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Shamim S, Mohsin AS, Rahman MM, Hossain Bhuian MB. Recent advances in the metamaterial and metasurface-based biosensor in the gigahertz, terahertz, and optical frequency domains. Heliyon 2024; 10:e33272. [PMID: 39040247 PMCID: PMC11260956 DOI: 10.1016/j.heliyon.2024.e33272] [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: 03/13/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Recently, metamaterials and metasurface have gained rapidly increasing attention from researchers due to their extraordinary optical and electrical properties. Metamaterials are described as artificially defined periodic structures exhibiting negative permittivity and permeability simultaneously. Whereas metasurfaces are the 2D analogue of metamaterials in the sense that they have a small but not insignificant depth. Because of their high optical confinement and adjustable optical resonances, these artificially engineered materials appear as a viable photonic platform for biosensing applications. This review paper discusses the recent development of metamaterial and metasurface in biosensing applications based on the gigahertz, terahertz, and optical frequency domains encompassing the whole electromagnetic spectrum. Overlapping features such as material selection, structure, and physical mechanisms were considered during the classification of our biosensing applications. Metamaterials and metasurfaces working in the GHz range provide prospects for better sensing of biological samples, THz frequencies, falling between GHz and optical frequencies, provide unique characteristics for biosensing permitting the exact characterization of molecular vibrations, with an emphasis on molecular identification, label-free analysis, and imaging of biological materials. Optical frequencies on the other hand cover the visible and near-infrared regions, allowing fine regulation of light-matter interactions enabling metamaterials and metasurfaces to offer excellent sensitivity and specificity in biosensing. The outcome of the sensor's sensitivity to an electric or magnetic field and the resonance frequency are, in theory, determined by the frequency domain and features. Finally, the challenges and possible future perspectives in biosensing application areas have been presented that use metamaterials and metasurfaces across diverse frequency domains to improve sensitivity, specificity, and selectivity in biosensing applications.
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Affiliation(s)
- Shadmani Shamim
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Abu S.M. Mohsin
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Md. Mosaddequr Rahman
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Mohammed Belal Hossain Bhuian
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
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Abu Saleh D, Sosnik A. Enhanced photoluminescence of boron nitride quantum dots by encapsulation within polymeric nanoparticles. NANOTECHNOLOGY 2021; 32:195104. [PMID: 33513592 DOI: 10.1088/1361-6528/abe155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Boron nitride quantum dots (BNQDs) have been proposed as probes for bioimaging owing their to outstanding photoluminescent properties, although their hydrophobic nature and strong aggregation tendency in aqueous media limit their application in the biomedical field. In this work, we synthesize BNQDs by a liquid exfoliation-solvothermal process under pressure from boron nitride nanoparticles in N,N-dimethylformamide. The BNQDs display an average size of 3.3 ± 0.6 nm, as measured by transmission electron microscopy, and a (100) crystalline structure. In addition, a quantum yield of 21.75 ± 0.20% was achieved. To ensure complete dispersibility in water and prevent possible elimination by renal filtration upon injection, the BNQDs (20% w/w) are encapsulated within poly(ethylene glycol)-b-poly(epsilon-caprolactone) nanoparticles by a simple and scalable nanoprecipitation method, and hybrid nanocomposite particles with significantly stronger photoluminescence than their free counterparts are produced. Finally, their optimal cell compatibility and bioimaging features are demonstrated in vitro in murine macrophage and human rhabdomyosarcoma cell lines.
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Affiliation(s)
- Doaa Abu Saleh
- Laboratory of Pharmaceutical Nanomaterials Science, Department of Materials Science and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Alejandro Sosnik
- Laboratory of Pharmaceutical Nanomaterials Science, Department of Materials Science and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
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Sarkis J, Vié V. Biomimetic Models to Investigate Membrane Biophysics Affecting Lipid-Protein Interaction. Front Bioeng Biotechnol 2020; 8:270. [PMID: 32373596 PMCID: PMC7179690 DOI: 10.3389/fbioe.2020.00270] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
Biological membranes are highly dynamic in their ability to orchestrate vital mechanisms including cellular protection, organelle compartmentalization, cellular biomechanics, nutrient transport, molecular/enzymatic recognition, and membrane fusion. Controlling lipid composition of different membranes allows cells to regulate their membrane characteristics, thus modifying their physical properties to permit specific protein interactions and drive structural function (membrane deformation facilitates vesicle budding and fusion) and signal transduction. Yet, how lipids control protein structure and function is still poorly understood and needs systematic investigation. In this review, we explore different in vitro membrane models and summarize our current understanding of the interplay between membrane biophysical properties and lipid-protein interaction, taken as example few proteins involved in muscular activity (dystrophin), digestion and Legionella pneumophila effector protein DrrA. The monolayer model with its movable barriers aims to mimic any membrane deformation while surface pressure modulation imitates lipid packing and membrane curvature changes. It is frequently used to investigate peripheral protein binding to the lipid headgroups. Examples of how lipid lateral pressure modifies protein interaction and organization within the membrane are presented using various biophysical techniques. Interestingly, the shear elasticity and surface viscosity of the monolayer will increase upon specific protein(s) binding, supporting the importance of such mechanical link for membrane stability. The lipid bilayer models such as vesicles are not only used to investigate direct protein binding based on the lipid nature, but more importantly to assess how local membrane curvature (vesicles with different size) influence the binding properties of a protein. Also, supported lipid bilayer model has been used widely to characterize diffusion law of lipids within the bilayer and/or protein/biomolecule binding and diffusion on the membrane. These membrane models continue to elucidate important advances regarding the dynamic properties harmonizing lipid-protein interaction.
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Affiliation(s)
- Joe Sarkis
- Department of Cell Biology, Harvard Medical School and Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, United States
- Univ Rennes, CNRS, IPR-UMR 6251, Rennes, France
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Wu D, Yang Y, Xu P, Xu D, Liu Y, Castillo R, Yan R, Ren J, Zhou G, Liu C, Qin M, Du J, Hou L, Chen I, Kang C, Jin L, Wen J, Chen W, Lu Y. Real-Time Quantification of Cell Internalization Kinetics by Functionalized Bioluminescent Nanoprobes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902469. [PMID: 31402525 DOI: 10.1002/adma.201902469] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/14/2019] [Indexed: 06/10/2023]
Abstract
Cells transport mass dynamically, crossing cell membranes to maintain metabolism and systemic homeostasis, through which biomolecules are also delivered to cells for gene editing, cell reprograming, therapy, and other purposes. Quantifying the translocation kinetics is fundamentally and clinically essential, but remains limited by fluorescence-based technologies, which are semi-quantitative and only provide kinetics information at cellular level or in discrete time. Herein, a real-time method of quantifying cell internalization kinetics is reported using functionalized firefly-luciferase nanocapsules as the probe. This quantitative assay will facilitate the rational design of delivery vectors and enable high-throughput screening of peptides and other functional molecules, constituting an effective tool for broad applications, including drug development and cancer therapy.
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Affiliation(s)
- Di Wu
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yilong Yang
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Pengcheng Xu
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Duo Xu
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Roxanne Castillo
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ran Yan
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jie Ren
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - George Zhou
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Chaoyong Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Meng Qin
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Lihua Hou
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Irvin Chen
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Chunsheng Kang
- Tianjin Neurological Institute, Key Laboratory of Post-Neurotrauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Lihua Jin
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jing Wen
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Wei Chen
- Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yunfeng Lu
- Department of Chemical and Biomolecular Engineering, School of Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Ulku AC, Bruschini C, Antolovic IM, Weiss S, Michalet X, Charbon E. Phasor-based widefield FLIM using a gated 512×512 single-photon SPAD imager. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10882. [PMID: 33859449 DOI: 10.1117/12.2511148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Single-photon avalanche diode (SPAD) imagers can perform fast time-resolved imaging in a compact form factor, by exploiting the processing capability and speed of integrated CMOS electronics. Developments in SPAD imagers have recently made them compatible with widefield microscopy, thanks to array formats approaching one megapixel and sensitivity and noise levels approaching those of established technologies. In this paper, phasor-based FLIM is demonstrated with a gated binary 512×512 SPAD imager, which can operate with a gate length as short as 5.75 ns, a minimum gate step of 17.9 ps, and up to 98 kfps readout rate (1-bit frames). Lifetimes of ATTO 550 and Rhodamine 6G (R6G) solutions were measured across a 472×256 sub-array using phasor analysis, acquiring data by shifting a 13.1 ns gate window across the 50 ns laser period. The measurement accuracy obtained when employing such a scheme based on long, overlapping gates was validated by comparison with TCSPC measurements and fitting analysis results based on a standard Levenberg-Marquardt algorithm (>90% accuracy for the lifetime of R6G and ATTO 550). This demonstrates the ability of the proposed method to measure short lifetimes without minimum gate length requirements. The FLIM frame rate of the overall system can be increased up to a few fps for phasor-based widefield FLIM (moving closer to real-time operation) by FPGA-based parallel computation with continuous acquisition at the full speed of 98 kfps.
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Affiliation(s)
| | | | | | - Shimon Weiss
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA USA
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Ardelean A, Ulku AC, Michalet X, Charbon E, Bruschini C. Fluorescence lifetime imaging with a single-photon SPAD array using long overlapping gates: an experimental and theoretical study. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10882:108820Y. [PMID: 33833477 PMCID: PMC8026147 DOI: 10.1117/12.2511287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Developing large arrays of single-photon avalanche diodes (SPADs) with on-chip time-correlated single-photon counting (TCSPC) capabilities continues to be a difficult task due to stringent silicon real estate constraints, high data rates and system complexity. As an alternative to TCSPC, time-gated architectures have been proposed, where the numbers of photons detected within different time gates are used as a replacement to the usual time-resolved luminescence decay. However, because of technological limitations, the minimum gate length implement is on the order of nanoseconds, longer than most fluorophore lifetimes of interest. However, recent FLIM measurements have shown that it is mainly the gate step and rise/fall time, rather than its length, which determine lifetime resolution. In addition, the large number of photons captured by longer gates results in higher SNR. In this paper, we study the effects of using long, overlapping gates on lifetime extraction by phasor analysis, using a recently developed 512×512 time-gated SPAD array. The experiments used Cy3B, Rhodamine 6G and Atto550 dyes as test samples. The gate window length was varied between 11.3 ns and 23 ns while the gate step was varied between 17.86 ps and 3 ns. We validated the results with a standard TCSPC setup and investigated the case of multi-exponential samples through simulations. Results indicate that lifetime extraction is not degraded by the use of longer gates, nor is the ability to resolve multi-exponential decays.
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Affiliation(s)
- Andrei Ardelean
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Arin Can Ulku
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, USA
| | - Edoardo Charbon
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
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Prabhakar A, Puglisi EV, Puglisi JD. Single-Molecule Fluorescence Applied to Translation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032714. [PMID: 29891562 DOI: 10.1101/cshperspect.a032714] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule fluorescence methods have illuminated the dynamics of the translational machinery. Structural and bulk biochemical experiments have provided detailed atomic and global mechanistic views of translation, respectively. Single-molecule studies of translation have bridged these views by temporally connecting the conformational and compositional states defined from structural data within the mechanistic framework of translation produced from biochemical studies. Here, we discuss the context for applying different single-molecule fluorescence experiments, and present recent applications to studying prokaryotic and eukaryotic translation. We underscore the power of observing single translating ribosomes to delineate and sort complex mechanistic pathways during initiation and elongation, and discuss future applications of current and improved technologies.
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Affiliation(s)
- Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Program in Biophysics, Stanford University, Stanford, California 94305
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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Patrone PN, Cooksey G, Kearsley A. Dynamic Measurement of Nanoflows: Analysis and Theory of an Optofluidic Flowmeter. PHYSICAL REVIEW APPLIED 2019; 11:10.1103/physrevapplied.11.034025. [PMID: 32166098 PMCID: PMC7067294 DOI: 10.1103/physrevapplied.11.034025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scientists must overcome fundamental measurement problems if microfluidic devices are to become reliable and commercially viable. In particular, microfluidic devices require precise control over operating conditions such as flow-rate, υυ , which is difficult to measure continuously and in situ. Given the small scales involved, state-of-the-art approaches generally require accurate models to infer υυ on the basis of indirect measurements. However, such methods necessarily introduce model-form errors that dominate at the nL/min scale being targeted by the community. To address these problems, we develop a robust and largely assumption-free scaling method that relates the fluorescence efficiency I of fluorophores to υυ through a dosage parameter ξ, which depends on the flow rate and laser power. Notably, we show that this scaling relationship emerges as a universal feature from a general class of partial differential equations (PDEs) describing the experimental setup, which consists of an excitation beam and fluorescence detector. As a result, our approach avoids uncertainties associated with most modeling assumptions, e.g. the exact system geometry, the flow profile, the physics of fluorescence, etc. Moreover, the corresponding measurements remain valid down to the scale of 10 nL/min, with some devices potentially capable of reaching 1 nL/min. As an added benefit, the measurement procedure is mathematically simple, requiring a few trivial computations, as opposed to the full solution of a PDE. To support these claims, we discuss and quantify uncertainties associated with our method and present experimental results that confirm its validity.
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Ulku AC, Bruschini C, Antolovic IM, Charbon E, Kuo Y, Ankri R, Weiss S, Michalet X. A 512×512 SPAD Image Sensor with Integrated Gating for Widefield FLIM. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2019; 25:6801212. [PMID: 31156324 PMCID: PMC6541425 DOI: 10.1109/jstqe.2018.2867439] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We report on SwissSPAD2, an image sensor with 512×512 photon-counting pixels, each comprising a single-photon avalanche diode (SPAD), a 1-bit memory, and a gating mechanism capable of turning the SPAD on and off, with a skew of 250ps and 344ps, respectively, for a minimum duration of 5.75ns. The sensor is designed to achieve a frame rate of up to 97,700 binary frames per second and sub-40ps gate shifts. By synchronizing it with a pulsed laser and using multiple successive overlapping gates, one can reconstruct a molecule's fluorescent response with picosecond temporal resolution. Thanks to the sensor's number of pixels (the largest to date) and the fully integrated gated operation, SwissSPAD2 enables widefield FLIM with an all-solid-state solution and at relatively high frame rates. This was demonstrated with preliminary results on organic dyes and semiconductor quantum dots using both decay fitting and phasor analysis. Furthermore, pixels with an exceptionally low dark count rate and high photon detection probability enable uniform and high quality imaging of biologically relevant fluorescent samples stained with multiple dyes. While future versions will feature the addition of microlenses and optimize firmware speed, our results open the way to low-cost alternatives to commercially available scientific time-resolved imagers.
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Affiliation(s)
- Arin C Ulku
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Claudio Bruschini
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Ivan Michel Antolovic
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Edoardo Charbon
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Yung Kuo
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Rinat Ankri
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
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Luitz MP, Barth A, Crevenna AH, Bomblies R, Lamb DC, Zacharias M. Covalent dye attachment influences the dynamics and conformational properties of flexible peptides. PLoS One 2017; 12:e0177139. [PMID: 28542243 PMCID: PMC5441599 DOI: 10.1371/journal.pone.0177139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022] Open
Abstract
Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP). Using the intrinsically disordered S-peptide as a model system, we investigate the impact of terminal fluorescence labeling on the molecular properties. We perform extensive molecular dynamics simulations on the labeled and unlabeled peptide and compare the results with in vitro PET-FCS measurements. Experimental and simulated timescales of end-to-end fluctuations were found in excellent agreement. Comparison between simulations with and without labels reveal that the π-stacking interaction between the fluorophore labels traps the conformation of S-peptide in a single dominant state, while the unlabeled peptide undergoes continuous conformational rearrangements. Furthermore, we find that the open to closed transition rate of S-peptide is decreased by at least one order of magnitude by the fluorophore attachment. Our approach combining experimental and in silico methods provides a benchmark for the simulations and reveals the significant effect that fluorescence labeling can have on the conformational dynamics of small biomolecules, at least for inherently flexible short peptides. The presented protocol is not only useful for comparing PET-FCS experiments with simulation results but provides a strategy to minimize the influence on molecular properties when chosing labeling positions for fluorescence experiments.
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Affiliation(s)
- Manuel P. Luitz
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
| | - Anders Barth
- Department Chemie, Physikalische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Alvaro H. Crevenna
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Rainer Bomblies
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
| | - Don C. Lamb
- Department Chemie, Physikalische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Martin Zacharias
- Department Physik, T38, Technische Universität München, 85748 Garching, Germany
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Cardarelli F. Time-resolved biophysical approaches to nucleocytoplasmic transport. Comput Struct Biotechnol J 2017; 15:299-306. [PMID: 28435614 PMCID: PMC5388937 DOI: 10.1016/j.csbj.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/25/2017] [Indexed: 12/26/2022] Open
Abstract
Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores). The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed.
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Cristino L, Imperatore R, Di Marzo V. Techniques for the Cellular and Subcellular Localization of Endocannabinoid Receptors and Enzymes in the Mammalian Brain. Methods Enzymol 2017; 593:61-98. [DOI: 10.1016/bs.mie.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Abstract
Cell biology came about with the ability to first visualize cells. As microscopy techniques advanced, the early microscopists became the first cell biologists to observe the inner workings and subcellular structures that control life. This ability to see organelles within a cell provided scientists with the first understanding of how cells function. The visualization of the dynamic architecture of subcellular structures now often drives questions as researchers seek to understand the intricacies of the cell. With the advent of fluorescent labeling techniques, better and new optical techniques, and more sensitive and faster cameras, a whole array of questions can now be asked. There has been an explosion of new light microscopic techniques, and the race is on to build better and more powerful imaging systems so that we can further our understanding of the spatial and temporal mechanisms controlling molecular cell biology.
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Affiliation(s)
- Kenneth A Myers
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, USA
| | - Christopher Janetopoulos
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, USA
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14
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Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional Studies of DNA-Protein Interactions Using FRET Techniques. Methods Mol Biol 2016; 1334:115-41. [PMID: 26404147 DOI: 10.1007/978-1-4939-2877-4_8] [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] [Indexed: 02/11/2023]
Abstract
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of protein-DNA interactions.
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Affiliation(s)
- Simon Blouin
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Daniel A Lafontaine
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1.
| | - J Carlos Penedo
- School of Physics and Astronomy, University of St. Andrews, St. Andrews, UK
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15
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Holzinger A, Steinbach C, Kranz C. Scanning Electrochemical Microscopy (SECM): Fundamentals and Applications in Life Sciences. ELECTROCHEMICAL STRATEGIES IN DETECTION SCIENCE 2015. [DOI: 10.1039/9781782622529-00125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In recent years, scanning electrochemical microscopy (SECM) has made significant contributions to the life sciences. Innovative developments focusing on high-resolution imaging, developing novel operation modes, and combining SECM with complementary optical or scanning probe techniques renders SECM an attractive analytical approach. This chapter gives an introduction to the essential instrumentation and operation principles of SECM for studying biologically-relevant systems. Particular emphasis is given to applications aimed at imaging the activity of biochemical constituents such as enzymes, antibodies, and DNA, which play a pivotal role in biomedical diagnostics. Furthermore, the unique advantages of SECM and combined techniques for studying live cells is highlighted by discussion of selected examples.
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Affiliation(s)
- Angelika Holzinger
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm 89069 Ulm Germany
| | - Charlotte Steinbach
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm 89069 Ulm Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, University of Ulm 89069 Ulm Germany
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16
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Abstract
Fluorescence microscopy is among the most widely utilized tools in cell and molecular biology due to its ability to noninvasively obtain time-resolved images of live cells with molecule-specific contrast. In this chapter, we describe a simple high-resolution technique, scanning angle interference microscopy (SAIM), for the imaging and localization of fluorescent molecules with nanometer precision along the optical axis. In SAIM, samples above a reflective surface are sequentially scanned with an excitation laser at varying angles of incidence. Interference patterns generated between the incident and reflected lights result in an emission intensity that depends on the height of a fluorophore above the silicon surface and the angle of the incident radiation. The measured fluorescence intensities are then fit to an optical model to localize the labeled molecules along the z-axis with 5-10 nm precision and diffraction-limited lateral resolution. SAIM is easily implemented on widely available commercial total internal reflection fluorescence microscopes, offering potential for widespread use in cell biology. Here, we describe the setup of SAIM and its application for imaging cellular structures near (<1 μm) the sample substrate.
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17
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Carson S, Wilson J, Aksimentiev A, Wanunu M. Smooth DNA transport through a narrowed pore geometry. Biophys J 2014; 107:2381-93. [PMID: 25418307 PMCID: PMC4241440 DOI: 10.1016/j.bpj.2014.10.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/02/2014] [Accepted: 10/15/2014] [Indexed: 12/13/2022] Open
Abstract
Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.
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Affiliation(s)
- Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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18
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Lu G, De Keersmaecker H, Su L, Kenens B, Rocha S, Fron E, Chen C, Van Dorpe P, Mizuno H, Hofkens J, Hutchison JA, Uji-i H. Live-cell SERS endoscopy using plasmonic nanowire waveguides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:5124-8. [PMID: 24866811 DOI: 10.1002/adma.201401237] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/30/2014] [Indexed: 05/22/2023]
Abstract
Live-cell surface-enhanced Raman spectroscopy (SERS) endoscopy is developed by using plasmonic nanowire waveguides as endoscopic probes. It is demonstrated that the probe insertion does not stress the cell. Opposed to conventional SERS endoscopy, with excitation at the hotspot within the cell, the remote excitation method yields low-background SERS spectra from specific cell compartments with minimal associated photodamage.
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Affiliation(s)
- Gang Lu
- KU Leuven, Departement Chemie, Celestijnenlaan 200G-F, B-3001, Heverlee, Belgium
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19
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Zheng D, Lu HP. Single-molecule enzymatic conformational dynamics: spilling out the product molecules. J Phys Chem B 2014; 118:9128-40. [PMID: 25025461 PMCID: PMC4126733 DOI: 10.1021/jp5014434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 07/14/2014] [Indexed: 12/19/2022]
Abstract
Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses.
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Affiliation(s)
- Desheng Zheng
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
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20
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Yu H, Shan X, Wang S, Chen H, Tao N. Plasmonic imaging and detection of single DNA molecules. ACS NANO 2014; 8:3427-3433. [PMID: 24593238 DOI: 10.1021/nn4062885] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The capability of imaging and detecting single DNA molecules is critical in the study, analysis, and applications of DNA. Fluorescence imaging is a widely used method, but it suffers from blinking and photobleaching, and fluorescence tags may block or affect binding sites on DNA. We report on label-free imaging of single DNA molecules with a differential plasmonic imaging technique. The technique produces high contrast images due to the scattering of surface plasmonic waves by the molecules and the removal of background noises and interference patterns, allowing for quantitative analysis of individual DNA molecules. Simulation of the images based on a scattering model shows good agreement with the experiment. We further demonstrate optical mapping of single DNA molecules.
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Affiliation(s)
- Hui Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
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21
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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22
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Tirloni B, Schulz Lang E, Manzoni de Oliveira G. Synthesis, crystal structure and optical features of new Hg–Se clusters. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Maliwal BP, Fudala R, Raut S, Kokate R, Sørensen TJ, Laursen BW, Gryczynski Z, Gryczynski I. Long-lived bright red emitting azaoxa-triangulenium fluorophores. PLoS One 2013; 8:e63043. [PMID: 23667570 PMCID: PMC3646960 DOI: 10.1371/journal.pone.0063043] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
The fluorescence lifetimes of most red emitting organic probes are under 4 nanoseconds, which is a limiting factor in studying interactions and conformational dynamics of macromolecules. In addition, the nanosecond background autofluorescence is a significant interference during fluorescence measurements in cellular environment. Therefore, red fluorophores with longer lifetimes will be immensely helpful. Azaoxa-triangulenium fluorophores ADOTA and DAOTA are red emitting small organic molecules with high quantum yield, long fluorescence lifetime and high limiting anisotropy. In aqueous environment, ADOTA and DAOTA absorption and emission maxima are respectively 540 nm and 556 nm, and 556 nm and 589 nm. Their emission extends beyond 700 nm. Both probes have the limiting anisotropy between 0.36-0.38 at their absorption peak. In both protic and aprotic solvents, their lifetimes are around 20 ns, making them among the longest-lived red emitting organic fluorophores. Upon labeling of avidin, streptavidin and immunoglobulin their absorption and fluorescence are red-shifted. Unlike in free form, the protein-conjugated probes have heterogeneous fluorescence decays, with the presence of both significantly quenched and unquenched populations. Despite the presence of significant local motions due to a flexible trimethylene linker, we successfully measured both intermediate nanosecond intra-protein motions and slower rotational correlation times approaching 100 ns. Their long lifetimes are unaffected by the cell membrane (hexadecyl-ADOTA) and the intra-cellular (DAOTA-Arginine) localization. Their long lifetimes also enabled successful time-gating of the cellular autofluorescence resulting in background-free fluorescence lifetime based images. ADOTA and DAOTA retain a long fluorescence lifetime when free, as protein conjugate, in membranes and inside the cell. Our successful measurements of intermediate nanosecond internal motions and long correlations times of large proteins suggest that these probes will be highly useful to study slower intra-molecular motions and interactions among macromolecules. The fluorescence lifetime facilitated gating of cellular nanosecond autofluorescence should be of considerable help in in vitro and in vivo applications.
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Affiliation(s)
- Badri P. Maliwal
- Center for Commercialization of Fluorescence Technologies, Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Rafal Fudala
- Center for Commercialization of Fluorescence Technologies, Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Sangram Raut
- Center for Commercialization of Fluorescence Technologies, Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Rutika Kokate
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Thomas J. Sørensen
- Nano-Science Center and Department of Chemistry, University of Copenhagen, København, Denmark
| | - Bo W. Laursen
- Nano-Science Center and Department of Chemistry, University of Copenhagen, København, Denmark
| | - Zygmunt Gryczynski
- Departments of Physics and Astronomy, Texas Christian University, Fort Worth, Texas, United States of America
| | - Ignacy Gryczynski
- Center for Commercialization of Fluorescence Technologies, Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Cell Biology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
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24
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Hambly AC, Henderson RK, Baker A, Stuetz RM, Khan SJ. Cross-connection detection in Australian dual reticulation systems by monitoring inherent fluorescent organic matter. ACTA ACUST UNITED AC 2012. [DOI: 10.1080/09593330.2012.696724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Shim TK, Lee MH, Kim D, Kim HS, Yoon KB. Fluorescence Characteristics of Isolated Dye Molecules within Silicalite-1 Channels. J Fluoresc 2012; 22:1475-82. [DOI: 10.1007/s10895-012-1084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 06/20/2012] [Indexed: 11/28/2022]
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26
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Balaz S. Does transbilayer diffusion have a role in membrane transport of drugs? Drug Discov Today 2012; 17:1079-87. [PMID: 22705388 DOI: 10.1016/j.drudis.2012.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/07/2012] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
Abstract
The existing consensus on coexistence of transbilayer diffusion and carrier-mediated transport as two main mechanisms for drugs crossing biological membranes was recently challenged by a systems biology group. Their transporters-only hypothesis is examined in this article using published experimental evidence. The main focus is on the key claim of their hypothesis, stating that 'the drug molecules cross pure phospholipid bilayers through transient pores that cannot form in the bilayers of cell membranes, and thus transbilayer drug transport does not exist in cells'. The analysis shows that the prior consensus remains a valid scientific view of the membrane transport of drugs.
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Affiliation(s)
- Stefan Balaz
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Department of Pharmaceutical Sciences, Colchester, VT 05446, USA.
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27
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Schlee C, Miedl M, Leiper KA, Stewart GG. The Potential of Confocal Imaging for Measuring Physiological Changes in Brewer's Yeast. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2006.tb00243.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Harke B, Bianchini P, Brandi F, Diaspro A. Photopolymerization inhibition dynamics for sub-diffraction direct laser writing lithography. Chemphyschem 2012; 13:1429-34. [PMID: 22392895 PMCID: PMC3491630 DOI: 10.1002/cphc.201200006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Indexed: 11/11/2022]
Abstract
Selective inhibition of the polymerization leads to sub-diffraction feature sizes in direct writing lithography-a principle based on the idea of stimulated emission depletion (STED) microscopy. However, the detailed understanding of the inhibition process is a key point to further enhance the resolution of the system. The authors present experiments focused on the time dynamics of the inhibition process, clarifying possible photophysical pathways.
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Affiliation(s)
- Benjamin Harke
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy.
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29
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Saurabh S, Maji S, Bruchez MP. Evaluation of sCMOS cameras for detection and localization of single Cy5 molecules. OPTICS EXPRESS 2012; 20:7338-49. [PMID: 22453414 PMCID: PMC3500109 DOI: 10.1364/oe.20.007338] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/23/2012] [Accepted: 03/05/2012] [Indexed: 05/25/2023]
Abstract
The ability to detect single molecules over the electronic noise requires high performance detector systems. Electron Multiplying Charge-Coupled Device (EMCCD) cameras have been employed successfully to image single molecules. Recently, scientific Complementary Metal Oxide Semiconductor (sCMOS) based cameras have been introduced with very low read noise at faster read out rates, smaller pixel sizes and a lower price compared to EMCCD cameras. In this study, we have compared the two technologies using two EMCCD and three sCMOS cameras to detect single Cy5 molecules. Our findings indicate that the sCMOS cameras perform similar to EMCCD cameras for detecting and localizing single Cy5 molecules.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
| | - Suvrajit Maji
- Lane Center for Computational Biology, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
| | - Marcel P. Bruchez
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
- Lane Center for Computational Biology, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
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30
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Chen T, Li S, Sun H. Metamaterials application in sensing. SENSORS (BASEL, SWITZERLAND) 2012; 12:2742-65. [PMID: 22736975 PMCID: PMC3376603 DOI: 10.3390/s120302742] [Citation(s) in RCA: 346] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/02/2012] [Accepted: 02/14/2012] [Indexed: 11/18/2022]
Abstract
Metamaterials are artificial media structured on a size scale smaller than wavelength of external stimuli, and they can exhibit a strong localization and enhancement of fields, which may provide novel tools to significantly enhance the sensitivity and resolution of sensors, and open new degrees of freedom in sensing design aspect. This paper mainly presents the recent progress concerning metamaterials-based sensing, and detailedly reviews the principle, detecting process and sensitivity of three distinct types of sensors based on metamaterials, as well as their challenges and prospects. Moreover, the design guidelines for each sensor and its performance are compared and summarized.
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Affiliation(s)
- Tao Chen
- Mechanical & Power Engineering College, Harbin University of Science and Technology, Harbin 150080, China
| | - Suyan Li
- Center for Engineering Training and Basic Experimentation, Heilongjiang Institute of Science and Technology, Harbin 150027, China; E-Mail:
| | - Hui Sun
- Mechanical & Power Engineering College, Harbin University of Science and Technology, Harbin 150080, China
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31
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Choi S, Dickson RM, Yu J. Developing luminescent silver nanodots for biological applications. Chem Soc Rev 2012; 41:1867-91. [DOI: 10.1039/c1cs15226b] [Citation(s) in RCA: 493] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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Abstract
Cells respond to biochemical and mechanical stimuli through a series of steps that begin at the molecular, nanometre level, and translate finally in global cell response. Defects in biochemical- and/or mechanical-sensing, transduction or cellular response are the cause of multiple diseases, including cancer and immune disorders among others. Within the booming field of regenerative medicine, there is an increasing need for developing and applying nanotechnology tools to bring understanding on the cellular machinery and molecular interactions at the nanoscale. Nanotechnology, nanophotonics and in particular, high-resolution-based fluorescence approaches are already delivering crucial information on the way that cells respond to their environment and how they organize their receptors to perform specialized functions. This chapter focuses on emerging super-resolution optical techniques, summarizing their principles, technical implementation, and reviewing some of the achievements reached so far.
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Affiliation(s)
- Maria F Garcia-Parajo
- BioNanoPhotonics Group, IBEC - Institute for Bioengineering of Catalonia and CIBER-BBN, Barcelona, Spain.
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33
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Colyer RA, Siegmund OHW, Tremsin AS, Vallerga JV, Weiss S, Michalet X. Phasor imaging with a widefield photon-counting detector. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:016008. [PMID: 22352658 PMCID: PMC3380817 DOI: 10.1117/1.jbo.17.1.016008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/06/2011] [Accepted: 11/15/2011] [Indexed: 05/18/2023]
Abstract
Fluorescence lifetime can be used as a contrast mechanism to distinguish fluorophores for localization or tracking, for studying molecular interactions, binding, assembly, and aggregation, or for observing conformational changes via Förster resonance energy transfer (FRET) between donor and acceptor molecules. Fluorescence lifetime imaging microscopy (FLIM) is thus a powerful technique but its widespread use has been hampered by demanding hardware and software requirements. FLIM data is often analyzed in terms of multicomponent fluorescence lifetime decays, which requires large signals for a good signal-to-noise ratio. This confines the approach to very low frame rates and limits the number of frames which can be acquired before bleaching the sample. Recently, a computationally efficient and intuitive graphical representation, the phasor approach, has been proposed as an alternative method for FLIM data analysis at the ensemble and single-molecule level. In this article, we illustrate the advantages of combining phasor analysis with a widefield time-resolved single photon-counting detector (the H33D detector) for FLIM applications. In particular we show that phasor analysis allows real-time subsecond identification of species by their lifetimes and rapid representation of their spatial distribution, thanks to the parallel acquisition of FLIM information over a wide field of view by the H33D detector. We also discuss possible improvements of the H33D detector's performance made possible by the simplicity of phasor analysis and its relaxed timing accuracy requirements compared to standard time-correlated single-photon counting (TCSPC) methods.
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Affiliation(s)
- Ryan A. Colyer
- UCLA, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California
| | | | - Anton S. Tremsin
- Space Sciences Laboratory, UCB, 7 Gauss Way, Berkeley, California
| | - John V. Vallerga
- Space Sciences Laboratory, UCB, 7 Gauss Way, Berkeley, California
| | - Shimon Weiss
- UCLA, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California
| | - Xavier Michalet
- UCLA, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California
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34
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Liu H, Wang Y, Liu C, Li H, Gao B, Zhang L, Bo F, Bai Q, Ba X. Fluorescent water-soluble probes based on dendritic PEG substituted perylene bisimides: synthesis, photophysical properties, and live cell images. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm30168g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Schuler B, Müller-Späth S, Soranno A, Nettels D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 2012; 896:21-45. [PMID: 22821515 DOI: 10.1007/978-1-4614-3704-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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36
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KOBITSKI ANDREIYU, NIERTH ALEXANDER, HENGESBACH MARTIN, JÄSCHKE ANDRES, HELM MARK, NIENHAUS GULRICH. EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048008000873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.
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Affiliation(s)
- ANDREI YU. KOBITSKI
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - ALEXANDER NIERTH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARTIN HENGESBACH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - ANDRES JÄSCHKE
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARK HELM
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - G. ULRICH NIENHAUS
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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37
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Layek A, De S, Thorat R, Chowdhury A. Spectrally Resolved Photoluminescence Imaging of ZnO Nanocrystals at Single-Particle Levels. J Phys Chem Lett 2011; 2:1241-1247. [PMID: 26295417 DOI: 10.1021/jz200370s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The intrinsic spectral line widths of defect-related transitions in quantum-confined semiconductor nanocrystals are often difficult to estimate using ensemble measurements because the extent of inhomogeneous broadening due to particle size distributions is not known precisely. To address this problem, we performed spectrally resolved photoluminescence (PL) microscopy of individual ZnO NC by directly populating the defects states using low-energy laser excitation. The temporal evolution of PL intensities shows discrete blinking behaviors, suggesting that the NCs are detected near single-particle levels. The transition energies of individual NCs are found to fluctuate around their mean position (2.25 eV) by ∼0.130 eV, which is attributed to particle size distribution and defects densities associated with each NC. The spectral line width associated with defect emission envelope of ZnO NCs is found to be inherently broad (200-400 meV), which further establishes the presence of multiple closely spaced defect energy levels within every ZnO NC.
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Affiliation(s)
- Arunasish Layek
- Department of Chemistry and National Center for Photovoltaic Research and Education (NCPRE), Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Suman De
- Department of Chemistry and National Center for Photovoltaic Research and Education (NCPRE), Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ruhi Thorat
- Department of Chemistry and National Center for Photovoltaic Research and Education (NCPRE), Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry and National Center for Photovoltaic Research and Education (NCPRE), Indian Institute of Technology Bombay, Mumbai 400076, India
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38
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Ferreon ACM, Deniz AA. Protein folding at single-molecule resolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1021-9. [PMID: 21303706 DOI: 10.1016/j.bbapap.2011.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/22/2011] [Accepted: 01/25/2011] [Indexed: 12/15/2022]
Abstract
The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Allan Chris M Ferreon
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines MB-19, La Jolla, CA 92037, USA
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39
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Davies M, Jung C, Wallis P, Schnitzler T, Li C, Müllen K, Bräuchle C. Photophysics of new photostable rylene derivatives: applications in single-molecule studies and membrane labelling. Chemphyschem 2010; 12:1588-95. [PMID: 21154947 DOI: 10.1002/cphc.201000666] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/11/2010] [Indexed: 11/08/2022]
Abstract
Three new photostable rylene dyes for applications in single molecule studies and membrane labelling have been synthesized and their photophysical properties were characterized. These dyes differ in the number of polyethylene glycol (PEG) chains attached to the core structure which is either a perylene derivate or a terrylene derivate. One perylene and one terrylene dye is modified with two PEG chains, and another terrylene derivate has four PEG chains. The results show that the terrylene dye with four PEG chains (4-PEG-TDI) forms soluble nonfluorescing H-aggregates in water, so that the absorption bands are blue-shifted with respect to those of the fluorescing monomeric form. The presence of a surfactant such as Pluronic P123 leads to the disruption of the aggregates due to the formation of monomers in micelles and a strong increase in fluorescence. Application for labelling cell membranes can be considered for this dye since it adsorbs in a similar way as monomer to a lipid bilayer. Furthermore a single-molecule study of all three rylene dyes in polymeric films of PMMA showed excellent photostability with respect to photobleaching, far above the photostability of other common water-soluble dyes, such as Oxazine-1, Atto647N, Cy5, Alexa647 and Rhodamin6G. Especially 4-PEG-TDI seems to be a promising dye for membrane labelling with its high photostability.
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Affiliation(s)
- Melari Davies
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 München, Germany
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40
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Göhler A, André S, Kaltner H, Sauer M, Gabius HJ, Doose S. Hydrodynamic properties of human adhesion/growth-regulatory galectins studied by fluorescence correlation spectroscopy. Biophys J 2010; 98:3044-53. [PMID: 20550917 DOI: 10.1016/j.bpj.2010.03.040] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 03/09/2010] [Accepted: 03/17/2010] [Indexed: 11/30/2022] Open
Abstract
Fluorescence correlation spectroscopy is applied on homologous human lectins (i.e., adhesion/growth-regulatory galectins) to detect influence of ligand binding and presence of the linker peptide in tandem-repeat-type proteins on hydrodynamic properties. Among five tested proteins, lactose binding increased the diffusion constant only in the cases of homodimeric galectin-1 and the linkerless variant of tandem-repeat-type galectin-4. To our knowledge, the close structural similarity among galectins does not translate into identical response to ligand binding. Kinetic measurements show association and dissociation rate constants in the order of 1 to 10(3) M(-1) s(-1) and 10(-4) s(-1), respectively. Presence of the linker peptide in tandem-repeat-type protein leads to anomalous scaling with molecular mass. These results provide what we believe to be new insights into lectin responses to glycan binding, detectable so far only by small angle neutron scattering, and the structural relevance of the linker peptide. Methodologically, fluorescence correlation spectroscopy is shown to be a rather simple technical tool to characterize hydrodynamic properties of these proteins at a high level of sensitivity.
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Affiliation(s)
- Antonia Göhler
- Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Bielefeld, Germany
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41
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Lang ES, Stieler R, de Oliveira GM. Synthesis, structural characterization and growth features of some (Ph)Se–Cd cluster compounds (Ph=phenyl). Polyhedron 2010. [DOI: 10.1016/j.poly.2010.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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McPhillips J, Murphy A, Jonsson MP, Hendren WR, Atkinson R, Höök F, Zayats AV, Pollard RJ. High-performance biosensing using arrays of plasmonic nanotubes. ACS NANO 2010; 4:2210-2216. [PMID: 20218668 DOI: 10.1021/nn9015828] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We show that aligned gold nanotube arrays capable of supporting plasmonic resonances can be used as high performance refractive index sensors in biomolecular binding reactions. A methodology to examine the sensing ability of the inside and outside walls of the nanotube structures is presented. The sensitivity of the plasmonic nanotubes is found to increase as the nanotube walls are exposed, and the sensing characteristic of the inside and outside walls is shown to be different. Finite element simulations showed good qualitative agreement with the observed behavior. Free standing gold nanotubes displayed bulk sensitivities in the region of 250 nm per refractive index unit and a signal-to-noise ratio better than 1000 upon protein binding which is highly competitive with state-of-the-art label-free sensors.
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Affiliation(s)
- John McPhillips
- Centre for Nanostructured Media, IRCEP, Queen's University of Belfast, BT71NN, United Kingdom.
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43
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Lee KH. Rapid detection of intracellular nanoparticles by electron microscopy. J Anal Sci Technol 2010. [DOI: 10.5355/jast.2010.71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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44
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Tracking single proteins in live cells using single-chain antibody fragment-fluorescent quantum dot affinity pair. Methods Enzymol 2010; 475:61-79. [PMID: 20627153 DOI: 10.1016/s0076-6879(10)75003-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quantum dots (QDs) are extremely bright fluorescent imaging probes that are particularly useful for tracking individual molecules in living cells. Here, we show how a two-component system composed of a high-affinity single-chain fragment antibody and its cognate hapten (fluorescein) can be utilized for tracking individual proteins in various cell types. The single-chain fragment antibody against fluorescein is genetically appended to the protein of interest, while the hapten fluorescein is attached to the end of the peptide that is used to coat the QDs. We describe (i) the method used to functionalize QDs with fluorescein peptides; (ii) the method used to control the stoichiometry of the hapten on the surface of the QD; and (iii) the technical details necessary to observe single molecules in living cells.
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45
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Doose S, Neuweiler H, Sauer M. Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules. Chemphyschem 2009; 10:1389-98. [PMID: 19475638 DOI: 10.1002/cphc.200900238] [Citation(s) in RCA: 373] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Photoinduced electron transfer (PET) between organic fluorophores and suitable electron donating moieties, for example, the amino acid tryptophan or the nucleobase guanine, can quench fluorescence upon van der Waals contact and thus report on molecular contact. PET-quenching has been used as reporter for monitoring conformational dynamics in polypeptides, proteins, and oligonucleotides. Whereas dynamic quenching transiently influences quantum yield and fluorescence lifetime of the fluorophore, static quenching in pi-stacked complexes efficiently suppresses fluorescence emission over time scales longer than the fluorescence lifetime. Static quenching therefore provides sufficient contrast to be observed at the single-molecule level. Here, we review complex formation and static quenching of different fluorophores by various molecular compounds, discuss applications as reporter system for macromolecular dynamics, and give illustrating examples.
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Affiliation(s)
- Sören Doose
- Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Universitätsstr. 25, 33619 Bielefeld, Germany
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46
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Schirra LK, Tackett BS, Blumenfeld ML, Monti OLA. Single molecule power-law behavior on a crystalline surface. J Chem Phys 2009; 131:124702. [DOI: 10.1063/1.3230558] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Srinivasa G, Fickus MC, Guo Y, Linstedt AD, Kovacević J. Active mask segmentation of fluorescence microscope images. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2009; 18:1817-29. [PMID: 19380268 PMCID: PMC2765110 DOI: 10.1109/tip.2009.2021081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the "contour" to that of "inside and outside," or masks, allowing for easy multidimensional segmentation. It adapts to the topology of the image through the use of multiple masks. The algorithm is almost invariant under initialization, allowing for random initialization, and uses a few easily tunable parameters. Experiments show that the active mask algorithm matches the ground truth well and outperforms the algorithm widely used in fluorescence microscopy, seeded watershed, both qualitatively, as well as quantitatively.
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Affiliation(s)
- Gowri Srinivasa
- Department of Information Science and Engineering and the Center for Pattern Recognition, PES School of Engineering, Bangalore, India
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48
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Boldyrev IA, Pavlova IB, Molotkovskiĭ IG. [Synthesis and characteristics of new fluorescent probes based on cardiolipin]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:239-44. [PMID: 19537175 DOI: 10.1134/s1068162009020101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
New fluorescent lipid probes, cardiolipin derivatives AV12-CL and B7-CL, bearing the residues of 12-(9-anthryl)-11E-dodecenoic and 7-(4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacen-8-yl)heptanoic acid, respectively, have been synthesized by acylation of 1-lysocardiolipin, which had been obtained from bovine heart cardiolipin by enzymatic hydrolysis with bacterial lipase. The resulting probes are intended for the study of protein-anionic phospholipid interactions.
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49
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Lang ES, Tirloni B, Oliveira GMD, Villetti MA. New examples of the exploitation of intermediary ligands in the synthesis of polymeric (μ-Se)Hg-clusters. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 2009; 96:2371-81. [PMID: 19289062 DOI: 10.1016/j.bpj.2008.11.061] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 01/12/2023] Open
Abstract
Organic fluorophores common to fluorescence-based investigations suffer from unwanted photophysical properties, including blinking and photobleaching, which limit their overall experimental performance. Methods to control such processes are particularly important for single-molecule fluorescence and fluorescence resonance energy transfer imaging where uninterrupted, stable fluorescence is paramount. Fluorescence and FRET-based assays have been carried out on dye-labeled DNA and RNA-based systems to quantify the effect of including small-molecule solution additives on the fluorescence and FRET behaviors of both cyanine and Alexa fluorophores. A detailed dwell time analysis of the fluorescence and FRET trajectories of more than 200,000 individual molecules showed that two compounds identified previously as triplet state quenchers, cyclooctatetraene, and Trolox, as well as 4-nitrobenzyl alcohol, act to favorably attenuate blinking, photobleaching, and influence the rate of photoresurrection in a concentration-dependent and context-dependent manner. In both biochemical systems examined, a unique cocktail of compounds was shown to be optimal for imaging performance. By simultaneously providing the most rapid and direct access to multiple photophysical kinetic parameters, smFRET imaging provides a powerful avenue for future investigations aimed at discovering new compounds, and effective combinations thereof. These efforts may ultimately facilitate tuning organic dye molecule performance according to each specific experimental demand.
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