1
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Sgouralis I, Xu LWQ, Jalihal AP, Kilic Z, Walter NG, Pressé S. BNP-Track: a framework for superresolved tracking. Nat Methods 2024:10.1038/s41592-024-02349-9. [PMID: 39039336 DOI: 10.1038/s41592-024-02349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/03/2024] [Indexed: 07/24/2024]
Abstract
Superresolution tools, such as PALM and STORM, provide nanoscale localization accuracy by relying on rare photophysical events, limiting these methods to static samples. By contrast, here, we extend superresolution to dynamics without relying on photodynamics by simultaneously determining emitter numbers and their tracks (localization and linking) with the same localization accuracy per frame as widefield superresolution on immobilized emitters under similar imaging conditions (≈50 nm). We demonstrate our Bayesian nonparametric track (BNP-Track) framework on both in cellulo and synthetic data. BNP-Track develops a joint (posterior) distribution that learns and quantifies uncertainty over emitter numbers and their associated tracks propagated from shot noise, camera artifacts, pixelation, background and out-of-focus motion. In doing so, we integrate spatiotemporal information into our distribution, which is otherwise compromised by modularly determining emitter numbers and localizing and linking emitter positions across frames. For this reason, BNP-Track remains accurate in crowding regimens beyond those accessible to other single-particle tracking tools.
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Affiliation(s)
- Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, TN, USA
| | - Lance W Q Xu
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Ameya P Jalihal
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA.
- Department of Physics, Arizona State University, Tempe, AZ, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
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2
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Li Y, Xu M, Qi Z. Deciphering molecular mechanisms of phase separation in RNA biology by single-molecule biophysical technologies. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1034-1041. [PMID: 37337634 PMCID: PMC10415185 DOI: 10.3724/abbs.2023113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 06/21/2023] Open
Abstract
Ribonucleic acid (RNA) biology has emerged as one of the most important areas in modern biology and biomedicine. RNA and RNA-binding proteins (RBPs) are involved in forming biomolecular condensates, which are crucial for RNA metabolism. To quantitively decipher the molecular mechanisms of RNP granules, researchers have turned to single-molecule biophysical techniques, such as single-molecule Förster resonance energy transfer (smFRET), in vivo single-molecule imaging technique with single particle tracking (SPT), DNA Curtains, optical tweezers, and atomic force microscopy (AFM). These methods are used to investigate the molecular biophysical properties within RNP granules, as well as the molecular interactions between RNA and RBPs and RBPs themselves, which are challenging to study using traditional experimental methods of the liquid-liquid phase separation (LLPS) field, such as fluorescence recovery after photobleaching (FRAP). In this work, we summarize the applications of single-molecule biophysical techniques in RNP granule studies and highlight how these methods can be used to reveal the molecular mechanisms of RNP granules.
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Affiliation(s)
- Yuchen Li
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
| | - Mengmeng Xu
- Tsinghua-Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Zhi Qi
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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3
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Sgouralis I, Xu (徐伟青) LW, Jalihal AP, Walter NG, Pressé S. BNP-Track: A framework for superresolved tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535459. [PMID: 37066320 PMCID: PMC10104004 DOI: 10.1101/2023.04.03.535459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Assessing dynamic processes at single molecule scales is key toward capturing life at the level of its molecular actors. Widefield superresolution methods, such as STORM, PALM, and PAINT, provide nanoscale localization accuracy, even when distances between fluorescently labeled single molecules ("emitters") fall below light's diffraction limit. However, as these superresolution methods rely on rare photophysical events to distinguish emitters from both each other and background, they are largely limited to static samples. In contrast, here we leverage spatiotemporal correlations of dynamic widefield imaging data to extend superresolution to simultaneous multiple emitter tracking without relying on photodynamics even as emitter distances from one another fall below the diffraction limit. We simultaneously determine emitter numbers and their tracks (localization and linking) with the same localization accuracy per frame as widefield superresolution does for immobilized emitters under similar imaging conditions (≈50nm). We demonstrate our results for both in cellulo data and, for benchmarking purposes, on synthetic data. To this end, we avoid the existing tracking paradigm relying on completely or partially separating the tasks of emitter number determination, localization of each emitter, and linking emitter positions across frames. Instead, we develop a fully joint posterior distribution over the quantities of interest, including emitter tracks and their total, otherwise unknown, number within the Bayesian nonparametric paradigm. Our posterior quantifies the full uncertainty over emitter numbers and their associated tracks propagated from origins including shot noise and camera artefacts, pixelation, stochastic background, and out-of-focus motion. Finally, it remains accurate in more crowded regimes where alternative tracking tools cannot be applied.
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Affiliation(s)
- Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, TN 37996, USA
| | - Lance W.Q. Xu (徐伟青)
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ameya P. Jalihal
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Nils G. Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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4
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Vo HD, Forero-Quintero LS, Aguilera LU, Munsky B. Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise. Front Cell Dev Biol 2023; 11:1133994. [PMID: 37305680 PMCID: PMC10250612 DOI: 10.3389/fcell.2023.1133994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction: Despite continued technological improvements, measurement errors always reduce or distort the information that any real experiment can provide to quantify cellular dynamics. This problem is particularly serious for cell signaling studies to quantify heterogeneity in single-cell gene regulation, where important RNA and protein copy numbers are themselves subject to the inherently random fluctuations of biochemical reactions. Until now, it has not been clear how measurement noise should be managed in addition to other experiment design variables (e.g., sampling size, measurement times, or perturbation levels) to ensure that collected data will provide useful insights on signaling or gene expression mechanisms of interest. Methods: We propose a computational framework that takes explicit consideration of measurement errors to analyze single-cell observations, and we derive Fisher Information Matrix (FIM)-based criteria to quantify the information value of distorted experiments. Results and Discussion: We apply this framework to analyze multiple models in the context of simulated and experimental single-cell data for a reporter gene controlled by an HIV promoter. We show that the proposed approach quantitatively predicts how different types of measurement distortions affect the accuracy and precision of model identification, and we demonstrate that the effects of these distortions can be mitigated through explicit consideration during model inference. We conclude that this reformulation of the FIM could be used effectively to design single-cell experiments to optimally harvest fluctuation information while mitigating the effects of image distortion.
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Affiliation(s)
- Huy D. Vo
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Linda S. Forero-Quintero
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Luis U. Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
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5
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Zhang Z, Xu H, Fan Y, Zhang X, Wang W, Zhu JJ, Min Q. Mass Nanotags Mediate Parallel Amplifications on Nanointerfaces for Multiplexed Profiling of RNAs. NANO LETTERS 2023; 23:1820-1829. [PMID: 36790360 DOI: 10.1021/acs.nanolett.2c04690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Multiplexed profiling of RNAs aids in a comprehensive understanding of multiparameter-defined cellular processes and pathological states. We herein present a mass nanotags-enabled interfacial assembly system (MNTs-AS) with parallel amplification motors for simultaneous assaying of multiple RNAs in biosystems by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Four kinds of MNTs encoding corresponding RNA can be cyclically assembled on magnetic beads by target-triggered catalytic hairpin assembly (CHA) machineries on nanointerfaces, generating multiplexed and amplified characteristic ion signals assigned to target RNAs upon MALDI MS interrogation. By virtue of high sensitivity and multiplexing capability, the MNTs-AS-based MS assay allows precision subtyping of diverse breast cancer cells and their exosomes by multiplexed profiling of miRNA-21, miRNA-373, miRNA-155, and manganese superoxide dismutase mRNA via a single MS inquiry. This method provides a promising tool for unraveling multiple RNA-involved biological events in fundamental research and distinguishing different cancer subtypes in clinical practice.
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Affiliation(s)
- Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hongmei Xu
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Yinyin Fan
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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6
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Saurabh A, Niekamp S, Sgouralis I, Pressé S. Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores. J Phys Chem B 2022; 126:10.1021/acs.jpcb.2c01889. [PMID: 35649158 PMCID: PMC9712593 DOI: 10.1021/acs.jpcb.2c01889] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative fluorescence analysis is often used to derive chemical properties, including stoichiometries, of biomolecular complexes. One fundamental underlying assumption in the analysis of fluorescence data─whether it be the determination of protein complex stoichiometry by super-resolution, or step-counting by photobleaching, or the determination of RNA counts in diffraction-limited spots in RNA fluorescence in situ hybridization (RNA-FISH) experiments─is that fluorophores behave identically and do not interact. However, recent experiments on fluorophore-labeled DNA origami structures such as fluorocubes have shed light on the nature of the interactions between identical fluorophores as these are brought closer together, thereby raising questions on the validity of the modeling assumption that fluorophores do not interact. Here, we analyze photon arrival data under pulsed illumination from fluorocubes where distances between dyes range from 2 to 10 nm. We discuss the implications of non-additivity of brightness on quantitative fluorescence analysis.
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Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stefan Niekamp
- Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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7
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Wang Y, Li B, Tian T, Liu Y, Zhang J, Qian K. Advanced on-site and in vitro signal amplification biosensors for biomolecule analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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Shi H, Grodner B, De Vlaminck I. Recent advances in tools to map the microbiome. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19:100289. [PMID: 34151052 PMCID: PMC8208594 DOI: 10.1016/j.cobme.2021.100289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microbes thrive in diverse habitats. They often form ecological niches with rich species diversity and complex spatial structure. These communities drive biogeochemical cycles in the environment and modulate host health in the human body. Much has been learned about the makeup of human and environmental microbiota via metagenomic DNA sequencing, but information on spatial interactions between microbes and between microbes and their environment remains scarce. Here, we review recent advances in tools to map the biogeography of microbiomes. We discuss methods to spatially map microbial genes, transcripts, and metabolites. We also examine future directions for microbiome mapping technologies that will allow improved understanding of both microbiome structure and function. Finally, we reflect on the impact of these methods in Biomedical Engineering.
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Affiliation(s)
- Hao Shi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Benjamin Grodner
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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9
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Depaix A, Mlynarska-Cieslak A, Warminski M, Sikorski PJ, Jemielity J, Kowalska J. RNA Ligation for Mono and Dually Labeled RNAs. Chemistry 2021; 27:12190-12197. [PMID: 34114681 DOI: 10.1002/chem.202101909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3'-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3',5'-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5'-fluorescently labeled m7 Gp3 Am -capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.
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Affiliation(s)
- Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Agnieszka Mlynarska-Cieslak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
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10
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Li M. Optimization of N-hydroxysuccinimide ester coupling with aminoallyl-modified RNA for fluorescent labeling. Bioengineered 2021; 11:599-606. [PMID: 32449472 PMCID: PMC8291868 DOI: 10.1080/21655979.2020.1765487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Site-specific fluorescent labeling of RNA is crucial for obtaining the structural and dynamic information of RNAs by fluorescence techniques. Post-synthetic modification of RNA based on N-hydroxysuccinimide (NHS) coupling reaction is an economic, efficient and simple strategy to introduce fluorophore to samples. However, this strategy are not that frequently used in RNA molecules, and the reported reaction conditions and yields varied among different systems. This study results mainly focused on screening the reaction conditions (reactants concentrations, dimethylsulfoxide concentration, solution conditions, pH and reaction time) between NHS-linked fluorophore and aminoallyl-RNA (aa-RNA) to optimize the yield of fluorescent RNA up to 55%, doubled the initial yield. What's more, as low as one tenth of fluorescent reagent was used in our protocol compared with the reported protocols, greatly reducing the experimental cost. The protocol can be applied as a general guide potentially for RNA labeling by NHS-ester coupling reaction.
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Affiliation(s)
- Mengyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
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11
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Solis-Santos M, Ordóñez M, Ochoa-Terán A, Morales-Cueto R, Labastida-Galván V. Synthesis of phthalimides, isoindolin-1-ones and isoindolines bearing aminobenzoic acids as a new fluorescent compounds. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Amplified electrochemical detection of circular RNA in breast cancer patients using ferrocene-capped gold nanoparticle/streptavidin conjugates. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Li P, Jia C, Guo X. Structural Transition Dynamics in Carbon
Electrode‐Based Single‐Molecule
Junctions. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Peihui Li
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
| | - Chuancheng Jia
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
| | - Xuefeng Guo
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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14
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Tian M, Zhang K, Zhang Y, Zhou H, Yuan Z, Lu C. Design of ratiometric monoaromatic fluorescence probe via modulating intramolecular hydrogen bonding: A case study of alkaline phosphatase sensing. Anal Chim Acta 2021; 1143:144-156. [PMID: 33384112 DOI: 10.1016/j.aca.2020.11.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/19/2022]
Abstract
Monoaromatic molecules are a category of molecules containing a single aromatic ring which generally emit light in the ultraviolet (UV) region. Despite their facile preparation, the UV emission greatly limits their application as organic probes. In this study, we developed a general method to red shift the emission of monoaromatic molecules. Significant fluorescence red-shift (∼100 nm per intramolecular hydrogen bonding) can be achieved by introducing intramolecular hydrogen bonding units to benzene, a typical monoaromatic molecule. Upon increasing the number of hydrogen bonding units on the benzene ring, UV, blue, and green emissions are screened, which are switchable by simply breaking/restoration the intramolecular hydrogen bonding. As a demonstration, with the breaking of one intramolecular H-bonding, the green emission (λemmax = 533 nm) of 2,5-dihydroxyterephthalic acid (DHTA) changed to cyan (λemmax = 463 nm) upon the formation of its phosphorylated form (denoted as PDHTA), which, in the presence of alkaline phosphatase (ALP), hydrolyzed and recovered the green emission. By taking advantage of the switchable emission colors, ratiometric in vitro and endogenous ALP sensing was achieved. This general approach offers a great promise to develop organic probes with tunable emissions for fluorescence analysis and imaging by different intramolecular hydrogen bonding.
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Affiliation(s)
- Mingce Tian
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Kai Zhang
- College of Preclinical Medicine, Southwest Medical University, Luzhou, 646000, China.
| | - Yanjun Zhang
- College of Preclinical Medicine, Southwest Medical University, Luzhou, 646000, China
| | - He Zhou
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhiqin Yuan
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Chao Lu
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China.
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15
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Jalihal AP, Schmidt A, Gao G, Little SR, Pitchiaya S, Walter NG. Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles. J Biol Chem 2021; 296:100044. [PMID: 33168632 PMCID: PMC7948973 DOI: 10.1074/jbc.rev120.010899] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/09/2023] Open
Abstract
Biological liquid-liquid phase separation has gained considerable attention in recent years as a driving force for the assembly of subcellular compartments termed membraneless organelles. The field has made great strides in elucidating the molecular basis of biomolecular phase separation in various disease, stress response, and developmental contexts. Many important biological consequences of such "condensation" are now emerging from in vivo studies. Here we review recent work from our group and others showing that many proteins undergo rapid, reversible condensation in the cellular response to ubiquitous environmental fluctuations such as osmotic changes. We discuss molecular crowding as an important driver of condensation in these responses and suggest that a significant fraction of the proteome is poised to undergo phase separation under physiological conditions. In addition, we review methods currently emerging to visualize, quantify, and modulate the dynamics of intracellular condensates in live cells. Finally, we propose a metaphor for rapid phase separation based on cloud formation, reasoning that our familiar experiences with the readily reversible condensation of water droplets help understand the principle of phase separation. Overall, we provide an account of how biological phase separation supports the highly intertwined relationship between the composition and dynamic internal organization of cells, thus facilitating extremely rapid reorganization in response to internal and external fluctuations.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Guoming Gao
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Biophysics Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Saffron R Little
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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16
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Aparin IO, Sergeeva OV, Mishin AS, Khaydukov EV, Korshun VA, Zatsepin TS. Excimer-FRET Cascade in Dual DNA Probes: Open Access to Large Stokes Shift, Enhanced Acceptor Light up, and Robust RNA Sensing. Anal Chem 2020; 92:7028-7036. [DOI: 10.1021/acs.analchem.0c00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ilya O. Aparin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Olga V. Sergeeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Evgeny V. Khaydukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Federal Scientific Research Centre “Crystallography and Photonics” RAS, 119333 Moscow, Russia
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, 119021 Moscow, Russia
- Department of Biology and Biotechnology, National Research University Higher School of Economics, 117312 Moscow, Russia
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
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17
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Abstract
A key approach to investigating RNA species in live mammalian cells is the ability to label them with fluorescent tags and track their dynamics in the complex cellular environment. The growing appreciation for the diversity of RNAs in nature, especially the roles of small, non-coding RNAs for cell function, calls for development of orthogonal RNA tagging systems. We previously developed Riboglow, a new RNA tagging system that features modular elements and hence the possibility to customize features for each application of choice. Riboglow consists of an RNA tag that is genetically fused to the RNA of interest and a small molecule that binds the RNA tag and elicits a fluorescence light up signal. Here, we present an overview of the Riboglow platform and compare and contrast the system with existing RNA tagging systems. Two step by step protocols for implementation of RNA imaging with Riboglow in live mammalian cells are presented, with special emphasis on guidelines that drive choices for modular elements in the Riboglow platform. Such modular elements include the RNA tag sequence and size, the number of RNA tag repeats per tagged RNA, the fluorescent color of the probe, the identity of the chemical linker in the probe, and the concentration of the probe used in live cells. Together, Riboglow is a new RNA tagging platform that enables robust live cell imaging of RNA dynamics, and this detailed protocol and guidelines for implementation will enable broad usage of Riboglow.
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18
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Schmidt A, Gao G, Little SR, Jalihal AP, Walter NG. Following the messenger: Recent innovations in live cell single molecule fluorescence imaging. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1587. [PMID: 31990126 DOI: 10.1002/wrna.1587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/19/2019] [Accepted: 01/04/2020] [Indexed: 01/16/2023]
Abstract
Messenger RNAs (mRNAs) convey genetic information from the DNA genome to proteins and thus lie at the heart of gene expression and regulation of all cellular activities. Live cell single molecule tracking tools enable the investigation of mRNA trafficking, translation and degradation within the complex environment of the cell and in real time. Over the last 5 years, nearly all tools within the mRNA tracking toolbox have been improved to achieve high-quality multi-color tracking in live cells. For example, the bacteriophage-derived MS2-MCP system has been improved to facilitate cloning and achieve better signal-to-noise ratio, while the newer PP7-PCP system now allows for orthogonal tracking of a second mRNA or mRNA region. The coming of age of epitope-tagging technologies, such as the SunTag, MoonTag and Frankenbody, enables monitoring the translation of single mRNA molecules. Furthermore, the portfolio of fluorogenic RNA aptamers has been expanded to improve cellular stability and achieve a higher fluorescence "turn-on" signal upon fluorogen binding. Finally, microinjection-based tools have been shown to be able to track multiple RNAs with only small fluorescent appendages and to track mRNAs together with their interacting partners. We systematically review and compare the advantages, disadvantages and demonstrated applications in discovering new RNA biology of this refined, expanding toolbox. Finally, we discuss developments expected in the near future based on the limitations of the current methods. This article is categorized under: RNA Export and Localization > RNA Localization RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Guoming Gao
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Biophysics Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Saffron R Little
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
| | - Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Cell and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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19
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Walter NG. Biological Pathway Specificity in the Cell-Does Molecular Diversity Matter? Bioessays 2019; 41:e1800244. [PMID: 31245864 PMCID: PMC6684156 DOI: 10.1002/bies.201800244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/09/2019] [Indexed: 01/07/2023]
Abstract
Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low-concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low-affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass-action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture of cellular components significantly shapes biological pathway specificity. In particular, on-pathway-i.e., "functional"-become those interactions thermodynamically and kinetically stable enough to survive the incessant onslaught of the many off-pathway ("nonfunctional") interactions. Consequently, to better understand the molecular biology of the cell a further paradigm shift is needed toward mechanistic experimental and computational approaches that probe intracellular diversity and complexity more directly. Also see the video abstract here https://youtu.be/T19X_zYaBzg.
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20
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. J Am Chem Soc 2019; 141:7562-7571. [PMID: 30986047 DOI: 10.1021/jacs.9b02697] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although genetically encoded light-up RNA aptamers have become promising tools for visualizing and tracking RNAs in living cells, aptamer/ligand pairs that emit in the far-red and near-infrared (NIR) regions are still rare. In this work, we developed a light-up RNA aptamer that binds silicon rhodamines (SiRs). SiRs are photostable, NIR-emitting fluorophores that change their open-closed equilibrium between the noncolored spirolactone and the fluorescent zwitterion in response to their environment. This property is responsible for their high cell permeability and fluorogenic behavior. Aptamers binding to SiR were in vitro selected from a combinatorial RNA library. Sequencing, bioinformatic analysis, truncation, and mutational studies revealed a 50-nucleotide minimal aptamer, SiRA, which binds with nanomolar affinity to the target SiR. In addition to silicon rhodamines, SiRA binds structurally related rhodamines and carborhodamines, making it a versatile tool spanning the far-red region of the spectrum. Photophysical characterization showed that SiRA is remarkably resistant to photobleaching and constitutes the brightest far-red light-up aptamer system known to date owing to its favorable features: a fluorescence quantum yield of 0.98 and an extinction coefficient of 86 000 M-1cm-1. Using the SiRA system, we visualized the expression of RNAs in bacteria in no-wash live-cell imaging experiments and also report stimulated emission depletion (STED) super-resolution microscopy images of aptamer-based, fluorescently labeled mRNA in live cells. This work represents, to our knowledge, the first application of the popular SiR dyes and of intramolecular spirocyclization as a means of background reduction in the field of aptamer-based RNA imaging. We anticipate a high potential for this novel RNA labeling tool to address biological questions.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Peng Gao
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Institute of Toxicology and Genetics (ITG) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
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21
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Pitchiaya S, Mourao MDA, Jalihal AP, Xiao L, Jiang X, Chinnaiyan AM, Schnell S, Walter NG. Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality. Mol Cell 2019; 74:521-533.e6. [PMID: 30952514 DOI: 10.1016/j.molcel.2019.03.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/21/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022]
Abstract
Cellular RNAs often colocalize with cytoplasmic, membrane-less ribonucleoprotein (RNP) granules enriched for RNA-processing enzymes, termed processing bodies (PBs). Here we track the dynamic localization of individual miRNAs, mRNAs, and long non-coding RNAs (lncRNAs) to PBs using intracellular single-molecule fluorescence microscopy. We find that unused miRNAs stably bind to PBs, whereas functional miRNAs, repressed mRNAs, and lncRNAs both transiently and stably localize within either the core or periphery of PBs, albeit to different extents. Consequently, translation potential and 3' versus 5' placement of miRNA target sites significantly affect the PB localization dynamics of mRNAs. Using computational modeling and supporting experimental approaches, we show that partitioning in the PB phase attenuates mRNA silencing, suggesting that physiological mRNA turnover occurs predominantly outside of PBs. Instead, our data support a PB role in sequestering unused miRNAs for surveillance and provide a framework for investigating the dynamic assembly of RNP granules by phase separation at single-molecule resolution.
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Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Marcio D A Mourao
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Consulting for Statistics, Computing and Analytics Research, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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22
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Murayama K, Kashida H, Asanuma H. The Use of Serinol Nucleic Acids as Ultrasensitive Molecular Beacons. Methods Mol Biol 2019; 1973:261-279. [PMID: 31016708 DOI: 10.1007/978-1-4939-9216-4_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular beacons composed of the artificial serinol nucleic acid (SNA) have demonstrated utility as novel fluorescence probes for visualization of RNA in fixed cells using both conventional fluorescence in situ hybridization (FISH) and wash-free FISH protocols. The SNA molecular beacons have higher affinity for target RNA and greater sensitivity than molecular beacons composed of DNA. Here we describe facile synthesis of the SNA using a conventional DNA synthesizer and protocols for purification by PAGE and HPLC as well as methods for use of the SNA molecular beacon in FISH.
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Affiliation(s)
- Keiji Murayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
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23
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RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications. Catalysts 2018. [DOI: 10.3390/catal8110550] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DNAzymes are catalytically active DNA molecules that are normally isolated through in vitro selection methods, among which RNA-cleaving DNAzymes that catalyze the cleavage of a single RNA linkage embedded within a DNA strand are the most studied group of this DNA enzyme family. Recent advances in DNA nanotechnology and engineering have generated many RNA-cleaving DNAzymes with unique recognition and catalytic properties. Over the past decade, numerous RNA-cleaving, DNAzymes-based functional probes have been introduced into many research areas, such as in vitro diagnostics, intracellular imaging, and in vivo therapeutics. This review focus on the fundamental insight into RNA-Cleaving DNAzymes and technical tricks for their intracellular and in vivo applications, highlighting the recent progress in the clinical trial of RNA-Cleaving DNAzymes with selected examples. The challenges and opportunities for the future translation of RNA-cleaving DNAzymes for biomedicine are also discussed.
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24
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Ishii A, Nakata N. Synthesis and Photophysical Property of 1-Chalcogeno-1,3-butadiene Derivatives and the Related Compounds Incorporated in a Dibenzobarrelene Skeleton. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.1042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akihiko Ishii
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University
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25
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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26
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Liu Y, Holmstrom E, Yu P, Tan K, Zuo X, Nesbitt DJ, Sousa R, Stagno JR, Wang YX. Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA. Nat Protoc 2018; 13:987-1005. [PMID: 29651055 DOI: 10.1038/nprot.2018.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Site-specific incorporation of labeled nucleotides is an extremely useful synthetic tool for many structural studies (e.g., NMR, electron paramagnetic resonance (EPR), fluorescence resonance energy transfer (FRET), and X-ray crystallography) of RNA. However, specific-position-labeled RNAs >60 nt are not commercially available on a milligram scale. Position-selective labeling of RNA (PLOR) has been applied to prepare large RNAs labeled at desired positions, and all the required reagents are commercially available. Here, we present a step-by-step protocol for the solid-liquid hybrid phase method PLOR to synthesize 71-nt RNA samples with three different modification applications, containing (i) a 13C15N-labeled segment; (ii) discrete residues modified with Cy3, Cy5, or biotin; or (iii) two iodo-U residues. The flexible procedure enables a wide range of downstream biophysical analyses using precisely localized functionalized nucleotides. All three RNAs were obtained in <2 d, excluding time for preparing reagents and optimizing experimental conditions. With optimization, the protocol can be applied to other RNAs with various labeling schemes, such as ligation of segmentally labeled fragments.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Erik Holmstrom
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Kemin Tan
- Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois, USA
| | - Xiaobing Zuo
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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28
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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29
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Abstract
The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression. Remarkably, the development of systems-level studies has been accompanied by tremendous progress in the visualization of individual RNA molecules in single cells, such that it is now possible to image RNA species with a single-molecule resolution from birth to translation or decay. Monitoring quantitatively, with unprecedented spatiotemporal resolution, the fate of individual molecules has been key to understanding the molecular mechanisms underlying the different steps of RNA regulation. This has also revealed biologically relevant, intracellular and intercellular heterogeneities in RNA distribution or regulation. More recently, the convergence of imaging and high-throughput technologies has led to the emergence of spatially resolved transcriptomic techniques that provide a means to perform large-scale analyses while preserving spatial information. By generating transcriptome-wide data on single-cell RNA content, or even subcellular RNA distribution, these methodologies are opening avenues to a wide range of network-level studies at the cell and organ-level, and promise to strongly improve disease diagnostic and treatment.In this introductory chapter, we highlight how recently developed technologies aiming at detecting and visualizing RNA molecules have contributed to the emergence of entirely new research fields, and to dramatic progress in our understanding of gene expression regulation.
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Affiliation(s)
- Caroline Medioni
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France.
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30
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Yoshimura H. Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications. Biochemistry 2017; 57:200-208. [PMID: 29164876 DOI: 10.1021/acs.biochem.7b00983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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31
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Synthetic biological approaches for RNA labelling and imaging: design principles and future opportunities. Curr Opin Biotechnol 2017; 48:153-158. [DOI: 10.1016/j.copbio.2017.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 12/15/2022]
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32
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Daher M, Widom JR, Tay W, Walter NG. Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding. J Mol Biol 2017; 430:509-523. [PMID: 29128594 DOI: 10.1016/j.jmb.2017.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Living cells contain diverse biopolymers, creating a heterogeneous crowding environment, the impact of which on RNA folding is poorly understood. Here, we have used single-molecule fluorescence resonance energy transfer to monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene glycol and yeast cell extract as crowding agents. As expected, polyethylene glycol stabilizes the docked, catalytically active state of the ribozyme, in part through excluded volume effects; unexpectedly, we found evidence that it additionally displays soft, non-specific interactions with the ribozyme. Yeast extract has a profound effect on folding at protein concentrations 1000-fold lower than found intracellularly, suggesting the dominance of specific interactions over volume exclusion. Gel shift assays and affinity pull-down followed by mass spectrometry identified numerous non-canonical RNA-binding proteins that stabilize ribozyme folding; the apparent chaperoning activity of these ubiquitous proteins significantly compensates for the low-counterion environment of the cell.
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Affiliation(s)
- May Daher
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Wendy Tay
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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33
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Gao HD, Thanasekaran P, Chen TH, Chang YH, Chen YJ, Lee HM. An Integrated System to Remotely Trigger Intracellular Signal Transduction by Upconversion Nanoparticle-mediated Kinase Photoactivation. J Vis Exp 2017. [PMID: 28892036 DOI: 10.3791/55769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Upconversion nanoparticle (UCNP)-mediated photoactivation is a new approach to remotely control bioeffectors with much less phototoxicity and with deeper tissue penetration. However, the existing instrumentation on the market is not readily compatible with upconversion application. Therefore, modifying the commercially available instrument is essential for this research. In this paper, we first illustrate the modifications of a conventional fluorimeter and fluorescence microscope to make them compatible for photon upconversion experiments. We then describe the synthesis of a near-infrared (NIR)-triggered caged protein kinase A catalytic subunit (PKA) immobilized on a UCNP complex. Parameters for microinjection and NIR photoactivation procedures are also reported. After the caged PKA-UCNP is microinjected into REF52 fibroblast cells, the NIR irradiation, which is significantly superior to conventional UV irradiation, efficiently triggers the PKA signal transduction pathway in living cells. In addition, positive and negative control experiments confirm that the PKA-induced pathway leading to the disintegration of stress fibers is specifically triggered by NIR irradiation. Thus, the use of protein-modified UCNP provides an innovative approach to remotely control light-modulated cellular experiments, in which direct exposure to UV light must be avoided.
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Affiliation(s)
- Hua-De Gao
- Institute of Chemistry, Academia Sinica; Department of Chemistry, National Taiwan University
| | | | - Tzu-Ho Chen
- Institute of Chemistry, Academia Sinica; Department of Chemistry, National Taiwan University
| | - Yu-Hsu Chang
- Department of Materials and Mineral Resources Engineering, National Taipei University of Technology;
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica; Department of Chemistry, National Taiwan University
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34
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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35
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Single-Molecule Counting of Point Mutations by Transient DNA Binding. Sci Rep 2017; 7:43824. [PMID: 28262827 PMCID: PMC5338343 DOI: 10.1038/srep43824] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022] Open
Abstract
High-confidence detection of point mutations is important for disease diagnosis and clinical practice. Hybridization probes are extensively used, but are hindered by their poor single-nucleotide selectivity. Shortening the length of DNA hybridization probes weakens the stability of the probe-target duplex, leading to transient binding between complementary sequences. The kinetics of probe-target binding events are highly dependent on the number of complementary base pairs. Here, we present a single-molecule assay for point mutation detection based on transient DNA binding and use of total internal reflection fluorescence microscopy. Statistical analysis of single-molecule kinetics enabled us to effectively discriminate between wild type DNA sequences and single-nucleotide variants at the single-molecule level. A higher single-nucleotide discrimination is achieved than in our previous work by optimizing the assay conditions, which is guided by statistical modeling of kinetics with a gamma distribution. The KRAS c.34 A mutation can be clearly differentiated from the wild type sequence (KRAS c.34 G) at a relative abundance as low as 0.01% mutant to WT. To demonstrate the feasibility of this method for analysis of clinically relevant biological samples, we used this technology to detect mutations in single-stranded DNA generated from asymmetric RT-PCR of mRNA from two cancer cell lines.
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36
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Custer TC, Walter NG. In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines. Protein Sci 2017; 26:1363-1379. [PMID: 28028853 PMCID: PMC5477532 DOI: 10.1002/pro.3108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
Abstract
RNA plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexes-"molecular machines"-used to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of RNAs involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular RNA functions, including those of protein coding messenger RNAs (mRNAs). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label RNA molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 RNA polymerase to body label an RNA with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2'-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mRNA, whereas protein coding is severely diminished in the case of body labeling.
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Affiliation(s)
- Thomas C Custer
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, 48109.,Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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37
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A Novel Method to Quantify RNA-Protein Interactions In Situ Using FMTRIP and Proximity Ligation. Methods Mol Biol 2017; 1468:155-70. [PMID: 27662876 DOI: 10.1007/978-1-4939-4035-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBP) and small RNAs regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNAs) through their interactions with specific cis-acting elements within target RNAs. Here, we describe a novel method to detect protein-mRNA interactions, which combines FLAG-peptide modified, multiply-labeled tetravalent RNA imaging probes (FMTRIPs) with proximity ligation (PLA), and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity.
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38
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Chen J, Wu J, Hong Y. The morpholino molecular beacon for specific RNA visualization in vivo. Chem Commun (Camb) 2016; 52:3191-4. [PMID: 26810703 DOI: 10.1039/c5cc07124k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A non-invasive fluorescent probe, morpholino molecular beacon (MO-MB), was designed for RNA visualization in vivo. Featuring negligible toxicity, stability, and high target specificity in living embryos, MO-MB is superior to conventional probes and has the potential for specific RNA visualization in basic biological and clinical research.
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Affiliation(s)
- Jianbin Chen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Jikui Wu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. and College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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39
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Vasilescu C, Tanase M, Dragomir M, Calin GA. From mobility to crosstalk. A model of intracellular miRNAs motion may explain the RNAs interaction mechanism on the basis of target subcellular localization. Math Biosci 2016; 280:50-61. [PMID: 27498347 DOI: 10.1016/j.mbs.2016.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/18/2016] [Accepted: 07/27/2016] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs), 22 nucleotides long molecules with the function to reduce gene expression by inhibiting mRNA translation through partial complementary to one or more messenger RNA (mRNA) molecules. A single miRNA can reduce the expression levels of hundreds of genes and one mRNA can be a target for many miRNAs. Despite the study models used so far, miRNAs and mRNAs cannot be seen as acting in an isolated manner or even "in pairs". They most likely exert their complex actions through numerous overlapping interrelations. One of the models depicting interdependence of intracytoplasmic RNAs is the crosstalk model. It is based on a competition between several target mRNAs which are regulated by the same miRNA. In this paper, we will discuss the mobility mechanism of miRNAs, recently suggested by data from "single particle tracking" experiments. These data suggests that miRNA intracellular mobility may be of "intermittent active transport"(IAT) type. IAT is a mobility model composed by alternation of active transport (AT) and Brownian motion (BM). Based on a mathematical model, we concluded that, AT phase may explain the efficiency in reaching far targets and the BM phase may explain the competition. Furthermore, we suggest that the interaction between miRNAs and their targets depends on the concentration of the molecules, the affinity between the molecules and also on the intracellular localization of the molecules. Hence, the probability that a miRNA interacts with its target depends also on the distance to the target and the macromolecular crowding. Taken together, our data proposes an intracytoplasmic mobility mechanism for miRNA and shows that this model can partially explain the RNA crosstalk.
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Affiliation(s)
- Catalin Vasilescu
- Department of Surgery, Fundeni Clinical Hospital, 258 Fundeni Street, Bucharest, 22328, Romania; "Carol Davila" University of Medicine and Pharmacy, Bulevardul Eroii Sanitari 8, Bucharest 050474, Romania.
| | - Mihai Tanase
- University Politehnica of Bucharest, Splaiul Independenei 313, Bucharest, 060042, Romania
| | - Mihnea Dragomir
- "Carol Davila" University of Medicine and Pharmacy, Bulevardul Eroii Sanitari 8, Bucharest 050474, Romania
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Center for RNA Interference and Non-coding RNAs, The University of Texas, MD Anderson Cancer Center, So Campus Research Bldg 3 (3SCR4.3424), 1881 East Road, Unit 1950, Houston 77030, TX, USA
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40
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Tsekouras K, Custer TC, Jashnsaz H, Walter NG, Pressé S. A novel method to accurately locate and count large numbers of steps by photobleaching. Mol Biol Cell 2016; 27:3601-3615. [PMID: 27654946 PMCID: PMC5221592 DOI: 10.1091/mbc.e16-06-0404] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/15/2016] [Indexed: 12/19/2022] Open
Abstract
Photobleaching event counting is a single-molecule fluorescence technique that is increasingly being used to determine the stoichiometry of protein and RNA complexes composed of many subunits in vivo as well as in vitro. By tagging protein or RNA subunits with fluorophores, activating them, and subsequently observing as the fluorophores photobleach, one obtains information on the number of subunits in a complex. The noise properties in a photobleaching time trace depend on the number of active fluorescent subunits. Thus, as fluorophores stochastically photobleach, noise properties of the time trace change stochastically, and these varying noise properties have created a challenge in identifying photobleaching steps in a time trace. Although photobleaching steps are often detected by eye, this method only works for high individual fluorophore emission signal-to-noise ratios and small numbers of fluorophores. With filtering methods or currently available algorithms, it is possible to reliably identify photobleaching steps for up to 20-30 fluorophores and signal-to-noise ratios down to ∼1. Here we present a new Bayesian method of counting steps in photobleaching time traces that takes into account stochastic noise variation in addition to complications such as overlapping photobleaching events that may arise from fluorophore interactions, as well as on-off blinking. Our method is capable of detecting ≥50 photobleaching steps even for signal-to-noise ratios as low as 0.1, can find up to ≥500 steps for more favorable noise profiles, and is computationally inexpensive.
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Affiliation(s)
- Konstantinos Tsekouras
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202
| | - Thomas C Custer
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109.,Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Hossein Jashnsaz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Steve Pressé
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 .,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202
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41
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Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 2016; 45:926-937. [PMID: 27625389 PMCID: PMC5314786 DOI: 10.1093/nar/gkw787] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 07/29/2016] [Accepted: 08/20/2016] [Indexed: 11/21/2022] Open
Abstract
Transfer RNA (tRNA) links messenger RNA nucleotide sequence with amino acid sequence during protein synthesis. Despite the importance of tRNA for translation, its subcellular distribution and diffusion properties in live cells are poorly understood. Here, we provide the first direct report on tRNA diffusion localization in live bacteria. We internalized tRNA labeled with organic fluorophores into live bacteria, applied single-molecule fluorescence imaging with single-particle tracking and localized and tracked single tRNA molecules over seconds. We observed two diffusive species: fast (with a diffusion coefficient of ∼8 μm2/s, consistent with free tRNA) and slow (consistent with tRNA bound to larger complexes). Our data indicate that a large fraction of internalized fluorescent tRNA (>70%) appears to diffuse freely in the bacterial cell. We also obtained the subcellular distribution of fast and slow diffusing tRNA molecules in multiple cells by normalizing for cell morphology. While fast diffusing tRNA is not excluded from the bacterial nucleoid, slow diffusing tRNA is localized to the cell periphery (showing a 30% enrichment versus a uniform distribution), similar to non-uniform localizations previously observed for mRNA and ribosomes.
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Affiliation(s)
- Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
| | - Ian Farrell
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA.,Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Zeev Smilansky
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
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42
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DeHaven AC, Norden IS, Hoskins AA. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:683-701. [PMID: 27198613 PMCID: PMC4990488 DOI: 10.1002/wrna.1358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/20/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
The process of removing intronic sequences from a precursor to messenger RNA (pre-mRNA) to yield a mature mRNA transcript via splicing is an integral step in eukaryotic gene expression. Splicing is carried out by a cellular nanomachine called the spliceosome that is composed of RNA components and dozens of proteins. Despite decades of study, many fundamentals of spliceosome function have remained elusive. Recent developments in single-molecule fluorescence microscopy have afforded new tools to better probe the spliceosome and the complex, dynamic process of splicing by direct observation of single molecules. These cutting-edge technologies enable investigators to monitor the dynamics of specific splicing components, whole spliceosomes, and even cotranscriptional splicing within living cells. WIREs RNA 2016, 7:683-701. doi: 10.1002/wrna.1358 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexander C. DeHaven
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Ian S. Norden
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Aaron A. Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
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43
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Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Applications of PLOR in labeling large RNAs at specific sites. Methods 2016; 103:4-10. [PMID: 27033177 PMCID: PMC10802919 DOI: 10.1016/j.ymeth.2016.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022] Open
Abstract
Incorporation of modified or labeled nucleotides at specific sites in RNAs is critical for gaining insights into the structure and function of RNAs. Preparation of site-specifically labeled large RNAs in amounts suitable for structural or functional studies is extremely difficult using current methodologies. The position-selective labeling of RNA, PLOR, is a recently developed method that makes such syntheses possible. PLOR allows incorporation of various probes, including (2)D/(13)C/(15)N-isotopic labels, Cy3/Cy5/Alexa488/Alexa555 fluorescent dyes, biotin and other chemical groups, into specific positions in long RNAs. Here, we describe in detail the use of PLOR to label RNAs at specific segment(s) or discrete sites.
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Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Ping Yu
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marzena Dyba
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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44
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Zurla C, Jung J, Santangelo PJ. Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes. Analyst 2016; 141:548-62. [PMID: 26605378 PMCID: PMC4701657 DOI: 10.1039/c5an01959a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.
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Affiliation(s)
- C Zurla
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - J Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - P J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
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45
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Almlie CK, Hsiao A, Burrows SM. Dye-Specific Wavelength Offsets to Resolve Spectrally Overlapping and Co-Localized Two-Photon Induced Fluorescence. Anal Chem 2016; 88:1462-7. [DOI: 10.1021/acs.analchem.5b04476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- C. Kyle Almlie
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Austen Hsiao
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Sean M. Burrows
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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46
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Harkiss AH, Sutherland A. Recent advances in the synthesis and application of fluorescent α-amino acids. Org Biomol Chem 2016; 14:8911-8921. [DOI: 10.1039/c6ob01715k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The design and synthesis of new fluorescent α-amino acids as well as their application in imaging of biological systems has been reviewed.
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Affiliation(s)
- Alexander H. Harkiss
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow G12 8QQ
| | - Andrew Sutherland
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow G12 8QQ
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47
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Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Deniz AA. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution. J Mol Biol 2015; 428:301-307. [PMID: 26707199 DOI: 10.1016/j.jmb.2015.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 01/12/2023]
Abstract
The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects.
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Affiliation(s)
- Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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50
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Ishii A, Makishima Y, Nakata N. Red and Near-Infrared Photoluminescence of D-π-A-Type Compounds Based on a 1,4-Diaryl-1-thio-1,3-butadiene Conjugated System in a Dibenzobarrelene Skeleton. J Org Chem 2015; 80:11598-604. [DOI: 10.1021/acs.joc.5b02189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Akihiko Ishii
- Department of Chemistry,
Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yukihiro Makishima
- Department of Chemistry,
Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Norio Nakata
- Department of Chemistry,
Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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