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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by mass photometry. SOFT MATTER 2024. [PMID: 38832814 DOI: 10.1039/d3sm01702h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Nathaniel J S Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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2
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572878. [PMID: 38187562 PMCID: PMC10769409 DOI: 10.1101/2023.12.21.572878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Nathaniel J. S. Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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3
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Pang HH, Huang CY, Chen PY, Li NS, Hsu YP, Wu JK, Fan HF, Wei KC, Yang HW. Bioengineered Bacteriophage-Like Nanoparticles as RNAi Therapeutics to Enhance Radiotherapy against Glioblastomas. ACS NANO 2023; 17:10407-10422. [PMID: 37120837 DOI: 10.1021/acsnano.3c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since glioblastomas (GBMs) are radioresistant malignancies and most GBM recurrences occur in radiotherapy, increasing the effectiveness of radiotherapy by gene-silencing has recently attracted attention. However, the difficulty in precisely tuning the composition and RNA loading in nanoparticles leads to batch-to-batch variations of the RNA therapeutics, thus significantly restricting their clinical translation. Here, we bioengineer bacteriophage Qβ particles with a designed broccoli light-up three-way junction (b-3WJ) RNA scaffold (contains two siRNA/miRNA sequences and one light-up aptamer) packaging for the silencing of genes in radioresistant GBM cells. The in vitro results demonstrate that the cleavage of de novo designed b-3WJ RNA by Dicer enzyme can be easily monitored in real-time using fluorescence microscopy, and the TrQβ@b-3WJLet-7gsiEGFR successfully knocks down EGFR and IKKα simultaneously and thereby inactivates NF-κB signaling to inhibit DNA repair. Delivery of TrQβ@b-3WJLet-7gsiEGFR through convection-enhanced delivery (CED) infusion followed by 2Gy X-ray irradiation demonstrated that the median survival was prolonged to over 60 days compared with the 2Gy X-ray irradiated group (median survival: 31 days). Altogether, the results of this study could be critical for the design of RNAi-based genetic therapeutics, and CED infusion serves as a powerful delivery system for promoting radiotherapy against GBMs without evidence of systemic toxicity.
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Affiliation(s)
- Hao-Han Pang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Chiung-Yin Huang
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
| | - Pin-Yuan Chen
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, 222 Maijin Rd., Keelung 20401, Taiwan
| | - Nan-Si Li
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Ying-Pei Hsu
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Department of Materials and Optoelectronic Science, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Jan-Kai Wu
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Hsiu-Fang Fan
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, 6, Sec 2, JunCheng Rd., New Taipei City 23652, Taiwan
| | - Hung-Wei Yang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
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4
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Milstein JN, Nino DF, Zhou X, Gradinaru CC. Single-molecule counting applied to the study of GPCR oligomerization. Biophys J 2022; 121:3175-3187. [PMID: 35927960 PMCID: PMC9463696 DOI: 10.1016/j.bpj.2022.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.
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Affiliation(s)
- Joshua N Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Daniel F Nino
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Xiaohan Zhou
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
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5
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Diffraction-limited molecular cluster quantification with Bayesian nonparametrics. NATURE COMPUTATIONAL SCIENCE 2022; 2:102-111. [PMID: 35874114 PMCID: PMC9302895 DOI: 10.1038/s43588-022-00197-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Life’s fundamental processes involve multiple molecules operating in close proximity within cells. To probe the composition and kinetics of molecular clusters confined within small (diffraction-limited) regions, experiments often report on the total fluorescence intensity simultaneously emitted from labeled molecules confined to such regions. Methods exist to enumerate total fluorophore numbers (e.g., step counting by photobleaching). However, methods aimed at step counting by photobleaching cannot treat photophysical dynamics in counting nor learn their associated kinetic rates. Here we propose a method to simultaneously enumerate fluorophores and determine their individual photophysical state trajectories. As the number of active (fluorescent) molecules at any given time is unknown, we rely on Bayesian nonparametrics and use specialized Monte Carlo algorithms to derive our estimates. Our formulation is benchmarked on synthetic and real data sets. While our focus here is on photophysical dynamics (in which labels transition between active and inactive states), such dynamics can also serve as a proxy for other types of dynamics such as assembly and disassembly kinetics of clusters. Similarly, while we focus on the case where all labels are initially fluorescent, other regimes, more appropriate to photoactivated localization microscopy, where fluorophores are instantiated in a non-fluorescent state, fall within the scope of the framework. As such, we provide a complete and versatile framework for the interpretation of complex time traces arising from the simultaneous activity of up to 100 fluorophores.
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6
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Su Z, Li T, Wu D, Wu Y, Li G. Recent Progress on Single-Molecule Detection Technologies for Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:458-469. [PMID: 34985271 DOI: 10.1021/acs.jafc.1c06808] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.
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Affiliation(s)
- Zhuoqun Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Tong Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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7
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Dey A, Maiti S. Determining the Stoichiometry of Amyloid Oligomers by Single-Molecule Photobleaching. Methods Mol Biol 2022; 2538:55-74. [PMID: 35951293 DOI: 10.1007/978-1-0716-2529-3_5] [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] [Indexed: 06/15/2023]
Abstract
Small oligomers are the initial intermediates in the pathway to amyloid fibril formation. They have a distinct identity from the monomers as well as from the protofibrils and the fibrils, both in their structure and in their properties. In many cases, they play a crucial biological role. However, due to their transient nature, they are difficult to characterize. "Oligomer" is a diffuse definition, encompassing aggregates of many different sizes, and this lack of precise definition causes much confusion and disagreement between different research groups. Here, we define the small oligomers as "n"-mers with n < 10, which is the size range in which the amyloid proteins typically exist at the initial phase of the aggregation process. Since the oligomers dynamically interconvert into each other, a solution of aggregating amyloid proteins will contain a distribution of sizes. A precise characterization of an oligomeric solution will, therefore, require quantification of the relative population of each size. Size-based separation methods, such as size-exclusion chromatography, are typically used to characterize this distribution. However, if the interconversion between oligomers of different sizes is fast, this would not yield reliable results. Single-molecule photobleaching (smPB) is a direct method to evaluate this size distribution in a heterogeneous solution without separation. In addition, understanding the mechanism of action of amyloid oligomers requires knowing the affinity of each oligomer type to different cellular components, such as the cell membrane. These measurements are also amenable to smPB. Here we show how to perform smPB, both for oligomers in solution and for oligomers attached to the membrane.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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8
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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9
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers SV. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol Microbiol 2021; 116:943-956. [PMID: 34219289 DOI: 10.1111/mmi.14781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Since autophosphorylation and dephosphorylation of KaiC are central properties for the function of KaiC, we asked whether autophosphorylation is also a property of ArlH proteins. We observed that both ArlH from the euryarchaeon Pyrococcus furiosus (PfArlH) and from the crenarchaeon Sulfolobus acidocaldarius (SaArlH) have autophosphorylation activity. Using a combination of single-molecule fluorescence measurements and biochemical assays, we show that autophosphorylation of ArlH is closely linked to its oligomeric state when bound to hexameric ArlI. These experiments also strongly suggest that ArlH is a hexamer in its ArlI-bound state. Mutagenesis of the putative catalytic residue (Glu-57 in SaArlH) in ArlH results in a reduced autophosphorylation activity and abolished archaellation and motility in S. acidocaldarius, indicating that optimum phosphorylation activity of ArlH is essential for archaellation and motility.
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Affiliation(s)
- J Nuno de Sousa Machado
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Leonie Vollmar
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rashmi Kumariya
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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10
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Das A, Vishvakarma V, Dey A, Dey S, Gupta A, Das M, Vishwakarma KK, Roy DS, Yadav S, Kesarwani S, Venkatramani R, Maiti S. Biophysical properties of the isolated spike protein binding helix of human ACE2. Biophys J 2021; 120:2785-2792. [PMID: 34214538 PMCID: PMC8241576 DOI: 10.1016/j.bpj.2021.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/22/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
The entry of the severe acute respiratory syndrome coronavirus 2 virus in human cells is mediated by the binding of its surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. A 23-residue long helical segment (SBP1) at the binding interface of human ACE2 interacts with viral spike protein and therefore has generated considerable interest as a recognition element for virus detection. Unfortunately, emerging reports indicate that the affinity of SBP1 to the receptor-binding domain of the spike protein is much lower than that of the ACE2 receptor itself. Here, we examine the biophysical properties of SBP1 to reveal factors leading to its low affinity for the spike protein. Whereas SBP1 shows good solubility (solubility > 0.8 mM), circular dichroism spectroscopy shows that it is mostly disordered with some antiparallel β-sheet content and no helicity. The helicity is substantial (>20%) only upon adding high concentrations (≥20% v/v) of 2,2,2-trifluoroethanol, a helix promoter. Fluorescence correlation spectroscopy and single-molecule photobleaching studies show that the peptide oligomerizes at concentrations >50 nM. We hypothesized that mutating the hydrophobic residues (F28, F32, and F40) of SBP1, which do not directly interact with the spike protein, to alanine would reduce peptide oligomerization without affecting its spike binding affinity. Whereas the mutant peptide (SBP1mod) shows substantially reduced oligomerization propensity, it does not show improved helicity. Our study shows that the failure of efforts, so far, to produce a short SBP1 mimic with a high affinity for the spike protein is not only due to the lack of helicity but is also due to the heretofore unrecognized problem of oligomerization.
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Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Mitradip Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | - Debsankar Saha Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Swati Yadav
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Shubham Kesarwani
- Centre for Cardiovascular Biology and Disease, Institute of Stem Cell Science and Regenerative Medicine (inStem), Gandhi Krishi Vigyan Kendra Campus, Bangalore, Karnataka, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.
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11
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Nguyen DP, Nguyen HTH, Do LH. Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells. ACS Catal 2021; 11:5148-5165. [PMID: 34824879 PMCID: PMC8612649 DOI: 10.1021/acscatal.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.
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Affiliation(s)
- Dat P. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Huong T. H. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Loi H. Do
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
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12
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers S. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum.. [DOI: 10.1101/2021.03.19.436134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeonPyrococcus furiosus (PfArlH)and the crenarchaeonSulfolobus acidocaldarius(SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 inSaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.
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13
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Zhang D, Liu SG, Fu Z, He Y, Gao W, Shi X. The method for integrating dual-color fluorescence colocalization and single molecule photobleaching technology on the theophylline sensing platform. MethodsX 2020; 7:101155. [PMID: 33304835 PMCID: PMC7708945 DOI: 10.1016/j.mex.2020.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/13/2020] [Indexed: 11/17/2022] Open
Abstract
• Smart usage of single molecule photobleaching technology and dual-color fluorescence colocalization is of critical importance for exploiting the sensing platform. Here, we provide the detailed protocols related to the article “A split aptamer sensing platform for highly sensitive detection of theophylline based on dual-color fluorescence colocalization and single molecule photobleaching” (published online by Biosensors and Bioelectronics) (Liu et al., 2020). The protocols contain: (1) how to clean the slides; (2) how to prepare the probe and detection sample; (3) Single molecule imaging; 4) Data processing by using the Image J. Finally, we used a simple model to confirm the feasibility of the method for integrating dual-color fluorescence colocalization and single molecule photobleaching technology on the theophylline sensing platform. • A simple, ultrasensitive method for the detection of theophylline. • The method is easily comprehensible. • Both strategy formulation and data processing are simple, learnability, and highly reproducible.
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Affiliation(s)
- Dong Zhang
- Laboratory of Micro and Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shi Gang Liu
- Laboratory of Micro and Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zhaodi Fu
- Analytical Testing Laboratory, Changsha Research Institute of Mining and Metallurgy CO., LTD., Changsha 410012, China
| | - Yu He
- Laboratory of Micro and Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Wenli Gao
- Laboratory of Micro and Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xingbo Shi
- Laboratory of Micro and Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
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14
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Eriksen MS, Nikolaienko O, Hallin EI, Grødem S, Bustad HJ, Flydal MI, Merski I, Hosokawa T, Lascu D, Akerkar S, Cuéllar J, Chambers JJ, O'Connell R, Muruganandam G, Loris R, Touma C, Kanhema T, Hayashi Y, Stratton MM, Valpuesta JM, Kursula P, Martinez A, Bramham CR. Arc self-association and formation of virus-like capsids are mediated by an N-terminal helical coil motif. FEBS J 2020; 288:2930-2955. [PMID: 33175445 DOI: 10.1111/febs.15618] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a protein interaction hub with diverse roles in intracellular neuronal signaling, and important functions in neuronal synaptic plasticity, memory, and postnatal cortical development. Arc has homology to retroviral Gag protein and is capable of self-assembly into virus-like capsids implicated in the intercellular transfer of RNA. However, the molecular basis of Arc self-association and capsid formation is largely unknown. Here, we identified a 28-amino-acid stretch in the mammalian Arc N-terminal (NT) domain that is necessary and sufficient for self-association. Within this region, we identified a 7-residue oligomerization motif, critical for the formation of virus-like capsids. Purified wild-type Arc formed capsids as shown by transmission and cryo-electron microscopy, whereas mutant Arc with disruption of the oligomerization motif formed homogenous dimers. An atomic-resolution crystal structure of the oligomerization region peptide demonstrated an antiparallel coiled-coil interface, strongly supporting NT-NT domain interactions in Arc oligomerization. The NT coil-coil interaction was also validated in live neurons using fluorescence lifetime FRET imaging, and mutation of the oligomerization motif disrupted Arc-facilitated endocytosis. Furthermore, using single-molecule photobleaching, we show that Arc mRNA greatly enhances higher-order oligomerization in a manner dependent on the oligomerization motif. In conclusion, a helical coil in the Arc NT domain supports self-association above the dimer stage, mRNA-induced oligomerization, and formation of virus-like capsids. DATABASE: The coordinates and structure factors for crystallographic analysis of the oligomerization region were deposited at the Protein Data Bank with the entry code 6YTU.
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Affiliation(s)
- Maria S Eriksen
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Oleksii Nikolaienko
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Norway
| | - Sverre Grødem
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Helene J Bustad
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Marte I Flydal
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Ian Merski
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Tomohisa Hosokawa
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Daniela Lascu
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Shreeram Akerkar
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Jorge Cuéllar
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts Amherst, MA, USA
| | - Rory O'Connell
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Christine Touma
- Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, USA
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway.,Faculty of Biochemistry and Molecular Biology & Biocenter Oulu, University of Oulu, Finland
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, Norway.,KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Norway
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15
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A split aptamer sensing platform for highly sensitive detection of theophylline based on dual-color fluorescence colocalization and single molecule photobleaching. Biosens Bioelectron 2020; 166:112461. [PMID: 32745928 DOI: 10.1016/j.bios.2020.112461] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 01/19/2023]
Abstract
A new split aptamer sensing platform is developed for highly sensitive and selective detection of theophylline based on single molecule photobleaching (SMPB) technique. The sensing system contains two probes. One is formed by one streptavidin and four biotinylated RNA fragments labelled with fluorescein isothiocyanate (FITC). Each biotinylated RNA fragment contains two repeating aptamer fragments. The other probe is the complementary aptamer fragment labelled with Cy5 dye. The existence of theophylline can trigger the first probe to bind as many as eight Cy5-labelled probes. The average combined number depends on the theophylline concentration and can be measured by SMPB technique. In the sensing system, the dual-color fluorescence colocalization is performed by the red fluorophore (Cy5) and green fluorophore (FITC), in which the red fluorophore is utilized for quantitative counting of photobleaching steps, while the green fluorophore serves as a counting reference to increase detection efficiency. On basis of the principle, an ultra-sensitive sensing platform of theophylline is created with a low limit of detection (LOD) of 0.092 nM. This work provides not only a highly sensitive method for theophylline detection but also a novel perspective for the applications of SMPB technology to construct biosensors.
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16
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Schaefer M, Kalwa H. Theoretical background of light-emitting diode total internal reflection fluorescence microscopy and photobleaching lifetime analysis of membrane-associated proteins-Part II. JOURNAL OF BIOPHOTONICS 2020; 13:e201960181. [PMID: 31965728 DOI: 10.1002/jbio.201960181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/16/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
The selective microscopic imaging of the plasma membrane and adjacent structures by total internal reflection fluorescence (TIRF) microscopy is a versatile and frequently used technique in cell biology. A reduction of imaging artifacts in objective-type TIRF microscopy can be achieved by circular or multi-spot laser illumination or by using noncoherent light sources that are projected into the back focal plane as a light annulus. Light-emitting diode (LED)-based TIRF excitation is a recent advancement of the latter strategy. While some basic principles of LED-TIRF remain the same as in laser-based methods, the calculation of penetration depth, the flatness of illumination and the amount of available illumination power differ. This study provides the theoretical framework for the construction and adjustment of LED-TIRF. Using state-of-the art high power LED emitters, LED-TIRF achieves excitation efficiencies that are comparable to laser-based systems and homogenously illuminate the entire field of view, thus, allowing variation of the penetration depth or quantitative photobleaching-assisted imaging protocols. Using autofluorescent transmembrane, soluble and membrane-attached fusion proteins, we provide examples for a photobleaching-based assessment of the exchange kinetics of proteins within living human endothelial cells.
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Affiliation(s)
- Michael Schaefer
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Universität Leipzig, Leipzig, Germany
| | - Hermann Kalwa
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Universität Leipzig, Leipzig, Germany
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17
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Yokota H. DNA-Unwinding Dynamics of Escherichia coli UvrD Lacking the C-Terminal 40 Amino Acids. Biophys J 2020; 118:1634-1648. [PMID: 32142643 DOI: 10.1016/j.bpj.2020.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
The E. coli UvrD protein is a nonhexameric DNA helicase that belongs to superfamily I and plays a crucial role in both nucleotide excision repair and methyl-directed mismatch repair. Previous data suggested that wild-type UvrD has optimal activity in its oligomeric form. However, crystal structures of the UvrD-DNA complex were only resolved for monomeric UvrD, using a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C). However, biochemical findings performed using UvrDΔ40C indicated that this mutant failed to dimerize, although its DNA-unwinding activity was comparable to that of wild-type UvrD. Although the C-terminus plays essential roles in nucleic acid binding for many proteins with helicase and dimerization activities, the exact function of the C-terminus is poorly understood. Thus, to understand the function of the C-terminal amino acids of UvrD, we performed single-molecule direct visualization. Photobleaching of dye-labeled UvrDΔ40C molecules revealed that two or three UvrDΔ40C molecules could bind simultaneously to an 18-bp double-stranded DNA with a 20-nucleotide, 3' single-stranded DNA tail in the absence of ATP. Simultaneous visualization of association/dissociation of the mutant with/from DNA and the DNA-unwinding dynamics of the mutant in the presence of ATP demonstrated that, as with wild-type UvrD, two or three UvrDΔ40C molecules were primarily responsible for DNA unwinding. The determined association/dissociation rate constants for the second bound monomer were ∼2.5-fold larger than that of wild-type UvrD. The involvement of multiple UvrDΔ40C molecules in DNA unwinding was also observed under a physiological salt concentration (200 mM NaCl). These results suggest that multiple UvrDΔ40C molecules, which may form an oligomer, play an active role in DNA unwinding in vivo and that deleting the C-terminal 40 residues altered the interaction of the second UvrD monomer with DNA without affecting the interaction with the first bound UvrD monomer.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Hamamatsu, Shizuoka, Japan.
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18
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Garry J, Li Y, Shew B, Gradinaru CC, Rutenberg AD. Bayesian counting of photobleaching steps with physical priors. J Chem Phys 2020; 152:024110. [DOI: 10.1063/1.5132957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jon Garry
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Yuchong Li
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Brandon Shew
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Claudiu C. Gradinaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Andrew D. Rutenberg
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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19
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Platnich CM, Hariri AA, Sleiman HF, Cosa G. Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques. Acc Chem Res 2019; 52:3199-3210. [PMID: 31675207 DOI: 10.1021/acs.accounts.9b00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.
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Affiliation(s)
- Casey M. Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Amani A. Hariri
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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20
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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21
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Dey S, Maiti S. Single-molecule photobleaching: Instrumentation and applications. J Biosci 2018; 43:447-454. [PMID: 30002264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule photobleaching (smPB) technique is a powerful tool for characterizing molecular assemblies. It can provide a direct measure of the number of monomers constituting a given oligomeric particle and generate the oligomer size distribution in a specimen. A major current application of this technique is in understanding protein aggregation, which is linked to many incurable diseases. Quantitative measurement of the size distribution of an aggregating protein in a physiological solution remains a difficult task, since techniques such as dynamic light scattering or fluorescence correlation spectroscopy (FCS) can provide an average size, but cannot accurately resolve the underlying size distribution. Here we describe the smPB method as implemented on a home-built total internal reflection fluorescence microscope (TIRF). We first describe the construction of a TIRF microscope, and then demonstrate the power of smPB by characterizing a solution of Amylin (hIAPP) oligomers, a 37-residue peptide whose aggregation is associated with Type II diabetes. We compare our results with FCS data obtained from the same specimen, and discuss the advantages and disadvantages of the two techniques.
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Affiliation(s)
- Simli Dey
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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22
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23
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Lee D, Hwang J, Seo Y, Gilad AA, Choi J. Optical Immunosensors for the Efficient Detection of Target Biomolecules. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0087-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Shi X, He Y, Gao W, Liu X, Ye Z, Liu H, Xiao L. Quantifying the Degree of Aggregation from Fluorescent Dye-Conjugated DNA Probe by Single Molecule Photobleaching Technology for the Ultrasensitive Detection of Adenosine. Anal Chem 2018; 90:3661-3665. [PMID: 29468866 DOI: 10.1021/acs.analchem.7b05317] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, we demonstrated a single molecule photobleaching-based strategy for the ultrasensitive detection of adenosine. A modified split aptamer was designed to specifically recognize individual adenosine molecules in solution. The specific binding of dye-labeled short strand DNA probes onto the elongated aptamer strand in the presence of adenosine resulted in a concentration-dependent self-aggregation process. The degree-of-aggregation (DOA) of the short DNA probes on the elongated aptamer strand could then be accurately determined based on the single molecule photobleaching measurement. Through statistically analyzing the DOA under different target concentrations, a well-defined curvilinear relationship between the DOA and target molecule concentration (e.g., adenosine) was established. The limit-of-detection (LOD) is down to 44.5 pM, which is lower than those recently reported results with fluorescence-based analysis. Owing to the high sensitivity and excellent selectivity, the sensing strategy described herein would find broad applications in biomolecule analysis under complicated surroundings.
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Affiliation(s)
- Xingbo Shi
- Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology , Hunan Agricultural University , Changsha , 410128 , China.,State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , China
| | - Yu He
- Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology , Hunan Agricultural University , Changsha , 410128 , China
| | - Wenli Gao
- Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology , Hunan Agricultural University , Changsha , 410128 , China
| | - Xiaoying Liu
- College of Science , Hunan Agricultural University , Changsha , 410128 , China
| | - Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin , 300071 , China
| | - Hua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin , 300071 , China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry , Nankai University , Tianjin , 300071 , China
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25
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Zagato E, Vermeulen L, Dewitte H, Van Imschoot G, Vandenbroucke RE, Demeester J, De Smedt SC, Neyts K, Remaut K, Braeckmans K. Quantifying the Average Number of Nucleic Acid Therapeutics per Nanocarrier by Single Particle Tracking Microscopy. Mol Pharm 2018; 15:1142-1149. [DOI: 10.1021/acs.molpharmaceut.7b00999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elisa Zagato
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Lotte Vermeulen
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Heleen Dewitte
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Griet Van Imschoot
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Roosmarijn E. Vandenbroucke
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Jo Demeester
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Stefaan C. De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Kristiaan Neyts
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University Ottergemsesteenweg 460, 9000 Ghent, Belgium
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26
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Xu C, Haque F, Jasinski DL, Binzel DW, Shu D, Guo P. Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy. Cancer Lett 2017; 414:57-70. [PMID: 28987384 DOI: 10.1016/j.canlet.2017.09.043] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 01/22/2023]
Abstract
The past decades have witnessed the successful transition of several nanotechnology platforms into the clinical trials. However, specific delivery of therapeutics to tumors is hindered by several barriers including cancer recognition and tissue penetration, particle heterogeneity and aggregation, and unfavorable pharmacokinetic profiles such as fast clearance and organ accumulation. With the advent of RNA nanotechnology, a series of RNA nanoparticles have been successfully constructed to overcome many of the aforementioned challenges for in vivo cancer targeting with favorable biodistribution profiles. Compared to other nanodelivery platforms, the physiochemical properties of RNA nanoparticles can be tuned with relative ease for investigating the in vivo behavior of nanoparticles upon systemic injection. The size, shape, and surface chemistry, especially hydrophobic modifications, exert significant impacts on the in vivo fate of RNA nanoparticles. Rationally designed RNA nanoparticles with defined stoichiometry and high homogeneity have been demonstrated to specifically target tumor cells while avoiding accumulation in healthy vital organs after systemic injection. RNA nanoparticles were proven to deliver therapeutics such as siRNA and anti-miRNA to block tumor growth in several animal models. Although the release of anti-miRNA from the RNA nanoparticles has achieved high efficiency of tumor regression in multiple animal models, the efficiency of endosomal escape for siRNA delivery needs further improvement. This review focuses on the advances and perspectives of this promising RNA nanotechnology platform for cancer targeting and therapy.
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Affiliation(s)
- Congcong Xu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Farzin Haque
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | - Daniel L Jasinski
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Dan Shu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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27
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Hariri AA, Hamblin GD, Hardwick JS, Godin R, Desjardins JF, Wiseman PW, Sleiman HF, Cosa G. Stoichiometry and Dispersity of DNA Nanostructures Using Photobleaching Pair-Correlation Analysis. Bioconjug Chem 2017; 28:2340-2349. [DOI: 10.1021/acs.bioconjchem.7b00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | - Jean-Francois Desjardins
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
| | - Paul W. Wiseman
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
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28
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Ryan J, Gerhold AR, Boudreau V, Smith L, Maddox PS. Introduction to Modern Methods in Light Microscopy. Methods Mol Biol 2017; 1563:1-15. [PMID: 28324598 DOI: 10.1007/978-1-4939-6810-7_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For centuries, light microscopy has been a key method in biological research, from the early work of Robert Hooke describing biological organisms as cells, to the latest in live-cell and single-molecule systems. Here, we introduce some of the key concepts related to the development and implementation of modern microscopy techniques. We briefly discuss the basics of optics in the microscope, super-resolution imaging, quantitative image analysis, live-cell imaging, and provide an outlook on active research areas pertaining to light microscopy.
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Affiliation(s)
- Joel Ryan
- LMU Munich, Biocenter Martinsried, Grosshadernerstr. 2, 82152, Martinsried, Munich, Germany
| | - Abby R Gerhold
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Vincent Boudreau
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lydia Smith
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul S Maddox
- Department of Biology, University of North Carolina at Chapel Hill, 4358 Genome Sciences Building, Chapel Hill, NC, 27599, USA.
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29
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Liesche C, Grussmayer KS, Ludwig M, Wörz S, Rohr K, Herten DP, Beaudouin J, Eils R. Automated Analysis of Single-Molecule Photobleaching Data by Statistical Modeling of Spot Populations. Biophys J 2016; 109:2352-62. [PMID: 26636946 DOI: 10.1016/j.bpj.2015.10.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/01/2015] [Accepted: 10/26/2015] [Indexed: 02/01/2023] Open
Abstract
The number of fluorophores within a molecule complex can be revealed by single-molecule photobleaching imaging. A widely applied strategy to analyze intensity traces over time is the quantification of photobleaching step counts. However, several factors can limit and bias the detection of photobleaching steps, including noise, high numbers of fluorophores, and the possibility that several photobleaching events occur almost simultaneously. In this study, we propose a new approach, to our knowledge, to determine the fluorophore number that correlates the intensity decay of a population of molecule complexes with the decay of the number of visible complexes. We validated our approach using single and fourfold Atto-labeled DNA strands. As an example we estimated the subunit stoichiometry of soluble CD95L using GFP fusion proteins. To assess the precision of our method we performed in silico experiments showing that the estimates are not biased for experimentally observed intensity fluctuations and that the relative precision remains constant with increasing number of fluorophores. In case of fractional fluorescent labeling, our simulations predicted that the fluorophore number estimate corresponds to the product of the true fluorophore number with the labeling fraction. Our method, denoted by spot number and intensity correlation (SONIC), is fully automated, robust to noise, and does not require the counting of photobleaching events.
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Affiliation(s)
- Clarissa Liesche
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Kristin S Grussmayer
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Michael Ludwig
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Stefan Wörz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Karl Rohr
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Dirk-Peter Herten
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Joël Beaudouin
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.
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30
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Single molecule fluorescence spectroscopy for quantitative biological applications. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0083-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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How can novel microscopic approaches shed light on the function of nucleic acid-based drugs? Future Med Chem 2015; 7:1623-5. [DOI: 10.4155/fmc.15.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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32
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Watt D, Dixit R, Cavalli V. JIP3 Activates Kinesin-1 Motility to Promote Axon Elongation. J Biol Chem 2015; 290:15512-15525. [PMID: 25944905 DOI: 10.1074/jbc.m115.651885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 11/06/2022] Open
Abstract
Kinesin-1 is a molecular motor responsible for cargo transport along microtubules and plays critical roles in polarized cells, such as neurons. Kinesin-1 can function as a dimer of two kinesin heavy chains (KHC), which harbor the motor domain, or as a tetramer in combination with two accessory light chains (KLC). To ensure proper cargo distribution, kinesin-1 activity is precisely regulated. Both KLC and KHC subunits bind cargoes or regulatory proteins to engage the motor for movement along microtubules. We previously showed that the scaffolding protein JIP3 interacts directly with KHC in addition to its interaction with KLC and positively regulates dimeric KHC motility. Here we determined the stoichiometry of JIP3-KHC complexes and observed approximately four JIP3 molecules binding per KHC dimer. We then determined whether JIP3 activates tetrameric kinesin-1 motility. Using an in vitro motility assay, we show that JIP3 binding to KLC engages kinesin-1 with microtubules and that JIP3 binding to KHC promotes kinesin-1 motility along microtubules. We tested the in vivo relevance of these findings using axon elongation as a model for kinesin-1-dependent cellular function. We demonstrate that JIP3 binding to KHC, but not KLC, is essential for axon elongation in hippocampal neurons as well as axon regeneration in sensory neurons. These findings reveal that JIP3 regulation of kinesin-1 motility is critical for axon elongation and regeneration.
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Affiliation(s)
- Dana Watt
- Department of Anatomy and Neurobiology, School of Medicine, Washington University, St. Louis, Missouri 63110
| | - Ram Dixit
- Department of Biology, Washington University, St. Louis, Missouri 63110
| | - Valeria Cavalli
- Department of Anatomy and Neurobiology, School of Medicine, Washington University, St. Louis, Missouri 63110.
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33
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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34
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Affiliation(s)
- Vasudha Aggarwal
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
| | - Taekjip Ha
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
- Department of Physics; University of Illinois Urbana Champaign; Urbana IL USA
- Howard Hughes Medical Institute; Urbana IL USA
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35
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De-Donatis GM, Zhao Z, Wang S, Huang LP, Schwartz C, Tsodikov OV, Zhang H, Haque F, Guo P. Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell Biosci 2014; 4:30. [PMID: 24940480 PMCID: PMC4060578 DOI: 10.1186/2045-3701-4-30] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022] Open
Abstract
Background Double-stranded DNA translocation is ubiquitous in living systems. Cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging and cell entry all involve biomotor-driven dsDNA translocation. Previously, biomotors have been primarily classified into linear and rotational motors. We recently discovered a third class of dsDNA translocation motors in Phi29 utilizing revolution mechanism without rotation. Analogically, the Earth rotates around its own axis every 24 hours, but revolves around the Sun every 365 days. Results Single-channel DNA translocation conductance assay combined with structure inspections of motor channels on bacteriophages P22, SPP1, HK97, T7, T4, Phi29, and other dsDNA translocation motors such as bacterial FtsK and eukaryotic mimiviruses or vaccinia viruses showed that revolution motor is widespread. The force generation mechanism for revolution motors is elucidated. Revolution motors can be differentiated from rotation motors by their channel size and chirality. Crystal structure inspection revealed that revolution motors commonly exhibit channel diameters larger than 3 nm, while rotation motors that rotate around one of the two separated DNA strands feature a diameter smaller than 2 nm. Phi29 revolution motor translocated double- and tetra-stranded DNA that occupied 32% and 64% of the narrowest channel cross-section, respectively, evidencing that revolution motors exhibit channel diameters significantly wider than the dsDNA. Left-handed oriented channels found in revolution motors drive the right-handed dsDNA via anti-chiral interaction, while right-handed channels observed in rotation motors drive the right-handed dsDNA via parallel threads. Tethering both the motor and the dsDNA distal-end of the revolution motor does not block DNA packaging, indicating that no rotation is required for motors of dsDNA phages, while a small-angle left-handed twist of dsDNA that is aligned with the channel could occur due to the conformational change of the phage motor channels from a left-handed configuration for DNA entry to a right-handed configuration for DNA ejection for host cell infection. Conclusions The revolution motor is widespread among biological systems, and can be distinguished from rotation motors by channel size and chirality. The revolution mechanism renders dsDNA void of coiling and torque during translocation of the lengthy helical chromosome, thus resulting in more efficient motor energy conversion.
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Affiliation(s)
- Gian Marco De-Donatis
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhengyi Zhao
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Lisa P Huang
- Current address: Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., Hamilton, NJ 08690, USA
| | - Chad Schwartz
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,William Farish Endowed Chair in Nanobiotechnology, School of Pharmacy, University of Kentucky, 565 Biopharmaceutical Complex, 789 S. Limestone Street, Lexington, KY 40536, USA
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36
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Nucleic Acids Nanotechnology. Methods 2014; 67:103-4. [DOI: 10.1016/j.ymeth.2014.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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