Article
Chemistry, Analytical
Yan Peng, Linjuan Shu, Xiongfei Deng, Xin Huang, Xianming Mo, Feng Du, Zhuo Tang
Summary: We developed a genetically encoded sensor for sensitive imaging and tracking of endogenous RNA in living cells. This sensor can specifically recognize target RNAs and induce structural changes to enable fluorescence imaging. We successfully demonstrated its application in monitoring mRNA expression and confirming RNA distribution in cancer cells and zebrafish embryos, respectively. This study provides an effective molecular tool for RNA imaging and has potential applications in disease diagnosis and treatment evaluation.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Wei Chen, Xiaoying Zhao, Nanyang Yang, Xing Li
Summary: Messenger RNA (mRNA) serves as the fundamental information transfer system in cells. Tracking single mRNA from transcription to degradation using fluorescent probes provides spatiotemporal information about how genetic information is transferred from DNA to proteins. RNA aptamers: small-molecule fluorophores (SFs) systems, as exciting alternatives for single mRNA imaging, offer advantages such as fluorogenic ability and minimal perturbation. This review summarizes the five reported RNA aptamers: SFs systems for single mRNA imaging in living cells so far, discusses challenges, and provides prospects for single mRNA imaging applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: This article introduces a method for real-time dynamic translation imaging using the CRISPR/dCas13 system. The method labels the unmodified coding regions of target mRNA, enabling real-time visualization of the translation process, and is promising for further investigations into translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: Translation is a critical cellular activity regulated by viruses, and studying its kinetics and subcellular localization requires real-time visualization techniques. This study presents a new method using the CRISPR/dCas13 system and specific complementary guide RNAs to dynamically image translation without altering the coding regions. This tool provides promising opportunities for further investigating translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Nien-Chen Huang, Kai-Ren Luo, Tien-Shin Yu
Summary: We developed a background-free RNA live-cell imaging system by using a split fluorescent protein-based approach. Our system successfully eliminates background fluorescence in the nucleus and enables visualization of subcellular mRNA distribution in living plant cells.
Article
Biochemistry & Molecular Biology
Robert M. Martin, Madalena R. de Almeida, Eduardo Gameiro, Sergio F. de Almeida
Summary: We developed RHINO, a genetically encoded sensor that can selectively bind RNA:DNA hybrids for live-cell imaging of cellular R-loops. With the help of RHINO, we investigated the dynamics of R-loops at nucleoli, telomeres, and protein-coding genes, and found significant variations across these regions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Fabio de Moliner, Zuzanna Konieczna, Lorena Mendive-Tapia, Rebecca S. Saleeb, Katie Morris, Juan Antonio Gonzalez-Vera, Takeshi Kaizuka, Seth G. N. Grant, Mathew H. Horrocks, Marc Vendrell
Summary: The multiple applications of super-resolution microscopy have led to the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. In this study, we have built a library of benzodiazole amino acids and examined their potential as background-free fluorescence microscopy probes. The results show that benzodiazole amino acids retain the binding capabilities of bioactive peptides and exhibit excellent signal-to-background ratios.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Tong Li, Mengxu Sun, Suping Xia, Ting Huang, Rong-Tian Li, Chunrong Li, Zong Dai, Jin-Xiang Chen, Jun Chen, Nuan Jia
Summary: Here, we developed a binary system based on DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. This system achieved high specificity label-free detection of nucleic acids with a detection limit of 1.34 nM. The method has potential applications in early disease diagnosis and new drug development.
Article
Chemistry, Multidisciplinary
Jingfang Zhao, Limin Xiang
Summary: This article introduces the latest advances in three main RNA imaging tools based on the species of interacting molecules, and discusses their advantages from a technical viewpoint. It also explores future directions and states that this emerging field will bring new insights to RNA biology research.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Laining Zhang, Qidong Si, Kejie Yang, Wenwei Zhang, Thomas W. Okita, Li Tian
Summary: Subcellular mRNA localization is an important mechanism that regulates gene expression and establishes functional networks. Although our understanding of mRNA localization in plant cells is limited, the targeting of mRNA to the endoplasmic reticulum (ER) has been well studied in cereal grains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Eduardo J. Pena, Gabriel Robles Luna, Manfred Heinlein
Summary: This study presents an in vivo plant RNA-labeling system based on the Escherichia coli RNA-binding protein BglG for investigating RNA transport and localization in plants. The research demonstrates the efficiency and specificity of mRNA detection by the BglG system when compared with other systems, showing its potential for studying mobile RNA particles and intercellular RNA transport.
Article
Chemistry, Multidisciplinary
Tom Baladi, Jesper R. Nilsson, Audrey Gallud, Emanuele Celauro, Cecile Gasse, Fabienne Levi-Acobas, Ivo Sarac, Marcel R. Hollenstein, Anders Dahlen, Elin K. Esbjorner, L. Marcus Wilhelmsson
Summary: The study introduces a stealth labeling strategy to efficiently generate RNA transcripts and translate them into correct proteins, providing an important tool for biological research and RNA delivery studies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Cell Biology
Igor Kukhtevich, Mariana Rivero-Romano, Namisha Rakesh, Poonam Bheda, Yagya Chadha, Paulina Rosales-Becerra, Stephan Hamperl, Daniela Bureik, Scarlett Dornauer, Catherine Dargemont, Antonis Kirmizis, Kurt M. Schmoller, Robert Schneider
Summary: RNA distribution during cell division is asymmetric and regulated by factors such as the lifespan regulator Sir2 and replicative age. This study establishes an approach to quantify RNA dynamics in single cells using the diSpinach aptamer in a microfluidics device and validates it using budding yeast as a model.
Article
Multidisciplinary Sciences
Charlotte A. Cialek, Gabriel Galindo, Tatsuya Morisaki, Ning Zhao, Taiowa A. Montgomery, Timothy J. Stasevich
Summary: The authors developed live-cell biosensors to investigate the impact of Argonaute proteins on single-mRNA translation dynamics. They found that Argonaute association gradually silences translation and leads to the clustering and coalescence of mRNA with P-bodies, maintaining a translationally silent state.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Changyu Zhang, Xiao Dong, Sing Yee Ong, Shao Q. Yao
Summary: The organic dark quencher-encapsulated surface-cross-linked micelles (qSCMs) reported in this study show promising potential as nanoquenchers for multicolor imaging of various endogenous biomarkers, with features including simple preparation, broad-spectrum quenching, high quenching efficiency, good stability, and easy surface modification. These nanoquenchers were successfully used to construct a mRNA-detecting nanosensor capable of simultaneous live-cell imaging of actin mRNA and survivin mRNA, with resistance to intracellular conditions and ability to quantify mRNA downregulation in response to treatment with YM155.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jin Wang, Bing Liang Alvin Chew, Yong Lai, Hongping Dong, Luang Xu, Seetharamsingh Balamkundu, Weiling Maggie Cai, Liang Cui, Chuan Fa Liu, Xin-Yuan Fu, Zhenguo Lin, Pei-Yong Shi, Timothy K. Lu, Dahai Luo, Samie R. Jaffrey, Peter C. Dedon
NUCLEIC ACIDS RESEARCH
(2019)
Article
Chemistry, Multidisciplinary
Xing Li, Hyaeyeong Kim, Jacob L. Litke, Jiahui Wu, Samie R. Jaffrey
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemistry & Molecular Biology
Sara Zaccara, Samie R. Jaffrey
Review
Biochemistry & Molecular Biology
Jiahui Wu, Samie R. Jaffrey
CURRENT OPINION IN CHEMICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Longteng Tang, Shuce Zhang, Yufeng Zhao, Nikita D. Rozanov, Liangdong Zhu, Jiahui Wu, Robert E. Campbell, Chong Fang
Summary: The study elucidated the working mechanism of a standalone red fluorescent protein-based Ca2+ biosensor using spectroscopic and computational methods, revealing the changes in excited-state proton transfer route upon Ca2+ binding. This enabled successful Ca2+ imaging in ionomycin-treated human HeLa cells with a significant red/green emission ratio change, outperforming other indicators and paving the way for next-generation biosensors with larger dynamic range and longer emission wavelengths.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Xing Li, Jiahui Wu, Samie R. Jaffrey
Summary: Fluorogenic aptamers can potentially show minimal photobleaching during continuous irradiation due to exchanges with fluorescent dyes, but designing fluorophores for optimized recycling can enhance fluorescence.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Bria S. VarnBuhler, Jared Moon, Sourav Kumar Dey, Jiahui Wu, Samie R. Jaffrey
Summary: This article describes a simplified method for RNA detection using simple unmodified DNA oligonucleotides, which can rapidly detect the target RNA's fluorescent signal. By developing a fluorogenic DNA aptamer called Lettuce, the researchers have achieved rapid detection of the target RNA by binding and activating the fluorescence of DFHBI-1T, a nonfluorescent molecule that resembles the chromophore found in green fluorescent protein.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jiahui Wu, Nina Svensen, Wenjiao Song, Hyaeyeong Kim, Sulei Zhang, Xing Li, Samie R. Jaffrey
Summary: DNA and RNA can self-assemble into various structures, and there are methods available to achieve RNA self-assembly in cells. The use of dimeric aptamers allows the creation of RNA and RNA-protein assemblies in cells. These studies provide an approach for inducing RNA self-assembly, demonstrate that proteins can be recruited to RNA assemblies to genetically encode intracellular RNA-protein assemblies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Immunology
Julien Moretti, Baosen Jia, Zachary Hutchins, Soumit Roy, Hilary Yip, Jiahui Wu, Meimei Shan, Samie R. Jaffrey, Jorn Coers, J. Magarian Blander
Summary: Caspase-11 can detect intracellular lipopolysaccharide (LPS) produced by invasive Gram-negative bacteria, leading to noncanonical activation of the NLRP3 inflammasome. This study found that bacterial mRNA signaling is necessary for the noncanonical activation of NLRP3 inflammasome in macrophages. Concurrent detection of bacterial RNA and LPS binding to pro-caspase-11 mediates the interaction between pro-caspase-11 and NLRP3, triggering the activation of the inflammasome.
Article
Multidisciplinary Sciences
Luiz F. M. Passalacqua, Mary R. Starich, Katie A. Link, Jiahui Wu, Jay R. Knutson, Nico Tjandra, Samie R. Jaffrey, Adrian R. Ferre-D'Amare
Summary: Beetroot, a homodimeric RNA, binds and activates DFAME, a conditional fluorophore derived from GFP. It binds two molecules of DFAME at sites separated by about 30 angstrom, and has distinct structural differences compared to the previously characterized homodimeric aptamer, Corn. Through structure-guided engineering, a variant of Beetroot with a 12-fold fluorescence activation selectivity switch towards DFHO was generated, and Beetroot and this variant form heterodimers that can be used to monitor RNA dimerization through inter-fluorophore interaction.
NATURE COMMUNICATIONS
(2023)
Correction
Cell Biology
Sara Zaccara, Ryan J. Ries, Samie R. Jaffrey
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jared D. Moon, Jiahui Wu, Sourav K. Dey, Jacob L. Litke, Xing Li, Hyaeyeong Kim, Samie R. Jaffrey
Summary: A versatile platform has been developed for designing RNA-based fluorescent small-molecule sensors using highly stable three-way junction RNAs. These sensors, which function as small-molecule-regulated fluorescent sensors, have been successfully utilized to measure the dynamics of S-adenosylmethionine levels in mammalian cells in real time. This strategy is compatible with a variety of metabolite-binding RNA aptamers, fluorogenic aptamers, and three-way junctions, demonstrating a versatile method for generating functional RNA devices in living cells.
CELL CHEMICAL BIOLOGY
(2021)
Article
Oncology
Dario Rizzotto, Sara Zaccara, Annalisa Rossi, Erik Dassi, Alberto Inga
MOLECULAR & CELLULAR ONCOLOGY
(2020)
