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live cell single molecule imaging

Nina G Bozhanova, Mikhail S Baranov, Natalia V Klementieva, Karen S Sarkisyan, Alexey S Gavrikov, Ilia V Yampolsky, Elena V Zagaynova, Sergey A Lukyanov, Konstantin A Lukyanov, Alexander S Mishin
We present protein-PAINT - the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes...
October 1, 2017: Chemical Science
Zhenghong Gao, Noémie Danné, Antoine Guillaume Godin, Brahim Lounis, Laurent Cognet
Fluorescence imaging of biological systems down to the single-molecule level has generated many advances in cellular biology. For applications within intact tissue, single-walled carbon nanotubes (SWCNTs) are emerging as distinctive single-molecule nanoprobes, due to their near-infrared photoluminescence properties. For this, SWCNT surfaces must be coated using adequate molecular moieties. Yet, the choice of the suspension agent is critical since it influences both the chemical and emission properties of the SWCNTs within their environment...
November 16, 2017: Nanomaterials
Mi Li, Dan Dang, Ning Xi, Yuechao Wang, Lianqing Liu
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution...
November 14, 2017: Nanoscale
Suzan Ruijtenberg, Tim A Hoek, Xiaowei Yan, Marvin E Tanenbaum
mRNA translation is a key step in decoding the genetic information stored in DNA. Regulation of translation efficiency contributes to gene expression control and is therefore important for cell fate and function. Here, we describe a recently developed microscopy-based method that allows for visualization of translation of single mRNAs in live cells. The ability to measure translation dynamics of single mRNAs will enable a better understanding of spatiotemporal control of translation, and will provide unique insights into translational heterogeneity of different mRNA molecules in single cells...
2018: Methods in Molecular Biology
Franka Voigt, Jan Eglinger, Jeffrey A Chao
Quantitative fluorescence microscopy techniques are frequently applied to answer fundamental biological questions. Single-molecule RNA imaging methods have enabled the direct observation of the initial steps of the mRNA life cycle in living cells, however, the dynamic mechanisms that regulate mRNA translation are still poorly understood. We have developed an RNA biosensor that can assess the translational state of individual mRNA transcripts with spatiotemporal resolution in living cells. In this chapter, we describe how to perform a TRICK (translating RNA imaging by coat protein knock-off) experiment and specifically focus on a detailed description of our image processing and data analysis procedure...
2018: Methods in Molecular Biology
Hideaki Yoshimura, Takeaki Ozawa
Visualizing RNA in living cells is increasingly important to facilitate accumulation of knowledge about the relation between specific RNA dynamics and physiological events. Single-molecule fluorescence imaging of target RNAs is an excellent approach to analyzing intracellular RNA motion, but it requires special techniques for probe design and microscope setup. Herein, we present a principle and protocol of an RNA visualization probe based on an RNA binding protein of the Pumilio homology domain (PUM-HD). We also describe the setup and operation of a microscope, and introduce an application to visualize telomeric repeats-containing RNA with telomeres and a telomere-related protein: hnRNPA1...
2018: Methods in Molecular Biology
Mingming Chen, Yantao Yang, Christopher J Krueger, Antony K Chen
Conventional molecular beacons (MBs) have been used extensively for imaging specific endogenous RNAs in living cells, but their tendency to generate false-positive signals as a result of nuclease degradation and/or nonspecific binding limits sensitive and accurate imaging of intracellular RNAs. In an attempt to overcome this limitation, MBs have been synthesized with various chemically modified oligonucleotide backbones to confer greater biostability. We have recently developed a new MB architecture composed of 2'-O-methyl RNA (2Me), a fully phosphorothioate (PS) modified loop domain and a phosphodiester stem (2Me/PSLOOP MB)...
2018: Methods in Molecular Biology
Yantao Yang, Mingming Chen, Christopher J Krueger, Andrew Tsourkas, Antony K Chen
Molecular beacons (MBs), a class of oligonucleotide-based probes, have enabled researchers to study various RNA molecules in their native live-cell contexts. However, it is also increasingly recognized that, when delivered into cells, MBs have the tendency to be sequestered into the nucleus where they may generate false positive signals. In an attempt to overcome this issue, MBs have been synthesized with chemically modified oligonucleotide backbones to confer greater biostability. Alternatively, strategies have been developed to minimize nuclear entry...
2018: Methods in Molecular Biology
Ryota Sato, Jun Kozuka, Masahiro Ueda, Reiko Mishima, Yutaro Kumagai, Akimasa Yoshimura, Masafumi Minoshima, Shin Mizukami, Kazuya Kikuchi
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared (NIR) fluorescent probes for protein-labeling, which specifically binds to a mutant β-lactamase tag...
November 9, 2017: Journal of the American Chemical Society
Jan Scrimgeour, Louis T McLane, Patrick S Chang, Jennifer E Curtis
The pericellular matrix is a robust, hyaluronan-rich polymer brush-like structure that controls access to the cell surface, and plays an important role in cell adhesion, migration, and proliferation. We report the observation of single bottlebrush proteoglycan dynamics in the pericellular matrix of living chondrocytes. Our investigations show that the pericellular matrix undergoes gross extension on the addition of exogenous aggrecan, and that this extension is significantly in excess of that observed in traditional particle exclusion assays...
October 25, 2017: Biophysical Journal
Wenqiang Chen, Xiuxiu Yue, Hui Zhang, Wenxiu Li, Liangliang Zhang, Qi Xiao, Chusheng Huang, Jiarong Sheng, Xiangzhi Song
Glutathione (GSH) and hydrogen polysulfides (H2Sn) play crucial roles in many physiological processes. To unravel the complicated interrelationship and cellular cross-talk between GSH and H2Sn, the development of single-molecule fluorescent probes that can selectively sense GSH and H2Sn simultaneously from different emission channels is highly desirable. In this report, we have developed the first dual-detection fluorescent probe, ACC-SePh, which responded to GSH with green fluorescence emission, whereas it reacted with H2Sn and emitted blue fluorescence...
November 15, 2017: Analytical Chemistry
Anne Beghin, Adel Kechkar, Corey Butler, Florian Levet, Marine Cabillic, Olivier Rossier, Gregory Giannone, Rémi Galland, Daniel Choquet, Jean-Baptiste Sibarita
Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software...
October 30, 2017: Nature Methods
Yuki Nakamura, Nobuhisa Umeki, Mitsuhiro Abe, Yasushi Sako
Noonan syndrome (NS) is a congenital hereditary disorder associated with developmental and cardiac defects. Some patients with NS carry mutations in SOS, a guanine nucleotide exchange factor (GEF) for the small GTPase RAS. NS mutations have been identified not only in the GEF domain, but also in various domains of SOS, suggesting that multiple mechanisms disrupt SOS function. In this study, we examined three NS mutations in different domains of SOS to clarify the abnormality in its translocation to the plasma membrane, where SOS activates RAS...
October 26, 2017: Scientific Reports
Ivana Horvathova, Franka Voigt, Anna V Kotrys, Yinxiu Zhan, Caroline G Artus-Revel, Jan Eglinger, Michael B Stadler, Luca Giorgetti, Jeffrey A Chao
RNA degradation plays a fundamental role in regulating gene expression. In order to characterize the spatiotemporal dynamics of RNA turnover in single cells, we developed a fluorescent biosensor based on dual-color, single-molecule RNA imaging that allows intact transcripts to be distinguished from stabilized degradation intermediates. Using this method, we measured mRNA decay in single cells and found that individual degradation events occur independently within the cytosol and are not enriched within processing bodies...
November 2, 2017: Molecular Cell
Titiwat Sungkaworn, Marie-Lise Jobin, Krzysztof Burnecki, Aleksander Weron, Martin J Lohse, Davide Calebiro
G-protein-coupled receptors mediate the biological effects of many hormones and neurotransmitters and are important pharmacological targets. They transmit their signals to the cell interior by interacting with G proteins. However, it is unclear how receptors and G proteins meet, interact and couple. Here we analyse the concerted motion of G-protein-coupled receptors and G proteins on the plasma membrane and provide a quantitative model that reveals the key factors that underlie the high spatiotemporal complexity of their interactions...
October 26, 2017: Nature
Michael J Lawson, Daniel Camsund, Jimmy Larsson, Özden Baltekin, David Fange, Johan Elf
In this work, we present a proof-of-principle experiment that extends advanced live cell microscopy to the scale of pool-generated strain libraries. We achieve this by identifying the genotypes for individual cells in situ after a detailed characterization of the phenotype. The principle is demonstrated by single-molecule fluorescence time-lapse imaging of Escherichia coli strains harboring barcoded plasmids that express a sgRNA which suppresses different genes in the E. coli genome through dCas9 interference...
October 17, 2017: Molecular Systems Biology
Varun K A Sreenivasan, Wan Aizuddin Wan Razali, Kai Zhang, Rashmi R Pillai, Avishkar Saini, Denitza Denkova, Marina Santiago, Hannah Brown, Jeremy Thompson, Mark Connor, Ewa M Goldys, Andrei V Zvyagin
At the forefront of developing fluorescent probes for biological imaging applications are enhancements aimed at increasing their brightness, contrast, and photostability, especially toward demanding applications of single-molecule detection. In comparison with existing probes, nanorubies exhibit unlimited photostability and a long emission lifetime (∼4 ms), which enable continuous imaging at single-particle sensitivity in highly scattering and fluorescent biological specimens. However, their wide application as fluorescence probes has so far been hindered by the absence of facile methods for scaled-up high-volume production and molecularly specific targeting...
November 2, 2017: ACS Applied Materials & Interfaces
Yoshiaki Suzuki, Kanako Tsutsumi, Tatsuya Miyamoto, Hisao Yamamura, Yuji Imaizumi
Two-pore-domain K+ (K2P) channels sense a wide variety of stimuli such as mechanical stress, inhalational anesthetics, and changes in extracellular pH or temperature. The K2P channel activity forms a background K+ current and, thereby, contributes to resting membrane potentials. Six subfamilies including fifteen subtypes of K2P channels have been identified. Each K2P channel molecule with two pores consists of a homodimer of each subtype. In addition, a few heterodimers mainly within the same subfamilies have been found recently...
2017: PloS One
Zejun Wang, Yao Luo, Xiaodong Xie, Xingjie Hu, Haiyun Song, Yun Zhao, Jiye Shi, Lihua Wang, Gennadi Glinsky, Nan Chen, Ratnesh Lal, Chunhai Fan
Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their functions and reveals novel mechanisms at the single-cell resolution. Here, we report the development of an aptamer-initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)-mimicking turn-on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, nascent mRNA molecules recruited split Broccoli and brought the two fragments to the spatial proximity, which in-situ formed a fluorophore-binding site and turned on fluorescence...
October 9, 2017: Angewandte Chemie
Liangqi Xie, Sharon E Torigoe, Jifang Xiao, Daniel H Mai, Li Li, Fred P Davis, Peng Dong, Herve Marie-Nelly, Jonathan Grimm, Luke Lavis, Xavier Darzacq, Claudia Cattoglio, Zhe Liu, Robert Tjian
Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular "dialog" between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Krüppel-like factor 4 (Klf4) expression in naïve pluripotency...
September 1, 2017: Genes & Development
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