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荧光RNA及其生物传感技术研究进展

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  • 1.华东理工大学光遗传学与合成生物学交叉学科研究中心,生物反应器工程国家重点实验室,上海 200237
    2.华东理工大学药学院,上海市细胞代谢光遗传学技术前沿科学研究基地,上海 200237
    3.华东理工大学生物工程学院,上海 200237
左方婷,博士后,研究方向:荧光RNA技术的开发与应用。E-mail: ftzuo@ecust.edu.cn.|杨弋,教授,博士生导师,长江学者特聘教授,国家杰出青年基金获得者,国家自然科学基金创新群体负责人,国家重点研发计划首席科学家。现任生物反应器工程国家重点实验室副主任,华东理工大学光遗传学与合成生物学交叉学科研究中心主任,中国生物化学与分子生物学会常务理事及酶学分会副主任、秘书长,中国生物物理学会理事。主要研究方向为光遗传控制方法、细胞代谢监控方法和生物大分子标记方法。系列前沿方法学研究成果发表于Nature Biotechnology、Nature Methods、Cell Metabolism等国际重要期刊,已被国内外实验室广泛应用。|陈显军,教授,博士生导师,国家高层次青年人才。研究方向主要为新型光遗传学技术的开发与应用和生物大分子荧光标记技术开发与应用,近年来聚焦活细胞RNA实时动态监测与时空精确调控的方法学关键难题,创新发展了系列高性能荧光RNA与RNA代谢光控因子,实现了活细胞RNA高时空分辨成像与精密控制。相关研究成果以第一或通讯作者发表在Nature Biotechnology、Nature Methods、Nature Chemical Biology、Nature Communications、Nature Protocols等国际重要期刊,授权多项国内外发明专利。研究成果在国际同行中产生重要影响,所发展技术被300余个国内外一流机构实验室跟踪应用。主持包括十余项国家与省部级基金项目。

收稿日期: 2023-12-12

  修回日期: 2024-01-25

  网络出版日期: 2024-01-29

基金资助

国家自然科学基金项目(32121005);国家自然科学基金项目(32150028);国家自然科学基金项目(21937004);国家自然科学基金项目(91857202);国家自然科学基金项目(32250009);国家重点研发计划(2022YFC3400100)

Progress on fluorescent RNA and fluorescent RNA-based biosensing technology

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  • 1. Interdisciplinary Research Center of Optogenetics and Synthetic Biology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
    2. Shanghai Advanced Research Base of Cell Metabolism Genetics, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
    3. School of Bioengineering, East China University of Science and Technology, Shanghai 200237, China

Received date: 2023-12-12

  Revised date: 2024-01-25

  Online published: 2024-01-29

Supported by

National Natural Science Foundation of China(32121005);National Natural Science Foundation of China(32150028);National Natural Science Foundation of China(21937004);National Natural Science Foundation of China(91857202);National Natural Science Foundation of China(32250009);National Key Research and Development Program of China(2022YFC3400100)

摘要

荧光RNA技术是一种新兴的RNA标记技术,可用于活细胞RNA的原位实时标记与成像,对于人们理解RNA的功能和调控机制发挥着至关重要的作用。基于荧光RNA的生物传感技术可用于活细胞内小分子代谢物以及蛋白质等靶标的实时动态检测,为生命科学基础研究以及生物医学传感技术开发提供极具价值的工具。本文对遗传编码的荧光RNA的发展历程、荧光RNA技术在活细胞RNA成像,以及基于荧光RNA的生物传感技术在活细胞代谢物检测等方面的应用进行了介绍和总结,并对该领域的发展现状和未来发展方向展开讨论和展望,以期为该技术的进一步发展和在相关领域的应用提供参考。

本文引用格式

左方婷, 张雅强, 杨慧敏, 杨弋, 陈显军 . 荧光RNA及其生物传感技术研究进展[J]. 遗传, 2024 , 46(2) : 92 -108 . DOI: 10.16288/j.yczz.23-306

Abstract

Fluorescent RNA is a kind of emerging RNA labeling technique that can be used for in situ labeling and imaging of RNA in live cells, which plays an important role in understanding the function and regulation mechanism of RNA. Biosensing technology based on fluorescent RNA can be applied in dynamic detection of small molecule metabolites and proteins in real time, offering valuable tools for basic life science research and biomedical sensing technology development. In this review, we introduce the development of genetically encoded fluorescent RNA, and the application of fluorescent RNA in RNA imaging and biosensing technology based on fluorescent RNA in biosensing in live cell. Meanwhile, we discuss the direction and challenge of future development of fluorescent RNA technology to provide valuable insights for further development and application of this technology in relevant fields.

参考文献

[1] Shimomura O, Johnson FH, Saiga Y. Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, aequorea. J Cell Comp Physiol, 1962, 59: 223-239.
[2] Prasher DC, Eckenrode VK, Ward WW, Prendergast FG, Cormier MJ. Primary structure of the aequorea victoria green-fluorescent protein. Gene, 1992, 111(2): 229-233.
[3] Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. Green fluorescent protein as a marker for gene expression. Science, 1994, 263(5148): 802-805.
[4] Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA. Fluorescent proteins from nonbioluminescent anthozoa species. Nat Biotechnol, 1999, 17(10): 969-973.
[5] Miyawaki A. Green fluorescent protein glows gold. Cell, 2008, 135(6): 987-990.
[6] Zimmer M. Green fluorescent protein (GFP): Applications, structure, and related photophysical behavior. Chem Rev, 2002, 102(3): 759-781.
[7] Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins—a review. Int J Biol Macromol, 2021, 191: 840-851.
[8] Shu XK, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science, 2009, 324(5928): 804-807.
[9] Auldridge ME, Satyshur KA, Anstrom DM, Forest KT. Structure-guided engineering enhances a phytochrome- based infrared fluorescent protein. J Biol Chem, 2012, 287(10): 7000-7009.
[10] Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc- Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu XK. An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging. Nat Commun, 2014, 5: 3626.
[11] Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. A bilirubin- inducible fluorescent protein from eel muscle. Cell, 2013, 153(7): 1602-1611.
[12] Mollwitz B, Brunk E, Schmitt S, et al. Directed evolution of the suicide protein O6-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability. Biochemistry, 2012, 51(5): 986-994.
[13] Los GV, Encell LP, Mcdougall MG, Hartzell DD, Karassina N, Zimprich C, Wood MG, Learish R, Ohana RF, Urh M, Simpson D, Mendez J, Zimmerman K, Otto P, Vidugiris G, Zhu J, Darzins A, Klaubert DH, Bulleit RF, Wood KV. Halotag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol, 2008, 3(6): 373-382.
[14] Plamont MA, Billon-Denis E, Maurin S, Gauron C, Pimenta FM, Specht CG, Shi J, Quérard J, Pan B, Rossignol J, Moncoq K, Morellet N, Volovitch M, Lescop E, Chen Y, Triller A, Vriz S, Le Saux T, Jullien L, Gautier A. Small fluorescence-activating and absorption- shifting tag for tunable protein imaging in vivo. Proc Natl Acad Sci USA, 2016, 113(3): 497-502.
[15] Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 1990, 249(4968): 505- 510.
[16] Robertson DL, Joyce GF. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 1990, 344(6265): 467-468.
[17] Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature, 1990, 346(6287): 818-822.
[18] Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev, 2010, 90(3): 1103-1163.
[19] Ward WW, Bokman SH. Reversible denaturation of aequorea green-fluorescent protein: physical separation and characterization of the renatured protein. Biochemistry, 1982, 21(19): 4535-4540.
[20] Grate D, Wilson C. Laser-mediated, site-specific inactivation of RNA transcripts. Proc Natl Acad Sci USA, 1999, 96(11): 6131-6136.
[21] Engelhart AE. RNA imaging: a tale of two G-quadruplexes. Nat Chem Biol, 2017, 13(11): 1140- 1141.
[22] Sando S, Narita A, Hayami M, Aoyama Y. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun (Camb), 2008(33): 3858-3860.
[23] Constantin TP, Silva GL, Robertson KL, Hamilton TP, Fague K, Waggoner AS, Armitage BA. Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org Lett, 2008, 10(8): 1561-1564.
[24] Tan XH, Constantin TP, Sloane KL, Waggoner AS, Bruchez MP, Armitage BA. Fluoromodules consisting of a promiscuous RNA aptamer and red or blue fluorogenic cyanine dyes: selection, characterization, and bioimaging. J Am Chem Soc, 2017, 139(26): 9001-9009.
[25] Dolgosheina EV, Jeng SCY, Panchapakesan SSS, Cojocaru R, Chen PSK, Wilson PD, Hawkins N, Wiggins PA, Unrau PJ. RNA Mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem Biol, 2014, 9(10): 2412-2420.
[26] Cawte AD, Unrau PJ, Rueda DS. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nat Commun, 2020, 11(1): 1283.
[27] Autour A, Jeng SCY, Cawte AD, Abdolahzadeh A, Galli A, Panchapakesan SSS, Rueda D, Ryckelynck M, Unrau PJ. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat Commun, 2018, 9(1): 656.
[28] Kong KYS, Jeng SCY, Rayyan B, Unrau PJ. RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands. RNA, 2021, 27(5): 604-615.
[29] Murata A, Sato SI, Kawazoe Y, Uesugi M. Small- molecule fluorescent probes for specific RNA targets. Chem Commun (Camb), 2011, 47(16): 4712-4714.
[30] Arora A, Sunbul M, J?schke A. Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers. Nucleic Acids Res, 2015, 43(21): e144.
[31] Sunbul M, J?schke A. SRB-2: a promiscuous rainbow aptamer for live-cell RNA imaging. Nucleic Acids Res, 2018, 46(18): e110.
[32] Sunbul M, J?schke A. Contact-mediated quenching for RNA imaging in bacteria with a fluorophore-binding aptamer. Angew Chem Int Ed Engl, 2013, 52(50): 13401-13404.
[33] Braselmann E, Wierzba AJ, Polaski JT, Chromiński M, Holmes ZE, Hung ST, Batan D, Wheeler JR, Parker R, Jimenez R, Gryko D, Batey RT, Palmer A E. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. Nat Chem Biol, 2018, 14(10): 964-971.
[34] Bouhedda F, Fam KT, Collot M, Autour A, Marzi S, Klymchenko A, Ryckelynck M. A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol, 2020, 16(1): 69-76.
[35] Paige JS, Wu KY, Jaffrey SR. RNA mimics of green fluorescent protein. Science, 2011, 333(6042): 642-646.
[36] Masuda I, Igarashi T, Sakaguchi R, Nitharwal RG, Takase R, Han KY, Leslie BJ, Liu CP, Gamper H, Ha T, Sanyal S, Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Res, 2017, 45(7): 4081-4093.
[37] Ilgu M, Ray J, Bendickson L, Wang TJ, Geraskin IM, Kraus GA, Nilsen-Hamilton M. Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells. Methods, 2016, 98: 26-33.
[38] Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C. Combining Spinach- tagged RNA and gene localization to image gene expression in live yeast. Nat Commun, 2015, 6: 8882.
[39] Han KY, Leslie BJ, Fei JY, Zhang JC, Ha T. Understanding the photophysics of the Spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging. J Am Chem Soc, 2013, 135(50): 19033- 19038.
[40] Guzmán-Zapata D, Domínguez-Anaya Y, Macedo- Osorio KS, Tovar-Aguilar A, Castrejón-Flores JL, Durán- Figueroa NV, Badillo-Corona JA. mRNA imaging in the chloroplast of chlamydomonas reinhardtii using the light-up aptamer Spinach. J Biotechnol, 2017, 251: 186-188.
[41] Song WJ, Strack RL, Svensen N, Jaffrey SR. Plug-and- play fluorophores extend the spectral properties of Spinach. J Am Chem Soc, 2014, 136(4): 1198-1201.
[42] Strack RL, Disney MD, Jaffrey SR. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods, 2013, 10(12): 1219-1224.
[43] Filonov GS, Moon JD, Svensen N, Jaffrey SR. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc, 2014, 136(46): 16299-16308.
[44] Warner KD, Chen MC, Song WJ, Strack RL, Thorn A, Jaffrey SR, Ferré-D'amaré AR. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol, 2014, 21(8): 658-663.
[45] Autour A, Westhof E, Ryckelynck M. iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res, 2016, 44(6): 2491- 2500.
[46] Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M. Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI. RNA, 2017, 23(12): 1788-1795.
[47] Song WJ, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, Jaffrey SR. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem Biol, 2017, 13(11): 1187-1194.
[48] Li X, Mo LT, Litke JL, Dey SK, Suter SR, Jaffrey SR. Imaging intracellular s-adenosyl methionine dynamics in live mammalian cells with a genetically encoded red fluorescent RNA-based sensor. J Am Chem Soc, 2020, 142(33): 14117-14124.
[49] Dey SK, Filonov GS, Olarerin-George AO, Jackson BT, Finley LWS, Jaffrey SR. Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat Chem Biol, 2022, 18(2): 180-190.
[50] Wu JH, Svensen N, Song WJ, Kim H, Zhang SL, Li X, Jaffrey SR. Self-assembly of intracellular multivalent RNA complexes using dimeric Corn and Beetroot aptamers. J Am Chem Soc, 2022, 144(12): 5471-5477.
[51] Steinmetzger C, Palanisamy N, Gore KR, H?bartner C. A multicolor large Stokes shift fluorogen-activating RNA aptamer with cationic chromophores. Chemistry, 2019, 25(8): 1931-1935.
[52] Wirth R, Gao P, Nienhaus GU, Sunbul M, J?schke A. SiRA: a silicon rhodamine-binding aptamer for live-cell super-resolution RNA imaging. J Am Chem Soc, 2019, 141(18): 7562-7571.
[53] Zhang JY, Wang L, J?schke A, Sunbul M. A color- shifting near-infrared fluorescent aptamer-fluorophore module for live-cell RNA imaging. Angew Chem Int Ed Engl, 2021, 60(39): 21441-21448.
[54] Chen HY, Shiroguchi K, Ge H, Xie XS. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol, 2015, 11(5): 808.
[55] Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA, 2002, 99(15): 9697-9702.
[56] Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res, 2003, 13(2): 216-223.
[57] Yang E, Van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res, 2003, 13(8): 1863-1872.
[58] Guo JU, Bartel DP. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science, 2016, 353(6306): aaf5371-5378.
[59] Chen XJ, Zhang DS, Su N, Bao BK, Xie X, Zuo FT, Yang LP, Wang H, Jiang L, Lin QN, Fang MY, Li NF, Hua X, Chen ZD, Bao CY, Xu JJ, Du WL, Zhang LX, Zhao YZ, Zhu LY, Loscalzo J, Yang Y. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat Biotechnol, 2019, 37(11): 1287-1293.
[60] Li X, Kim H, Litke JL, Wu JH, Jaffrey SR. Fluorophore-promoted RNA folding and photostability enables imaging of single Broccoli-tagged mRNAs in live mammalian cells. Angew Chem Int Ed Engl, 2020, 59(11): 4511-4518.
[61] Li X, Wu JH, Jaffrey SR. Engineering fluorophore recycling in a fluorogenic RNA aptamer. Angew Chem Int Ed Engl, 2021, 60(45): 24153-24161.
[62] Sunbul M, Lackner J, Martin A, Englert D, Hacene B, Grün F, Nienhaus K, Nienhaus GU, J?schke A. Super- resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics. Nat Biotechnol, 2021, 39(6): 686-690.
[63] Bühler B, Schokolowski J, Benderoth A, Englert D, Grün F, J?schke A, Sunbul M. Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging. Nat Chem Biol, 2023, 19(4): 478-487.
[64] Englert D, Burger EM, Grün F, Verma MS, Lackner J, Lampe M, Bühler B, Schokolowski J, Nienhaus GU, J?schke A, Sunbul M. Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging. Nat Commun, 2023, 14(1): 3879.
[65] Jiang L, Xie X, Su N, Zhang DS, Chen XJ, Xu XC, Zhang BB, Huang KY, Yu JW, Fang MY, Bao BK, Zuo FT, Yang LP, Zhang R, Li HW, Huang XY, Chen ZD, Zeng QM, Liu RM, Lin QN, Zhao YZ, Ren AM, Zhu LY, Yang Y. Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells. Nat Methods, 2023, 20(10): 1563-1572.
[66] Ying ZM, Tu B, Liu L, Tang H, Tang LJ, Jiang JH. Spinach-based fluorescent light-up biosensors for multiplexed and label-free detection of microRNAs. Chem Commun (Camb), 2018, 54(24): 3010-3013.
[67] Ong WQ, Citron YR, Sekine S, Huang B. Live cell imaging of endogenous mRNA using RNA-based fluorescence "turn-on" probe. ACS Chem Biol, 2017, 12(1): 200-205.
[68] Wang Q, Xiao F, Su HM, Liu H, Xu JL, Tang H, Qin SS, Fang ZT, Lu ZA, Wu J, Weng XC, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res, 2022, 50(14): e84.
[69] Wang ZJ, Luo Y, Xie XD, Hu XJ, Song HY, Zhao Y, Shi JY, Wang LH, Glinsky G, Chen N, Lal R, Fan CH. In situ spatial complementation of aptamer-mediated recognition enables live-cell imaging of native RNA transcripts in real time. Angew Chem Int Ed Engl, 2018, 57(4): 972-976.
[70] Karunanayake Mudiyanselage APKK, Yu QK, Leon-Duque MA, Zhao B, Wu R, You MX. Genetically encoded catalytic hairpin assembly for sensitive RNA imaging in live cells. J Am Chem Soc, 2018, 140(28): 8739-8745.
[71] Ren KW, Wu R, Karunanayake Mudiyanselage APKK, Yu QK, Zhao B, Xie YW, Bagheri Y, Tian Q, You MX. In situ genetically cascaded amplification for imaging RNA subcellular locations. J Am Chem Soc, 2020, 142(6): 2968-2974.
[72] Rogers TA, Andrews GE, Jaeger L, Grabow WW. Fluorescent monitoring of RNA assembly and processing using the split-Spinach aptamer. ACS Synth Biol, 2015, 4(2): 162-166.
[73] Tsvetkova IB, Yi GH, Yi Y, Kao CC, Dragnea BG. Segmented GFP-like aptamer probes for functional imaging of viral genome trafficking. Virus Res, 2015, 210: 291-297.
[74] Furukawa A, Tanaka T, Furuta H, Matsumura S, Ikawa Y. Use of a fluorescent aptamer RNA as an exonic sequence to analyze self-splicing ability of agroup I intron from structured RNAs. Biology (Basel), 2016, 5(4): 43.
[75] Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A fluorescent split aptamer for visualizing RNA-RNA assembly in vivo. ACS Synth Biol, 2017, 6(9): 1710-1721.
[76] Chandler M, Lyalina T, Halman J, Rackley L, Lee L, Dang D, Ke WN, Sajja S, Woods S, Acharya S, Baumgarten E, Christopher J, Elshalia E, Hrebien G, Kublank K, Saleh S, Stallings B, Tafere M, Striplin C, Afonin KA. Broccoli fluorets: split aptamers as a user-friendly fluorescent toolkit for dynamic RNA nanotechnology. Molecules, 2018, 23(12): 3178.
[77] Ying ZM, Wu Z, Tu B, Tan WH, Jiang JH. Genetically encoded fluorescent RNA sensor for ratiometric imaging of microRNA in living tumor cells. J Am Chem Soc, 2017, 139(29): 9779-9782.
[78] Huang K, Doyle F, Wurz ZE, Tenenbaum SA, Hammond RK, Caplan JL, Meyers BC. FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs. Nucleic Acids Res, 2017, 45(14): e130.
[79] Newman RH, Fosbrink MD, Zhang J. Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells. Chem Rev, 2011, 111(5): 3614-3666.
[80] Zhang J, Campbell RE, Ting AY, Tsien RY. Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol, 2002, 3(12): 906-918.
[81] Zhao YZ, Jin J, Hu QX, Zhou HM, Yi J, Yu ZH, Xu L, Wang X, Yang Y, Loscalzo J. Genetically encoded fluorescent sensors for intracellular NADH detection. Cell Metab, 2011, 14(4): 555-566.
[82] Zhao YZ, Hu QX, Cheng FX, Su N, Wang AX, Zou YJ, Hu HY, Chen XJ, Zhou HM, Huang XZ, Yang K, Zhu Q, Wang X, Yi J, Zhu LY, Qian XH, Chen LX, Tang Y, Loscalzo J, Yang Y. SoNar, a highly responsive NAD+/NADH sensor, allows high-throughput metabolic screening of anti-tumor agents. Cell Metab, 2015, 21(5): 777-789.
[83] Tao RK, Zhao YZ, Chu HY, Wang AX, Zhu JH, Chen XJ, Zou YJ, Shi M, Liu RM, Su N, Du JL, Zhou HM, Zhu LY, Qian XH, Liu HY, Loscalzo J, Yang Y. Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism. Nat Methods, 2017, 14(7): 720-728.
[84] Zou YJ, Wang AX, Huang L, Zhu XD, Hu QX, Zhang YN, Chen XJ, Li FW, Wang QH, Wang H, Liu RM, Zuo FT, Li T, Yao J, Qian YJ, Shi M, Yue X, Chen WC, Zhang Z, Wang CR, Zhou Y, Zhu LY, Ju ZY, Loscalzo J, Yang Y, Zhao YZ. Illuminating NAD+ metabolism in live cells and in vivo using a genetically encoded fluorescent sensor. Dev Cell, 2020, 53(2): 240-252.e7.
[85] Li X, Zhang YN, Xu LY, Wang AX, Zou YJ, Li T, Huang L, Chen WC, Liu SN, Jiang K, Zhang XZ, Wang DM, Zhang LJ, Zhang Z, Zhang ZY, Chen XJ, Jia W, Zhao AH, Yan XF, Zhou HM, Zhu LY, Ma XR, Ju ZY, Jia WP, Wang CR, Loscalzo J, Yang Y, Zhao YZ. Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease. Cell Metab, 2023, 35(1): 200-211.e9.
[86] Song WJ, Strack RL, Jaffrey SR. Imaging bacterial protein expression using genetically encoded RNA sensors. Nat Methods, 2013, 10(9): 873-875.
[87] You MX, Litke JL, Jaffrey SR. Imaging metabolite dynamics in living cells using a Spinach-based riboswitch. Proc Natl Acad Sci USA, 2015, 112(21): E2756-E2765.
[88] Kellenberger CA, Wilson SC, Sales-Lee J, Hammond MC. RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP. J Am Chem Soc, 2013, 135(13): 4906-4909.
[89] Kellenberger CA, Chen C, Whiteley AT, Portnoy DA, Hammond MC. RNA-based fluorescent biosensors for live cell imaging of second messenger cyclic di-AMP. J Am Chem Soc, 2015, 137(20): 6432-6435.
[90] Su YC, Hickey SF, Keyser SGL, Hammond MC. In vitro and in vivo enzyme activity screening via RNA-based fluorescent biosensors for s-adenosyl-l-homocysteine (SAH). J Am Chem Soc, 2016, 138(22): 7040-7047.
[91] Moon JD, Wu JH, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chem Biol, 2021, 28(11): 1569-1580.e4.
[92] Ying ZM, Yuan YY, Tu B, Tang LJ, Yu RQ, Jiang JH. A single promoter system co-expressing RNA sensor with fluorescent proteins for quantitative mRNA imaging in living tumor cells. Chem Sci, 2019, 10(18): 4828-4833.
[93] Wu R, Karunanayake Mudiyanselage APKK, Shafiei F, Zhao B, Bagheri Y, Yu QK, Mcauliffe K, Ren KW, You MX. Genetically encoded ratiometric RNA-based sensors for quantitative imaging of small molecules in living cells. Angew Chem Int Ed Engl, 2019, 58(50): 18271-18275.
[94] Wu R, Karunanayake Mudiyanselage APKK, Ren KW, Sun ZN, Tian Q, Zhao B, Bagheri Y, Lutati D, Keshri P, You MX. Ratiometric fluorogenic RNA-based sensors for imaging live-cell dynamics of small molecules. ACS Appl Bio Mater, 2020, 3(5): 2633-2642.
[95] Fang MY, Li HW, Xie X, Wang H, Jiang Y, Li TY, Zhang BB, Jiang X, Cao YY, Zhang R, Zhang DS, Zhao YZ, Zhu LY, Chen XJ, Yang Y. Imaging intracellular metabolite and protein changes in live mammalian cells with bright fluorescent RNA-based genetically encoded sensors. Biosens Bioelectron, 2023, 235: 115411.
[96] Chen ZY, Chen W, Reheman Z, Jiang HD, Wu JH, Li X. Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer. Nucleic Acids Res, 2023, 51(16): 8322-8336.
[97] Yang K, Mitchell NM, Banerjee S, Cheng ZZ, Taylor S, Kostic AM, Wong I, Sajjath S, Zhang YM, Stevens J, Mohan S, Landry DW, Worgall TS, Andrews AM, Stojanovic MN. A functional group-guided approach to aptamers for small molecules. Science, 2023, 380(6648): 942-948.
[98] Singh NK, Wang YX, Wen C, Davis B, Wang XL, Lee K, Wang Y. High-affinity one-step aptamer selection using a non-fouling porous hydrogel. Nat Biotechnol, 2023, doi: 10.1038/s41587-023-01973-8.
[99] Filonov GS, Kam CW, Song WJ, Jaffrey SR. In-gel imaging of RNA processing using Broccoli reveals optimal aptamer expression strategies. Chem Biol, 2015, 22(5): 649-660.
[100] Jepsen MDE, Sparvath SM, Nielsen TB, Langvad AH, Grossi G, Gothelf KV, Andersen ES. Development of a genetically encodable FRET system using fluorescent RNA aptamers. Nat Commun, 2018, 9(1): 18.
[101] Litke JL, Jaffrey SR. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts. Nat Biotechnol, 2019, 37(6): 667-675.
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