T. Soh, Nat. Commun. 2019, 10, 5079;
A.-X. Zheng, J.-R. Wang, J. Li, X.-R. Song, G.-N. Chen, H.-H. Yang, Biosens. Bioelectron. 2012, 36, 217-221;
J. Zhu, L. Zhang, Z. Zhou, S. Dong, E. Wang, Chem. Commun. 2014, 50, 3321-3323;
L. Yang, C. W. Fung, E. J. Cho, A. D. Ellington, Anal. Chem. 2007, 79, 3320-3329;
R. M. Dirks, N. A. Pierce, Proc. Nat. Acad. Sci. 2004, 101, 15275-15278;
Y. Xing, Z. Yang, D. Liu, Angew. Chem. Int. Ed. 2011, 50, 11934-11936.
L. A. Wurmthaler, M. Sack, K. Gense, J. S. Hartig, M. Gamerdinger, Nat. Commun. 2019, 10, 491;
A. Serganov, D. J. Patel, Nat. Rev. Genet. 2007, 8, 776-790;
K. Kavita, R. R. Breaker, Trends Biochem. Sci. 2022, 48, 119-141;
Z. F. Hallberg, Y. Su, R. Z. Kitto, M. C. Hammond, Annu. Rev. Biochem. 2017, 86, 515-539.
Z. Tang, P. Mallikaratchy, R. Yang, Y. Kim, Z. Zhu, H. Wang, W. Tan, J. Am. Chem. Soc. 2008, 130, 11268-11269;
E. J. Cho, J.-W. Lee, A. D. Ellington, Annu. Rev. Anal. Chem. 2009, 2, 241-264.
Y. Zhao, K. Yavari, J. Liu, TrAC Trends Anal. Chem. 2022, 146, 116480;
S. Liu, Y. Xu, X. Jiang, H. Tan, B. Ying, Biosens. Bioelectron. 2022, 208, 114168.
A. A. Green, J. Kim, D. Ma, P. A. Silver, J. J. Collins, P. Yin, Nature 2017, 548, 117-121;
G. Domin, S. Findeiß, M. Wachsmuth, S. Will, P. F. Stadler, M. Mörl, Nucleic Acids Res. 2017, 45, 4108-4119;
K. Fukunaga, V. Dhamodharan, N. Miyahira, Y. Nomura, K. Mustafina, Y. Oosumi, K. Takayama, A. Kanai, Y. Yokobayashi, J. Am. Chem. Soc. 2023, 145, 7820-7828;
S. K. Desai, J. P. Gallivan, J. Am. Chem. Soc. 2004, 126, 13247-13254.
Q.-L. Zhang, L.-L. Wang, Y. Liu, J. Lin, L. Xu, Nat. Commun. 2021, 12, 4654.
Q. L. Zhang, Y. Wang, L. L. Wang, F. Xie, R. Y. Wu, X. Y. Ma, H. Li, Y. Liu, S. Yao, L. Xu, Angew. Chem. 2023, 135, e202214698.
A. J. Genot, J. Bath, A. J. Turberfield, Angew. Chem. Int. Ed. 2013, 52, 1189-1192.
X. Chen, J. Am. Chem. Soc. 2012, 134, 263-271.
S. Zhao, L. Yu, S. Yang, X. Tang, K. Chang, M. Chen, Nanoscale Horiz. 2021, 6, 298-310;
F. Wang, C.-H. Lu, I. Willner, Chem. Rev. 2014, 114, 2881-2941;
Z. Li, C. Wang, J. Li, J. Zhang, C. Fan, I. Willner, H. Tian, CCS Chem. 2020, 2, 707-728;
L. Yue, S. Wang, Z. Zhou, I. Willner, J. Am. Chem. Soc. 2020, 142, 21577-21594;
L. Chen, W. Chen, G. Liu, J. Li, C. Lu, J. Li, W. Tan, H. Yang, Chem. Soc. Rev. 2021, 50, 12551-12575.
L. Qian, E. Winfree, Science 2011, 332, 1196-1201.
J. Wu, S. Zaccara, D. Khuperkar, H. Kim, M. E. Tanenbaum, S. R. Jaffrey, Nat. Methods 2019, 16, 862-865;
G. Werstuck, M. R. Green, Science 1998, 282, 296-298.
W. Tang, J. H. Hu, D. R. Liu, Nat. Commun. 2017, 8, 15939;
J. L. Vinkenborg, N. Karnowski, M. Famulok, Nat. Chem. Biol. 2011, 7, 519-527;
J. Feng, J. Wang, J. Lin, Y. Diao, Mol. Ther. 2015, 23, S66.
J. Lin, Y. Liu, P. Lai, H. Ye, L. Xu, Nucleic Acids Res. 2020, 48, 11773-11784;
K.-H. Siu, W. Chen, Nat. Chem. Biol. 2019, 15, 217-220;
Y. Liu, Y. Wang, J. Lin, L. Xu, Chem. Commun. 2021, 57, 5418-5421;
K. Kundert, J. E. Lucas, K. E. Watters, C. Fellmann, A. H. Ng, B. M. Heineike, C. M. Fitzsimmons, B. L. Oakes, J. Qu, N. Prasad, Nat. Commun. 2019, 10, 2127.