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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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2
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Chicea D, Nicolae-Maranciuc A, Doroshkevich AS, Chicea LM, Ozkendir OM. Comparative Synthesis of Silver Nanoparticles: Evaluation of Chemical Reduction Procedures, AFM and DLS Size Analysis. MATERIALS (BASEL, SWITZERLAND) 2023; 16:5244. [PMID: 37569948 PMCID: PMC10419401 DOI: 10.3390/ma16155244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
The size of silver nanoparticles plays a crucial role in their ultimate application in the medical and industrial fields, as their efficacy is enhanced by decreasing dimensions. This study presents two chemical synthesis procedures for obtaining silver particles and compares the results to a commercially available Ag-based product. The first procedure involves laboratory-based chemical reduction using D-glucose (C6H12O6) and NaOH as reducing agents, while the second approach utilizes trisodium citrate dehydrate (C6H5Na3O7·2H2O, TSC). The Ag nanoparticle suspensions were examined using FT-IR and UV-VIS spectroscopy, which indicated the formation of Ag particles. The dimensional properties were investigated using Atomic Force Microscopy (AFM) and confirmed by Dynamic Light Scattering (DLS). The results showed particle size from microparticles to nanoparticles, with a particle size of approximately 60 nm observed for the laboratory-based TSC synthesis approach.
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Affiliation(s)
- Dan Chicea
- Research Center for Complex Physical Systems, Faculty of Sciences, Lucian Blaga University of Sibiu, 550012 Sibiu, Romania
| | - Alexandra Nicolae-Maranciuc
- Research Center for Complex Physical Systems, Faculty of Sciences, Lucian Blaga University of Sibiu, 550012 Sibiu, Romania
- Institute for Interdisciplinary Studies and Research (ISCI), Lucian Blaga University of Sibiu, 550024 Sibiu, Romania
| | - Aleksandr S. Doroshkevich
- Donetsk Institute for Physics and Engineering Named after O.O. Galkin, NAS of Ukraine, 46, Prospect Nauky, 03028 Kyiv, Ukraine;
| | - Liana Maria Chicea
- Faculty of Medicine, Lucian Blaga University of Sibiu, 550169 Sibiu, Romania;
| | - Osman Murat Ozkendir
- Faculty of Engineering, Department of Natural and Mathematical Sciences, Tarsus University, Tarsus 33400, Turkey;
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3
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Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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4
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Ishii S, Yoshimoto S, Hori K. Single-cell adhesion force mapping of a highly sticky bacterium in liquid. J Colloid Interface Sci 2022; 606:628-634. [PMID: 34416455 DOI: 10.1016/j.jcis.2021.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/25/2021] [Accepted: 08/07/2021] [Indexed: 11/18/2022]
Abstract
The sticky bacterium Acinetobacter sp. Tol 5 adheres to various material surfaces via its cell surface nanofiber protein, AtaA. This adhesiveness has only been evaluated based on the amount of cells adhering to a surface. In this study, the adhesion force mapping of a single Tol 5 cell in liquid using the quantitative imaging mode of atomic force microscopy (AFM) revealed that the adhesion of Tol 5 was near 2 nN, which was 1-2 orders of magnitude higher than that of other adhesive bacteria. The adhesion force of a cell became stronger with the increase in AtaA molecules present on the cell surface. Many fibers of peritrichate AtaA molecules simultaneously interact with a surface, strongly attaching the cell to the surface. The adhesion force of a Tol 5 cell was drastically reduced in the presence of 1% casamino acids but not in deionized water (DW), although both liquids decrease the adhesiveness of Tol 5 cells, suggesting that DW and casamino acids inhibit the cell approaching step and the subsequent direct interaction step of AtaA with surfaces, respectively. Heterologous production of AtaA provided non-adhesive Acinetobacter baylyi ADP1 cells with a strong adhesion force to AFM tip surfaces of silicon and gold.
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Affiliation(s)
- Satoshi Ishii
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
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Abstract
AbstractAtomic force microscopy (AFM) has been widely used to acquire surface topography upon different scanning modes and to quantify mechanical properties of a cell using single-point ramp force mode. However, these traditional measurements need massive force curves originating from multiple points of a cell to exclude the potential errors resulted from limited and factitious selections of testing points, making the measurements time-consuming and highly localized. PeakForce Quantitative NanoMechanics (PF QNM) is a high-speed (faster by 3–4 order of magnitude) and global surface mechanical property mapping method with high spatial resolution, overcoming the drawbacks of traditional ramp mode especially used for a live cell with high heterogeneity. In this protocol, we elaborated how to run PF QNM measurements for live cells and relevant modification may be needed when extending this method to other cell-like soft materials.
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Atomic Force Microscopy of Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 2073:247-285. [PMID: 31612446 DOI: 10.1007/978-1-4939-9869-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Atomic force microscopy (AFM) enables imaging of surface-deposited proteins and protein structures under physiological conditions, which is a benefit compared to ultra-high vacuum techniques such as electron microscopy. AFM also has the potential to provide more information from the phase in tapping mode or from functional AFM modes. The sample preparation, probe selection, and imaging conditions are crucial for successful imaging of proteins. Here we give a detailed account of the steps toward imaging of soft samples in both air and liquid along with the basic theory underpinning these details.
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Biophysical Techniques to Analyze Elastic Tissue Extracellular Matrix Proteins Interacting with ADAMTS Proteins. Methods Mol Biol 2019. [PMID: 31463915 DOI: 10.1007/978-1-4939-9698-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Multidomain matrix-associated zinc extracellular proteases ADAMTS and ADAMTS-like proteins have important biological activities in cells and tissues. Beyond their traditional role in procollagen and von Willebrand factor processing and proteoglycan cleavage, ADAMTS/ADAMTSL likely participate in or at least have some role in ECM assembly as some of these proteins bind ECM proteins including fibrillins, fibronectin, and LTBPs. In this chapter, we present four biophysical techniques largely used for the characterization, multimerization, and interaction of proteins: surface plasmon resonance spectroscopy, dynamic light scattering, atomic force microscopy, and circular dichroism spectroscopy.
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Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS NANO 2019; 13:4220-4229. [PMID: 30938988 DOI: 10.1021/acsnano.8b09234] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl2 and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl2-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl2. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Physics , University of Colorado , Boulder , Colorado 80309 , United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Molecular, Cellular, and Developmental Biology , University of Colorado , Boulder , Colorado 80309 , United States
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Angeli E, Buzio R, Firpo G, Magrassi R, Mussi V, Repetto L, Valbusa U. Nanotechnology Applications in Medicine. TUMORI JOURNAL 2018; 94:206-15. [DOI: 10.1177/030089160809400213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In recent years there has been a rapid increase in nanotechnology applications to medicine in order to prevent and treat diseases in the human body. The established and future applications have the potential to dramatically change medical science. The present paper will give a few examples that could transform common medical procedures.
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Affiliation(s)
- Elena Angeli
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Renato Buzio
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Giuseppe Firpo
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Raffaella Magrassi
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Valentina Mussi
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Luca Repetto
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Ugo Valbusa
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
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Abstract
OBJECTIVES Survivors of critical illness have an increased prevalence of bone fractures. However, early changes in bone strength, and their relationship to structural changes, have not been described. We aimed to characterize early changes in bone functional properties in critical illness and their relationship to changes in bone structure, using a sepsis rodent model. DESIGN Experimental study. SETTING Animal research laboratory. SUBJECTS Adult Sprague-Dawley rats. INTERVENTIONS Forty Sprague-Dawley rats were randomized to cecal ligation and puncture or sham surgery. Twenty rodents (10 cecal ligation and puncture, 10 sham) were killed at 24 hours, and 20 more at 96 hours. MEASUREMENTS AND MAIN RESULTS Femoral bones were harvested for strength testing, microCT imaging, histologic analysis, and multifrequency scanning probe microscopy. Fracture loads at the femoral neck were significantly reduced for cecal ligation and puncture-exposed rodents at 24 hours (83.39 ± 10.1 vs 103.1 ± 17.6 N; p = 0.014) and 96 hours (81.60 ± 14.2 vs 95.66 ± 14.3 N; p = 0.047). Using multifrequency scanning probe microscopy, collagen elastic modulus was lower in cecal ligation and puncture-exposed rats at 24 hours (1.37 ± 0.2 vs 6.13 ± 0.3 GPa; p = 0.001) and 96 hours (5.57 ± 0.5 vs 6.13 ± 0.3 GPa; p = 0.006). Bone mineral elastic modulus was similar at 24 hours but reduced in cecal ligation and puncture-exposed rodents at 96 hours (75.34 ± 13.2 vs 134.4 ± 8.2 GPa; p < 0.001). There were no bone architectural or bone mineral density differences by microCT. Similarly, histologic analysis demonstrated no difference in collagen and elastin staining, and C-X-C chemokine receptor type 4, nuclear factor kappa beta, and tartrate-resistant acid phosphatase immunostaining. CONCLUSIONS In a rodent sepsis model, trabecular bone strength is functionally reduced within 24 hours and is associated with a reduction in collagen and mineral elastic modulus. This is likely to be the result of altered biomechanical properties, rather than increased bone mineral turnover. These data offer both mechanistic insights and may potentially guide development of therapeutic interventions.
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Gade Malmos K, Blancas-Mejia LM, Weber B, Buchner J, Ramirez-Alvarado M, Naiki H, Otzen D. ThT 101: a primer on the use of thioflavin T to investigate amyloid formation. Amyloid 2017; 24:1-16. [PMID: 28393556 DOI: 10.1080/13506129.2017.1304905] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thioflavin T (ThT) has been widely used to investigate amyloid formation since 1989. While concerns have recently been raised about its use as a probe specific for amyloid, ThT still continues to be a very valuable tool for studying kinetic aspects of fibrillation and associated inhibition mechanisms. This review aims to provide a conceptual instruction manual, covering appropriate considerations and pitfalls related to the use of ThT. We start by giving a brief introduction to amyloid formation with focus on the morphology of different aggregate species, followed by a discussion of the quality of protein needed to obtain reliable fibrillation data. After an overview of the photochemical basis for ThT's amyloid binding properties and artifacts that may arise from this, we describe how to plan and analyze ThT assays. We conclude with recommendations for complementary techniques to address shortcomings in the ThT assay.
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Affiliation(s)
- Kirsten Gade Malmos
- a Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN) , Aarhus University , Aarhus C , Denmark.,b Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
| | - Luis M Blancas-Mejia
- c Department of Biochemistry and Molecular Biology , Mayo Clinic , Rochester , MN , USA
| | - Benedikt Weber
- d Center for Integrated Protein Science Munich at the Department Chemie , Technische Universität München , Garching , Germany
| | - Johannes Buchner
- d Center for Integrated Protein Science Munich at the Department Chemie , Technische Universität München , Garching , Germany
| | | | - Hironobu Naiki
- e Department of Molecular Pathology, Faculty of Medical Sciences , University of Fukui , Fukui , Japan
| | - Daniel Otzen
- a Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN) , Aarhus University , Aarhus C , Denmark
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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Abyaneh MK, Parisse P, Casalis L. Direct formation of gold nanorods on surfaces using polymer-immobilised gold seeds. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:809-16. [PMID: 27547597 PMCID: PMC4979766 DOI: 10.3762/bjnano.7.72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/14/2016] [Indexed: 12/27/2022]
Abstract
Herein, we present the formation of gold nanorods (GNRs) on novel gold-poly(methyl methacrylate) (Au-PMMA) nanocomposite substrates with unprecedented growth control through the polymer molecular weight (M w) and gold-salt-to-polymer weight ratio. For the first time, GNRs have been produced by seed-mediated direct growth on surfaces that were pre-coated with polymer-immobilised gold seeds. A Au-PMMA nanocomposite formed by UV photoreduction has been used as the gold seed. The influence of polymer M w and gold concentration on the formation of GNRs has been investigated and discussed. The polymer nanocomposite formed with a lower M w PMMA and 20 wt % gold salt provides a suitable medium for growing well-dispersed GNRs. In this sample, the average dimension of produced GNRs is 200 nm in length with aspect ratios up to 10 and a distribution of GNRs to nanoparticles of nearly 22%. Suitable characterization techniques such as AFM and SEM have been used to support concept of the proposed growth method.
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Affiliation(s)
- Majid K Abyaneh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, Oxfordshire, UK
| | - Pietro Parisse
- Elettra - Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, 34149, Trieste, Italy
| | - Loredana Casalis
- Elettra - Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, 34149, Trieste, Italy
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Methods for Improving Aptamer Binding Affinity. Molecules 2016; 21:421. [PMID: 27043498 PMCID: PMC6273865 DOI: 10.3390/molecules21040421] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers.
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Carvalho FA, Freitas T, Santos NC. Taking nanomedicine teaching into practice with atomic force microscopy and force spectroscopy. ADVANCES IN PHYSIOLOGY EDUCATION 2015; 39:360-366. [PMID: 26628660 DOI: 10.1152/advan.00119.2014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Atomic force microscopy (AFM) is a useful and powerful tool to study molecular interactions applied to nanomedicine. The aim of the present study was to implement a hands-on atomic AFM course for graduated biosciences and medical students. The course comprises two distinct practical sessions, where students get in touch with the use of an atomic force microscope by performing AFM scanning images of human blood cells and force spectroscopy measurements of the fibrinogen-platelet interaction. Since the beginning of this course, in 2008, the overall rating by the students was 4.7 (out of 5), meaning a good to excellent evaluation. Students were very enthusiastic and produced high-quality AFM images and force spectroscopy data. The implementation of the hands-on AFM course was a success, giving to the students the opportunity of contact with a technique that has a wide variety of applications on the nanomedicine field. In the near future, nanomedicine will have remarkable implications in medicine regarding the definition, diagnosis, and treatment of different diseases. AFM enables students to observe single molecule interactions, enabling the understanding of molecular mechanisms of different physiological and pathological processes at the nanoscale level. Therefore, the introduction of nanomedicine courses in bioscience and medical school curricula is essential.
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Affiliation(s)
- Filomena A Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Freitas
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Kilpatrick JI, Revenko I, Rodriguez BJ. Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy. Adv Healthc Mater 2015. [PMID: 26200464 DOI: 10.1002/adhm.201500229] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications.
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Affiliation(s)
- Jason I. Kilpatrick
- Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin 4 Ireland
| | - Irène Revenko
- Asylum Research an Oxford Instruments Company; 6310 Hollister Avenue Santa Barbara CA 93117 USA
| | - Brian J. Rodriguez
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin; Belfield, Dublin 4, Ireland; School of Physics; University College Dublin; Belfield Dublin 4 Ireland
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Koebley SR, Thorpe D, Pang P, Chrisochoides P, Greving I, Vollrath F, Schniepp HC. Silk Reconstitution Disrupts Fibroin Self-Assembly. Biomacromolecules 2015; 16:2796-804. [DOI: 10.1021/acs.biomac.5b00732] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sean R. Koebley
- The College of William & Mary, Department of Applied Science, P.O. Box 8795, Williamsburg, Virginia 23187-8795, United States
| | - Daniel Thorpe
- The College of William & Mary, Department of Applied Science, P.O. Box 8795, Williamsburg, Virginia 23187-8795, United States
| | - Pei Pang
- The College of William & Mary, Department of Applied Science, P.O. Box 8795, Williamsburg, Virginia 23187-8795, United States
| | - Panos Chrisochoides
- The College of William & Mary, Department of Applied Science, P.O. Box 8795, Williamsburg, Virginia 23187-8795, United States
| | - Imke Greving
- Oxford Silk Group, Department of Zoology, Oxford University, Tinbergen
Building, South Parks Road, Oxford, Oxfordshire OX1 3PS, United Kingdom
| | - Fritz Vollrath
- Oxford Silk Group, Department of Zoology, Oxford University, Tinbergen
Building, South Parks Road, Oxford, Oxfordshire OX1 3PS, United Kingdom
| | - Hannes C. Schniepp
- The College of William & Mary, Department of Applied Science, P.O. Box 8795, Williamsburg, Virginia 23187-8795, United States
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18
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Garai A, Saurabh S, Lansac Y, Maiti PK. DNA Elasticity from Short DNA to Nucleosomal DNA. J Phys Chem B 2015; 119:11146-56. [DOI: 10.1021/acs.jpcb.5b03006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashok Garai
- Centre
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Suman Saurabh
- Centre
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
| | - Prabal K. Maiti
- Centre
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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19
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Modification by UV radiation of the surface of thin films based on collagen extracted from fish scales. Biointerphases 2014; 9:029003. [DOI: 10.1116/1.4865753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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21
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Tovee PD, Kolosov OV. Mapping nanoscale thermal transfer in-liquid environment-immersion scanning thermal microscopy. NANOTECHNOLOGY 2013; 24:465706. [PMID: 24164803 DOI: 10.1088/0957-4484/24/46/465706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nanoscale heat transport is of increasing importance as it often defines performance of modern processors and thermoelectric nanomaterials, and affects functioning of chemical sensors and biosensors. Scanning thermal microscopy (SThM) is the leading tool for nanoscale mapping of thermal properties, but it is often negatively affected by unstable tip-surface thermal contacts. While operating SThM in-liquid environment may allow unimpeded thermal contact and open new application areas, it has so far been regarded as impossible due to increased heat dissipation into the liquid, and the perceived reduced spatial thermal resolution. Nevertheless, in this paper we show that such liquid immersion SThM (iSThM) is fully feasible and, while its thermal sensitivity and spatial resolution is somewhat below that of in-air SThM, it has sufficient thermal contrast to detect thermal conductivity variations in few tens of nm thick graphite nanoflake and metal-polymer nanostructured interconnects. Our results confirm that thermal sensing in iSThM can provide nanoscale resolution on the order of 30 nm, that, coupled with the absence of tip snap-in due to the elimination of capillary forces, opens the possibility for nanoscale thermal mapping in liquids, including thermal phenomena in energy storage devices, catalysts and biosystems.
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Affiliation(s)
- Peter D Tovee
- Physics Department, Lancaster University, Lancaster, LA1 4YB, UK
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22
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Sionkowska A, Płanecka A. Surface properties of thin films based on the mixtures of chitosan and silk fibroin. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.07.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Jacobson KH, Kuech TR, Pedersen JA. Attachment of pathogenic prion protein to model oxide surfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:6925-34. [PMID: 23611152 PMCID: PMC4091914 DOI: 10.1021/es3045899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Prions are the infectious agents in the class of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies, which affect humans, deer, sheep, and cattle. Prion diseases of deer and sheep can be transmitted via environmental routes, and soil is has been implicated in the transmission of these diseases. Interaction with soil particles is expected to govern the transport, bioavailability and persistence of prions in soil environments. A mechanistic understanding of prion interaction with soil components is critical for understanding the behavior of these proteins in the environment. Here, we report results of a study to investigate the interactions of prions with model oxide surfaces (Al2O3, SiO2) using quartz crystal microbalance with dissipation monitoring and optical waveguide light mode spectroscopy. The efficiency of prion attachment to Al2O3 and SiO2 depended strongly on pH and ionic strength in a manner consistent with electrostatic forces dominating interaction with these oxides. The presence of the N-terminal portion of the protein appeared to promote attachment to Al2O3 under globally electrostatically repulsive conditions. We evaluated the utility of recombinant prion protein as a surrogate for prions in attachment experiments and found that its behavior differed markedly from that of the infectious agent. Our findings suggest that prions would tend to associate with positively charged mineral surfaces in soils (e.g., iron and aluminum oxides).
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Affiliation(s)
- Kurt H. Jacobson
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, WI 53706
| | - Thomas R. Kuech
- Environmental Chemistry and Technology Program, University of Wisconsin, Madison, WI 53706
| | - Joel A. Pedersen
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, WI 53706
- Environmental Chemistry and Technology Program, University of Wisconsin, Madison, WI 53706
- Department of Soil Science, University of Wisconsin, Madison, WI 53706
- Corresponding author address: Department of Soil Science, University of Wisconsin, 1525 Observatory Drive, Madison, WI 53706 1299; phone: (608) 263-4971; fax: (608) 265-2595;
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Schön P, Kutnyanszky E, ten Donkelaar B, Santonicola MG, Tecim T, Aldred N, Clare AS, Vancso GJ. Probing biofouling resistant polymer brush surfaces by atomic force microscopy based force spectroscopy. Colloids Surf B Biointerfaces 2013; 102:923-30. [DOI: 10.1016/j.colsurfb.2012.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 09/07/2012] [Accepted: 09/12/2012] [Indexed: 12/17/2022]
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25
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Fasting C, Schalley CA, Weber M, Seitz O, Hecht S, Koksch B, Dernedde J, Graf C, Knapp EW, Haag R. Multivalenz als chemisches Organisations- und Wirkprinzip. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201114] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Fasting C, Schalley CA, Weber M, Seitz O, Hecht S, Koksch B, Dernedde J, Graf C, Knapp EW, Haag R. Multivalency as a Chemical Organization and Action Principle. Angew Chem Int Ed Engl 2012; 51:10472-98. [DOI: 10.1002/anie.201201114] [Citation(s) in RCA: 688] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Indexed: 12/26/2022]
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Nanocolloidal albumin-IRDye 800CW: a near-infrared fluorescent tracer with optimal retention in the sentinel lymph node. Eur J Nucl Med Mol Imaging 2012; 39:1161-8. [PMID: 22349719 PMCID: PMC3369133 DOI: 10.1007/s00259-012-2080-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/31/2012] [Indexed: 12/13/2022]
Abstract
Purpose At present, the only approved fluorescent tracer for clinical near-infrared fluorescence-guided sentinel node (SN) detection is indocyanine green (ICG), but the use of this tracer is limited due to its poor retention in the SN resulting in the detection of higher tier nodes. We describe the development and characterization of a next-generation fluorescent tracer, nanocolloidal albumin-IRDye 800CW that has optimal properties for clinical SN detection Methods The fluorescent dye IRDye 800CW was covalently coupled to colloidal human serum albumin (HSA) particles present in the labelling kit Nanocoll in a manner compliant with current Good Manufacturing Practice. Characterization of nanocolloidal albumin-IRDye 800CW included determination of conjugation efficiency, purity, stability and particle size. Quantum yield was determined in serum and compared to that of ICG. For in vivo evaluation a lymphogenic metastatic tumour model in rabbits was used. Fluorescence imaging was performed directly after peritumoral injection of nanocolloidal albumin-IRDye 800CW or the reference ICG/HSA (i.e. ICG mixed with HSA), and was repeated after 24 h, after which fluorescent lymph nodes were excised. Results Conjugation of IRDye 800CW to nanocolloidal albumin was always about 50% efficient and resulted in a stable and pure product without affecting the particle size of the nanocolloidal albumin. The quantum yield of nanocolloidal albumin-IRDye 800CW was similar to that of ICG. In vivo evaluation revealed noninvasive detection of the SN within 5 min of injection of either nanocolloidal albumin-IRDye 800CW or ICG/HSA. No decrease in the fluorescence signal from SN was observed 24 h after injection of the nanocolloidal albumin-IRDye 800CW, while a strong decrease or complete disappearance of the fluorescence signal was seen 24 h after injection of ICG/HSA. Fluorescence-guided SN biopsy was very easy. Conclusion Nanocolloidal albumin-IRDye 800CW is a promising fluorescent tracer with optimal kinetic features for SN detection. Electronic supplementary material The online version of this article (doi:10.1007/s00259-012-2080-5) contains supplementary material, which is available to authorized users.
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te Riet J, Katan AJ, Rankl C, Stahl SW, van Buul AM, Phang IY, Gomez-Casado A, Schön P, Gerritsen JW, Cambi A, Rowan AE, Vancso GJ, Jonkheijm P, Huskens J, Oosterkamp TH, Gaub H, Hinterdorfer P, Figdor CG, Speller S. Interlaboratory round robin on cantilever calibration for AFM force spectroscopy. Ultramicroscopy 2011; 111:1659-69. [DOI: 10.1016/j.ultramic.2011.09.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/12/2011] [Accepted: 09/16/2011] [Indexed: 01/30/2023]
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29
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Heuveling DA, Visser GWM, Baclayon M, Roos WH, Wuite GJL, Hoekstra OS, Leemans CR, de Bree R, van Dongen GAMS. 89Zr-nanocolloidal albumin-based PET/CT lymphoscintigraphy for sentinel node detection in head and neck cancer: preclinical results. J Nucl Med 2011; 52:1580-4. [PMID: 21890880 DOI: 10.2967/jnumed.111.089557] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Identifying sentinel nodes near the primary tumor remains a problem in, for example, head and neck cancer because of the limited resolution of current lymphoscintigraphic imaging when using (99m)Tc-nanocolloidal albumin. This study describes the development and evaluation of a nanocolloidal albumin-based tracer specifically dedicated for high-resolution PET detection. METHODS (89)Zr was coupled to nanocolloidal albumin via the bifunctional chelate p-isothiocyanatobenzyldesferrioxamine B. Quality control tests, including particle size measurements, and in vivo biodistribution and imaging experiments in a rabbit lymphogenic metastasis model were performed. RESULTS Coupling of (89)Zr to nanocolloidal albumin appeared to be efficient, resulting in a stable product with a radiochemical purity greater than 95%, without affecting the particle size. PET showed distinguished uptake of (89)Zr-nanocolloidal albumin in the sentinel nodes, with visualization of lymphatic vessels, and with a biodistribution comparable to (99m)Tc-nanocolloidal albumin. CONCLUSION (89)Zr-nanocolloidal albumin is a promising tracer for sentinel node detection by PET.
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Affiliation(s)
- Derrek A Heuveling
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
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30
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Allison DP, Mortensen NP, Sullivan CJ, Doktycz MJ. Atomic force microscopy of biological samples. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2011; 2:618-34. [PMID: 20672388 DOI: 10.1002/wnan.104] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).
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Affiliation(s)
- David P Allison
- Biosciences Division, Oak Ridge National Laboratory, TN 37831-6445, USA
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31
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Diezmann F, Seitz O. DNA-guided display of proteins and protein ligands for the interrogation of biology. Chem Soc Rev 2011; 40:5789-801. [DOI: 10.1039/c1cs15054e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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32
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Atomic force microscopy study of DNA conformation in the presence of drugs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:59-68. [PMID: 20882274 DOI: 10.1007/s00249-010-0627-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/27/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug-DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.
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Baclayon M, Roos WH, Wuite GJL. Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 2010; 9:1678-88. [PMID: 20562411 PMCID: PMC2938060 DOI: 10.1074/mcp.r110.001461] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 12/17/2022] Open
Abstract
To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.
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Affiliation(s)
- Marian Baclayon
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Gijs J. L. Wuite
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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McConney ME, Singamaneni S, Tsukruk VV. Probing Soft Matter with the Atomic Force Microscopies: Imaging and Force Spectroscopy. POLYM REV 2010. [DOI: 10.1080/15583724.2010.493255] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
The phase imaging atomic force microscopy is a powerful tool in surface characterization of the biomaterials, and the resulting phase image is able to detect chemical variation and reveal more detailed surface properties than the morphological image. However, the chemical- and morphological-dependent phase images were still not distinguished well. In order to better understand actual occurring phase images, we examined non-carious human maxillary incisor, microphase separated polyurethane and self-assembling peptide nanofibres. We herein reported that phase image mainly plotted the morphological change: the phase peak corresponding to the morphological valley, and the morphological peak to the phase valley, and exhibited fine surface structures of materials. The chemical-dependent phase contrast was generally masked by their inherent roughness. For the sample being very rough and having great phase separation, its chemical-dependent phase contrast could be detected at the hard tapping mode ('Amp. Ref. "set point ratio"': -0.4 to -0.8), for the sample with medium roughness only at the light tapping mode ('Amp. Ref.': -0.1 to -0.4). These results will help us understand and determine actual occurring phase images of natural or fabricated biomaterials, even, other materials.
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Affiliation(s)
- Z Ye
- Institute for NanoBiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Science Park No.1, Ke Yuan 4th St., Gao Peng Road, Hi-tech Industrial Development Zone, Chengdu, 610041, Sichuan, China
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Uemura H, Ichikawa M, Kimura Y. Crossover behavior in static and dynamic properties of a single DNA molecule from three to quasi-two dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:051801. [PMID: 20866253 DOI: 10.1103/physreve.81.051801] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Indexed: 05/29/2023]
Abstract
We studied the conformation and dynamics of a single DNA molecule in a thin slit by a fluorescent microscope. In a slit thinner than the Flory radius in three dimensions, the length of the major axis, the translational self-diffusion coefficient and the rotational relaxation time in a dilute solution show the apparent dependence on the thickness of the slit. The observed dependence is in agreement with that predicted by blob theory, despite the number of blobs is very small. The radial distribution of the segments around the center of mass of a single molecule was also studied and compared with that calculated for a Gaussian and an excluded volume chain. The influence of the polymer concentration on the geometrical confinement by slits was also studied in a semidilute solution near the overlap concentration c∗. The confinement effect is found to be not so serious near c∗ and is only significant in the so-called "two-dimensional pancake" region.
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Affiliation(s)
- Hitoshi Uemura
- Department of Physics, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Ikai A. A review on: atomic force microscopy applied to nano-mechanics of the cell. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 119:47-61. [PMID: 19343307 DOI: 10.1007/10_2008_41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Since its introduction in 1986, AFM has been applied to biological studies along with its widespread use in physics, chemistry and engineering fields. Due to its dual capabilities of imaging nano-materials with an atomic level resolution and of directly manipulating samples with high precision, AFM is now considered an indispensable instrument for nano-technological researchers especially in physically oriented fields. In biology in general, however, and in biotechnology in particular, its usefulness must be critically examined and, if necessary as it certainly is, further explored from a practical point of view. In this review, a new trend of applying AFM based technology to elucidate the mechanical basis of the cellular structure and its interaction with the extracellular matrix including cell to cell interaction is reviewed. Some of the recent studies done by using other force measuring or force exerting methods are also covered in the hope that all the nano-mechanical work on the cellular level will eventually contribute to the emergence of the mechano-chemical view of the cell in a unified manner.
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Affiliation(s)
- Atsushi Ikai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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WU J, DENG X, ZHANG Y, WANG L, TIAN BQ, XIE BJ. Application of Atomic Force Microscopy in the Study of Polysaccharide. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60359-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Goldsbury CS, Scheuring S, Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2009; Chapter 17:17.7.1-17.7.19. [DOI: 10.1002/0471140864.ps1707s58] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Laurent Kreplak
- Dalhousie University, Department of Physics & Atmospheric Science Halifax Canada
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40
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Chandraprabha MN, Somasundaran P, Natarajan KA. Modeling and analysis of nanoscale interaction forces between Acidithiobacillus ferrooxidans and AFM tip. Colloids Surf B Biointerfaces 2009; 75:310-8. [PMID: 19800769 DOI: 10.1016/j.colsurfb.2009.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/30/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
Abstract
The specificity exhibited by Acidithiobacillus ferrooxidans, a chemolithoautotrophic acidophile, in their attachment to different sulphide minerals has resulted in effective physical separation of these minerals. This can be explained in terms of surface forces of interaction between the cells and substrates using AFM. In the light of this, the present study reports interaction studies with A. ferrooxidans cells and an AFM silicon nitride tip. The aim of the present investigation is to probe the nanoscale interactions between A. ferrooxidans cells and silicon nitride tip of an AFM, model the approach and retraction forces, and elucidate the effects of pH, ionic strength and surface biopolymers on interfacial forces.
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Affiliation(s)
- M N Chandraprabha
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bangalore 560054, India.
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Yadavalli VK, Forbes JG, Wang K. Nanomechanics of full-length nebulin: an elastic strain gauge in the skeletal muscle sarcomere. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:7496-505. [PMID: 19463013 PMCID: PMC2998391 DOI: 10.1021/la9009898] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nebulin, a family of giant modular proteins (MW 700-800 kDa), acts as a F-actin thin filament ruler and calcium-linked regulator of actomyosin interaction. The nanomechanics of full length, native rabbit nebulin was investigated with an atomic force microscope by tethering, bracketing, and stretching full-length molecules via pairs of site-specific antibodies that were attached covalently, one to a protein resistant self-assembled monolayer of oligoethylene glycol and the other to the cantilever. Using this new nanomechanics platform that enables the identification of single molecule events via an unbiased analysis of detachment force and distance of all force curves, we showed that nebulin is elastic and extends to approximately 1 microm by external force up to an antibody detachment force of approximately 300-400 pN. Upon stretching, nebulin unravels and yields force spectra with craggy mountain range profiles with variable numbers and heights of force peaks. The peak spacings, analyzed by the model-independent, empirical Hilbert-Huang transform method, displayed underlying periodicities at approximately 15 and approximately 22 nm that may result from the unfolding of one or more nebulin modules between force peaks. Nebulin may act as an elastic strain gauge that interacts optimally with actin only under appropriate strain and stress. This stretch to match protein ruler may also exert a compressive force that stabilizes thin filaments against stress during contraction. We propose that the elasticity of nebulin is integral and essential in the muscle sarcomere.
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Affiliation(s)
- Vamsi K Yadavalli
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Abstract
Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23°C to 42°C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.
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Affiliation(s)
- Robert A Forties
- Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117, USA
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Rittman M, Gilroy E, Koohy H, Rodger A, Richards A. Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review. Sci Prog 2009; 92:163-204. [PMID: 19697713 PMCID: PMC10361128 DOI: 10.3184/003685009x462205] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.
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Affiliation(s)
- Martyn Rittman
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Emma Gilroy
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Hashem Koohy
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Adair Richards
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
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Plant AL, Bhadriraju K, Spurlin TA, Elliott JT. Cell response to matrix mechanics: focus on collagen. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:893-902. [PMID: 19027042 DOI: 10.1016/j.bbamcr.2008.10.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 10/27/2008] [Indexed: 01/16/2023]
Abstract
Many model systems and measurement tools have been engineered for observing and quantifying the effect of mechanics on cellular response. These have contributed greatly to our current knowledge of the molecular events by which mechanical cues affect cell biology. Cell responses to the mechanical properties of type 1 collagen gels are discussed, followed by a description of a model system of very thin, mechanically tunable collagen films that evoke similar responses from cells as do gel systems, but have additional advantages. Cell responses to thin films of collagen suggest that at least some of the mechanical cues that cells can respond to in their environment occur at the sub-micron scale. Mechanical properties of thin films of collagen can be tuned without altering integrin engagement, and in some cases without altering topology, making them useful in addressing questions regarding the roles of specific integrins in transducing or mitigating responses to mechanical cues. The temporal response of cells to differences in ECM may provide insight into mechanisms of signal transduction.
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Affiliation(s)
- Anne L Plant
- National Institute of Standards and Technology, Biochemical Science Division, Gaithersburg, MD 20899, USA.
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Harding JH, Duffy DM, Sushko ML, Rodger PM, Quigley D, Elliott JA. Computational Techniques at the Organic−Inorganic Interface in Biomineralization. Chem Rev 2008; 108:4823-54. [DOI: 10.1021/cr078278y] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- John H. Harding
- Department of Engineering Materials, University of Sheffield, Sheffield, U.K
| | | | | | | | | | - James A. Elliott
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, U.K
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47
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Nanotechnology, nanotoxicology, and neuroscience. Prog Neurobiol 2008; 87:133-70. [PMID: 18926873 DOI: 10.1016/j.pneurobio.2008.09.009] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 07/02/2008] [Accepted: 09/18/2008] [Indexed: 12/19/2022]
Abstract
Nanotechnology, which deals with features as small as a 1 billionth of a meter, began to enter into mainstream physical sciences and engineering some 20 years ago. Recent applications of nanoscience include the use of nanoscale materials in electronics, catalysis, and biomedical research. Among these applications, strong interest has been shown to biological processes such as blood coagulation control and multimodal bioimaging, which has brought about a new and exciting research field called nanobiotechnology. Biotechnology, which itself also dates back approximately 30 years, involves the manipulation of macroscopic biological systems such as cells and mice in order to understand why and how molecular level mechanisms affect specific biological functions, e.g., the role of APP (amyloid precursor protein) in Alzheimer's disease (AD). This review aims (1) to introduce key concepts and materials from nanotechnology to a non-physical sciences community; (2) to introduce several state-of-the-art examples of current nanotechnology that were either constructed for use in biological systems or that can, in time, be utilized for biomedical research; (3) to provide recent excerpts in nanotoxicology and multifunctional nanoparticle systems (MFNPSs); and (4) to propose areas in neuroscience that may benefit from research at the interface of neurobiologically important systems and nanostructured materials.
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Ierardi V, Niccolini A, Alderighi M, Gazzano A, Martelli F, Solaro R. AFM characterization of rabbit spermatozoa. Microsc Res Tech 2008; 71:529-35. [DOI: 10.1002/jemt.20584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Goldsbury C, Scheuring S. Introduction to atomic force microscopy (AFM) in biology. ACTA ACUST UNITED AC 2008; Chapter 17:17.7.1-17.7.17. [PMID: 18429225 DOI: 10.1002/0471140864.ps1707s29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The atomic force microscope has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated. Importantly, the measurements are made in buffer solutions, allowing biological samples to stay alive within a physiological-like environment while temporal changes in structure are measured. This overview provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins. The physical principles of the technique and methodological aspects of its practical use and applications are also described.
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Affiliation(s)
- Claire Goldsbury
- Cytoskeleton Group, Max Planck Unit for Structural Molecular Biology, Hamburg, Germany
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