Module Assembly Strategy for Single-Cell Nucleic Acid Imaging at the Sub-Molecule Level.

Tytuł:: Module Assembly Strategy for Single-Cell Nucleic Acid Imaging at the Sub-Molecule Level.
Autorzy:: Teng X; Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.
Dai Y; Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.
Li J; Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.
Źródło:: Chemistry (Weinheim an der Bergstrasse, Germany) [Chemistry] 2022 May 16; Vol. 28 (28), pp. e202104628. Date of Electronic Publication: 2022 Mar 25.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Original Publication: Weinheim, Germany : Wiley-VCH
MeSH Terms:: G-Quadruplexes*
Nucleic Acids*/chemistry
Nucleic Acid Conformation ; RNA/chemistry
References:: X. Pichon, M. Lagha, F. Mueller, E. Bertrand, Mol. Cell 2018, 71, 468-480.
.
J. Shendure, S. Balasubramanian, G. M. Church, W. Gilbert, J. Rogers, J. A. Schloss, R. H. Waterston, Nature 2017, 550, 345-353;.
T. Nawy, Nat. Methods 2014, 11, 18.
A. R. Buxbaum, G. Haimovich, R. H. Singer, Nat. Rev. Mol. Cell Biol. 2015, 16, 95-109.
A. M. Femino, F. S. Fay, K. Fogarty, R. H. Singer, Science 1998, 280, 585-590.
D. S. Seferos, D. A. Giljohann, H. D. Hill, A. E. Prigodich, C. A. Mirkin, J. Am. Chem. Soc. 2007, 129, 15477-15479.
.
E. Braselmann, A. J. Wierzba, J. T. Polaski, M. Chrominski, Z. E. Holmes, S. T. Hung, D. Batan, J. R. Wheeler, R. Parker, R. Jimenez, D. Gryko, R. T. Batey, A. E. Palmer, Nat. Chem. Biol. 2018, 641, 343-372;.
F. Tomoike, H. Abe, Adv. Drug Delivery Rev. 2019, 147, 44-58.
R. Lin, Q. Feng, P. Li, P. Zhou, R. Wang, Z. Liu, Z. Wang, X. Qi, N. Tang, F. Shao, M. Luo, Nat. Methods 2018, 15, 275-278.
A. Karunanayake Mudiyanselage, Q. Yu, M. A. Leon-Duque, B. Zhao, R. Wu, M. You, J. Am. Chem. Soc. 2018, 140, 8739-8745.
.
R. Deng, K. Zhang, L. Wang, X. Ren, Y. Sun, J. Li, Chem 2018, 4, 1373-1386;.
K. H. Chen, A. N. Boettiger, J. R. Moffitt, S. Wang, X. Zhuang, Science 2015, 348, aaa6090.
C. N. Ravarani, G. Chalancon, M. Breker, N. S. de Groot, M. M. Babu, Nat. Commun. 2016, 7, 10417.
.
P. Murat, G. Marsico, B. Herdy, A. Ghanbarian, G. Portella, S. Balasubramanian, Genome Biol. 2018, 19, 229-229;.
A. L. Wolfe, K. Singh, Y. Zhong, P. Drewe, V. K. Rajasekhar, V. R. Sanghvi, K. J. Mavrakis, M. Jiang, J. E. Roderick, J. Van der Meulen, J. H. Schatz, C. M. Rodrigo, C. Zhao, P. Rondou, E. de Stanchina, J. Teruya-Feldstein, M. A. Kelliher, F. Speleman, J. A. Porco, Jr., J. Pelletier, G. Ratsch, H. G. Wendel, Nature 2014, 513, 65-70.
B. Chen, W. Zou, H. Xu, Y. Liang, B. Huang, Nat. Commun. 2018, 9, 5065.
Y. Dai, A. Furst, C. C. Liu, Trends Biotechnol. 2019, 37, 1367-1382.
.
R. Kempfer, A. Pombo, Nat. Rev. Genet. 2020, 21, 207-226;.
H. Zhang, F. Li, B. Dever, X. F. Li, X. C. Le, Chem. Rev. 2013, 113, 2812-2841.
.
A. H. El-Sagheer, T. Brown, Acc. Chem. Res. 2012, 45, 1258-1267;.
A. P. Silverman, E. T. Kool, Chem. Rev. 2006, 106, 3775-3789;.
K. Gorska, N. Winssinger, Angew. Chem. Int. Ed. 2013, 52, 6820-6843;.
K. Gorska, N. Winssinger, Angew. Chem. 2013, 125, 6956-6980.
J. Jana, S. Mondal, P. Bhattacharjee, P. Sengupta, T. Roychowdhury, P. Saha, P. Kundu, S. Chatterjee, Sci. Rep. 2017, 7, 40706-40706.
D. Y. Vargas, K. Shah, M. Batish, M. Levandoski, S. Sinha, S. A. Marras, P. Schedl, S. Tyagi, Cell 2011, 147, 1054-1065.
K. Lee, Y. Cui, L. P. Lee, J. Irudayaraj, Nat. Nanotechnol. 2014, 9, 474-480.
X. Ren, R. Deng, K. Zhang, Y. Sun, X. Teng, J. Li, ACS Cent. Sci. 2018, 4, 680-687.
.
Y. Dai, X. Teng, J. Li, Angew. Chem. Int. Ed. 2022, 61, e202111132;.
Y. Dai, X. Teng, J. Li, Angew. Chem. 2022, 61, e202111132.
K. Zhang, R. Deng, X. Teng, Y. Li, Y. Sun, X. Ren, J. Li, J. Am. Chem. Soc. 2018, 140, 11293-11301.
.
X. Ren, R. Deng, K. Zhang, Y. Sun, Y. Li, J. Li, Angew. Chem. Int. Ed. 2021, 60, 22646-22651;.
X. Ren, R. Deng, K. Zhang, Y. Sun, Y. Li, J. Li, Angew. Chem. 2021, 133, 22828-22833.
.
S. C. Lee, O. Abdel-Wahab, Nat. Med. 2016, 22, 976-986;.
Y. Lee, D. C. Rio, Annu. Rev. Biochem. 2015, 84, 291-323.
X. Ren, K. Zhang, R. Deng, J. Li, Chem 2019, 5, 2571-2592.
G. W. Collie, S. M. Haider, S. Neidle, G. N. Parkinson, Nucleic Acids Res. 2010, 38, 5569-5580.
D. Varshney, J. Spiegel, K. Zyner, D. Tannahill, S. Balasubramanian, Nat. Rev. Mol. Cell Biol. 2020, 21, 459-474.
.
S. Balasubramanian, L. H. Hurley, S. Neidle, Nat. Rev. Drug Discovery 2011, 10, 261-275;.
J. Amato, T. W. Madanayake, N. Iaccarino, E. Novellino, A. Randazzo, L. H. Hurley, B. Pagano, Chem. Commun. 2018, 54, 9442-9445.
.
P. Silva-Pinheiro, M. Minczuk, Nat. Rev. Genet. 2022, 23, 199-214;.
C. Y. Chung, G. E. Valdebenito, A. R. Chacko, M. R. Duchen, Trends Cell Biol. 2021, https://doi.org/10.1016/j.tcb.2021.10.005.
.
R. Deng, L. Tang, Q. Tian, Y. Wang, L. Lin, J. Li, Angew. Chem. Int. Ed. 2014, 53, 2389-2393;.
R. Deng, L. Tang, Q. Tian, Y. Wang, L. Lin, J. Li, Angew. Chem. 2014, 126, 2421-2425;.
R. Deng, K. Zhang, J. Li, Acc. Chem. Res. 2017, 50, 1059-1068;.
R. Deng, K. Zhang, Y. Sun, X. Ren, J. Li, Chem. Sci. 2017, 8, 3668-3675;.
C. Larsson, J. Koch, A. Nygren, G. Janssen, A. K. Raap, U. Landegren, M. Nilsson, Nat. Methods 2004, 1, 227-232.
.
S. Zaccara, R. J. Ries, S. R. Jaffrey, Nat. Rev. Mol. Cell Biol. 2019, 20, 608-624;.
Y. Fu, D. Dominissini, G. Rechavi, C. He, Nat. Rev. Genet. 2014, 15, 293-306.
.
K. D. Meyer, Y. Saletore, P. Zumbo, O. Elemento, C. E. Mason, S. R. Jaffrey, Cell 2012, 149, 1635-1646;.
D. Dominissini, S. Moshitch-Moshkovitz, S. Schwartz, M. Salmon-Divon, L. Ungar, S. Osenberg, K. Cesarkas, J. Jacob-Hirsch, N. Amariglio, M. Kupiec, R. Sorek, G. Rechavi, Nature 2012, 485, 201-206.
N. Liu, M. Parisien, Q. Dai, G. Zheng, C. He, T. Pan, RNA 2013, 19, 1848-1856.
.
Y. Xiao, Y. Wang, Q. Tang, L. Wei, X. Zhang, G. Jia, Angew. Chem. Int. Ed. 2018, 57, 15995-16000;.
Y. Xiao, Y. Wang, Q. Tang, L. Wei, X. Zhang, G. Jia, Angew. Chem. 2018, 130, 16227-16232.
Grant Information:: 2021YFA1200104 National Key R&D Program of China; 22027807 National Natural Science Foundation of China; 22034004 National Natural Science Foundation of China; 21621003 National Natural Science Foundation of China; XDB36000000 Strategic Priority Research Program of Chinese Academy of Sciences; 2020Z99CFZ019 Tsinghua University Spring Breeze Fund
Contributed Indexing:: Keywords: imaging agents; molecular recognition; nucleic acids; single-cell imaging; sub-molecule level
Substance Nomenclature:: 0 (Nucleic Acids)
63231-63-0 (RNA)
Entry Date(s):: Date Created: 20220310 Date Completed: 20220517 Latest Revision: 20220517
Update Code:: 20240104
DOI:: 10.1002/chem.202104628
PMID:: 35267217
: Czasopismo naukowe

Pełny tekst

Single-cell imaging has unique advantages of maintaining the in situ physiological state, morphology, and microenvironment, becoming a powerful tool to unravel the nature of intracellular nucleic acids. The analysis of nucleic acids unprecedentedly demands the sub-molecule details at segment or subunit, secondary structure and monomer levels, instead of just probing the sequence and the abundance of nucleic acids. Detection of nucleic acids at the sub-molecule level requires higher specificity and higher sensitivity, which becomes a new challenge in nucleic acid analysis. Herein, we summarize the recent progress in the design and the application of single-cell nucleic acid imaging methods at the sub-molecule level, including the visualization of RNA splicing variants, RNA G-quadruplexes in an individual gene, single nucleotide variation of mitochondrial DNA, and RNA m 6 A methylation. Remarkably, we highlight the key strategy, "Module Assembly", for high-performance molecular recognition and demonstrate the required improvements in future research.
(© 2022 Wiley-VCH GmbH.)

Zaloguj się, aby uzyskać dostęp do pełnego tekstu.

Informacja