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Vobornik D, Chen M, Zou S, Lopinski GP. Measuring the Diameter of Single-Wall Carbon Nanotubes Using AFM. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:477. [PMID: 36770438 PMCID: PMC9921789 DOI: 10.3390/nano13030477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
In this work, we identify two issues that can significantly affect the accuracy of AFM measurements of the diameter of single-wall carbon nanotubes (SWCNTs) and propose a protocol that reduces errors associated with these issues. Measurements of the nanotube height under different applied forces demonstrate that even moderate forces significantly compress several different types of SWCNTs, leading to errors in measured diameters that must be minimized and/or corrected. Substrate and nanotube roughness also make major contributions to the uncertainty associated with the extraction of diameters from measured images. An analysis method has been developed that reduces the uncertainties associated with this extraction to <0.1 nm. This method is then applied to measure the diameter distribution of individual highly semiconducting enriched nanotubes in networks prepared from polyfluorene/SWCNT dispersions. Good agreement is obtained between diameter distributions for the same sample measured with two different commercial AFM instruments, indicating the reproducibility of the method. The reduced uncertainty in diameter measurements based on this method facilitates: (1) determination of the thickness of the polymer layer wrapping the nanotubes and (2) measurement of nanotube compression at tube-tube junctions within the network.
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2
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Revealing DNA Structure at Liquid/Solid Interfaces by AFM-Based High-Resolution Imaging and Molecular Spectroscopy. Molecules 2021; 26:molecules26216476. [PMID: 34770895 PMCID: PMC8587808 DOI: 10.3390/molecules26216476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
DNA covers the genetic information in all living organisms. Numerous intrinsic and extrinsic factors may influence the local structure of the DNA molecule or compromise its integrity. Detailed understanding of structural modifications of DNA resulting from interactions with other molecules and surrounding environment is of central importance for the future development of medicine and pharmacology. In this paper, we review the recent achievements in research on DNA structure at nanoscale. In particular, we focused on the molecular structure of DNA revealed by high-resolution AFM (Atomic Force Microscopy) imaging at liquid/solid interfaces. Such detailed structural studies were driven by the technical developments made in SPM (Scanning Probe Microscopy) techniques. Therefore, we describe here the working principles of AFM modes allowing high-resolution visualization of DNA structure under native (liquid) environment. While AFM provides well-resolved structure of molecules at nanoscale, it does not reveal the chemical structure and composition of studied samples. The simultaneous information combining the structural and chemical details of studied analyte allows achieve a comprehensive picture of investigated phenomenon. Therefore, we also summarize recent molecular spectroscopy studies, including Tip-Enhanced Raman Spectroscopy (TERS), on the DNA structure and its structural rearrangements.
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3
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Prasad J, Viollet S, Gurunatha KL, Urvoas A, Fournier AC, Valerio-Lepiniec M, Marcelot C, Baris B, Minard P, Dujardin E. Directed evolution of artificial repeat proteins as habit modifiers for the morphosynthesis of (111)-terminated gold nanocrystals. NANOSCALE 2019; 11:17485-17497. [PMID: 31532442 DOI: 10.1039/c9nr04497c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Natural biocomposites are shaped by proteins that have evolved to interact with inorganic materials. Protein directed evolution methods which mimic Darwinian evolution have proven highly successful to generate improved enzymes or therapeutic antibodies but have rarely been used to evolve protein-material interactions. Indeed, most reported studies have focused on short peptides and a wide range of oligopeptides with chemical binding affinity for inorganic materials have been uncovered by phage display methods. However, their small size and flexible unfolded structure prevent them from dictating the shape and crystallinity of the growing material. In the present work, a specific set of artificial repeat proteins (αRep), which exhibit highly stable 3D folding with a well-defined hypervariable interacting surface, is selected by directed evolution of a very efficient home-built protein library for their high and selective affinity for the Au(111) surface. The proteins are built from the extendable concatenation of self-compatible repeated motifs idealized from natural HEAT proteins. The high-yield synthesis of Au(111)-faceted nanostructures mediated by these αRep proteins demonstrates their chemical affinity and structural selectivity that endow them with high crystal habit modification performances. Importantly, we further exploit the protein shell spontaneously assembled on the nanocrystal facets to drive protein-mediated colloidal self-assembly and on-surface enzymatic catalysis. Our method constitutes a generic tool for producing nanocrystals with determined faceting, superior biocompatibility and versatile bio-functionalization towards plasmon-based devices and (bio)molecular sensors.
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Affiliation(s)
- Janak Prasad
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Sébastien Viollet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Kargal L Gurunatha
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Agathe C Fournier
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Cécile Marcelot
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Bulent Baris
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Erik Dujardin
- CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France.
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4
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Papkov D, Delpouve N, Delbreilh L, Araujo S, Stockdale T, Mamedov S, Maleckis K, Zou Y, Andalib MN, Dargent E, Dravid VP, Holt MV, Pellerin C, Dzenis YA. Quantifying Polymer Chain Orientation in Strong and Tough Nanofibers with Low Crystallinity: Toward Next Generation Nanostructured Superfibers. ACS NANO 2019; 13:4893-4927. [PMID: 31038925 DOI: 10.1021/acsnano.8b08725] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Advanced fibers revolutionized structural materials in the second half of the 20th century. However, all high-strength fibers developed to date are brittle. Recently, pioneering simultaneous ultrahigh strength and toughness were discovered in fine (<250 nm) individual electrospun polymer nanofibers (NFs). This highly desirable combination of properties was attributed to high macromolecular chain alignment coupled with low crystallinity. Quantitative analysis of the degree of preferred chain orientation will be crucial for control of NF mechanical properties. However, quantification of supramolecular nanoarchitecture in NFs with low crystallinity in the ultrafine diameter range is highly challenging. Here, we discuss the applicability of traditional as well as emerging methods for quantification of polymer chain orientation in nanoscale one-dimensional samples. Advantages and limitations of different techniques are critically evaluated on experimental examples. It is shown that straightforward application of some of the techniques to sub-wavelength-diameter NFs can lead to severe quantitative and even qualitative artifacts. Sources of such size-related artifacts, stemming from instrumental, materials, and geometric phenomena at the nanoscale, are analyzed on the example of polarized Raman method but are relevant to other spectroscopic techniques. A proposed modified, artifact-free method is demonstrated. Outstanding issues and their proposed solutions are discussed. The results provide guidance for accurate nanofiber characterization to improve fundamental understanding and accelerate development of nanofibers and related nanostructured materials produced by electrospinning or other methods. We expect that the discussion in this review will also be useful to studies of many biological systems that exhibit nanofilamentary architectures and combinations of high strength and toughness.
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Affiliation(s)
- Dimitry Papkov
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
| | - Nicolas Delpouve
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Laurent Delbreilh
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Steven Araujo
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Taylor Stockdale
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Sergey Mamedov
- Division of HORIBA Instruments, Inc. , HORIBA Scientific , 20 Knightsbridge Road , Piscataway , New Jersey 08854 , United States
| | - Kaspars Maleckis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Yan Zou
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Mohammad Nahid Andalib
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Eric Dargent
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Vinayak P Dravid
- Department of Materials Science and Engineering , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martin V Holt
- Center for Nanoscale Materials , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Christian Pellerin
- Département de chimie , Université de Montréal , Montréal , QC H3C 3J7 , Canada
| | - Yuris A Dzenis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
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5
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Pawlak R, Vilhena JG, Hinaut A, Meier T, Glatzel T, Baratoff A, Gnecco E, Pérez R, Meyer E. Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold. Nat Commun 2019; 10:685. [PMID: 30737410 PMCID: PMC6368621 DOI: 10.1038/s41467-019-08531-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/16/2019] [Indexed: 01/02/2023] Open
Abstract
Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, structure alone is insufficient to understand the function of native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens of pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy and computer simulations in cryogenic conditions to quantify adhesion and intra-molecular properties of spray-deposited single-strand DNA oligomers on Au(111). Sub-nanometer resolution images reveal folding conformations confirmed by simulations. Lifting shows a decay of the measured stiffness with sharp dips every 0.2-0.3 nm associated with the sequential peeling and detachment of single nucleotides. A stiffness of 30-35 N m-1 per stretched repeat unit is deduced in the nano-newton range. This combined study suggests how to better control cryo-force spectroscopy of adsorbed heterogeneous (bio)polymer and to potentially enable single-base recognition in DNA strands only few nanometers long.
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Affiliation(s)
- Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Antoine Hinaut
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Tobias Meier
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Alexis Baratoff
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Enrico Gnecco
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, D-07742, Jena, Germany
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain.
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
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6
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Kasas S, Dietler G. DNA-protein interactions explored by atomic force microscopy. Semin Cell Dev Biol 2017; 73:231-239. [PMID: 28716606 DOI: 10.1016/j.semcdb.2017.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022]
Abstract
DNA-protein interactions play an important role in all living organisms on Earth. The advent of atomic force microscopy permitted for the first time to follow and to characterize interaction forces between these two molecular species. After a short description of the AFM and its imaging modes we review, in a chronological order some of the studies that we think importantly contributed to the field.
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Affiliation(s)
- S Kasas
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Plateforme de Morphologie, Faculté de Médecine, Université de Lausanne, Bugnion 9, 1005 Lausanne, Switzerland.
| | - G Dietler
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Japaridze A, Renevey S, Sobetzko P, Stoliar L, Nasser W, Dietler G, Muskhelishvili G. Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein. J Biol Chem 2017; 292:7607-7618. [PMID: 28316324 PMCID: PMC5418058 DOI: 10.1074/jbc.m117.780239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Indexed: 11/28/2022] Open
Abstract
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.
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Affiliation(s)
- Aleksandre Japaridze
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | - Sylvain Renevey
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | | | | | - William Nasser
- UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003 INSA Lyon, Villeurbanne F-69621, France, and
| | - Giovanni Dietler
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland,
| | - Georgi Muskhelishvili
- Jacobs University, D-28759 Bremen, Germany, .,Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159 Tbilisi, Republik of Georgia
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8
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Frequency-modulated atomic force microscopy localises viscoelastic remodelling in the ageing sheep aorta. J Mech Behav Biomed Mater 2016; 64:10-7. [PMID: 27479890 PMCID: PMC5020410 DOI: 10.1016/j.jmbbm.2016.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/23/2022]
Abstract
Age-related aortic stiffening is associated with cardiovascular diseases such as heart failure. The mechanical functions of the main structural components of the aorta, such as collagen and elastin, are determined in part by their organisation at the micrometer length scale. With age and disease both components undergo aberrant remodelling, hence, there is a need for accurate characterisation of the biomechanical properties at this length scale. In this study we used a frequency-modulated atomic force microscopy (FM-AFM) technique on a model of ageing in female sheep aorta (young: ~18 months, old: >8 years) to measure the micromechanical properties of the medial layer of the ascending aorta. The novelty of our FM-AFM method, operated at 30 kHz, is that it is non-contact and can be performed on a conventional AFM using the ׳cantilever tune’ mode, with a spatial (areal) resolution of around 1.6 μm2. We found significant changes in the elastic and viscoelastic properties within the medial lamellar unit (elastic lamellae and adjacent inter-lamellar space) with age. In particular, there was an increase in elastic modulus (Young; geometric mean (geometric SD)=42.9 (2.26) kPa, Old=113.9 (2.57) kPa, P<0.0001), G′ and G″ (storage and loss modulus respectively) (Young; G′=14.3 (2.26) kPa, Old G′=38.0 (2.57) kPa, P<0.0001; Young; G″=14.5 (2.56) kPa, Old G″=32.8 (2.52) kPa, P<0.0001). The trends observed in the elastic properties with FM-AFM matched those we have previously found using scanning acoustic microscopy (SAM). The utility of the FM-AFM method is that it does not require custom AFM hardware and can be used to simultaneously determine the elastic and viscoelastic behaviour of a biological sample.
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9
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Al-Ta’ii HMJ, Amin YM, Periasamy V. Humidity influenced capacitance and resistance of an Al/DNA/Al Schottky diode irradiated by alpha particles. Sci Rep 2016; 6:25519. [PMID: 27160654 PMCID: PMC4861926 DOI: 10.1038/srep25519] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/15/2016] [Indexed: 11/10/2022] Open
Abstract
Deoxyribonucleic acid or DNA based sensors, especially as humidity and alpha particle sensors have become quite popular in recent times due to flexible and highly optimizable nature of this fundamental biomaterial. Application of DNA electronics allow for more sensitive, accurate and effective sensors to be developed and fabricated. In this work, we examined the effect of different humidity conditions on the capacitive and resistive response of Aluminum (Al)/DNA/Al Schottky barrier structure when bombarded by time-dependent dosages of alpha particles. Based on current-voltage profiles, which demonstrated rectifying behaviours, Schottky diode parameters such as ideality factor, barrier height and series resistance was calculated. Results observed generally pointed towards a decrease in the resistance value from the pristine to the radiated structures. It was also demonstrated that under the effect of humidity, the capacitance of the DNA thin film increased from 0.05894 to 92.736 nF, with rising relative humidity level. We also observed the occurrence of the hypersensitivity phenomena after alpha irradiation between 2 to 4 min by observing a drop in the series resistance, crucial in the study of DNA damage and repair mechanisms. These observations may also suggest the exciting possibility of utilizing Al/DNA/Al Schottky diodes as potentially sensitive humidity sensors.
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Affiliation(s)
- Hassan Maktuff Jaber Al-Ta’ii
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Physics, Faculty of Science, University of Al-Muthanna, 66001, Iraq
| | - Yusoff Mohd Amin
- Department of Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Vengadesh Periasamy
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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10
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Japaridze A, Vobornik D, Lipiec E, Cerreta A, Szczerbinski J, Zenobi R, Dietler G. Toward an Effective Control of DNA’s Submolecular Conformation on a Surface. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b01827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dusan Vobornik
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ewelina Lipiec
- The
Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | - Andrea Cerreta
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacek Szczerbinski
- Laboratory
of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory
of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Giovanni Dietler
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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11
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Kim D, Sahin O. Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy. NATURE NANOTECHNOLOGY 2015; 10:264-9. [PMID: 25664622 PMCID: PMC4429059 DOI: 10.1038/nnano.2014.335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 12/17/2014] [Indexed: 05/24/2023]
Abstract
Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.
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12
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Calculation of the electronic parameters of an Al/DNA/p-Si Schottky barrier diode influenced by alpha radiation. SENSORS 2015; 15:4810-22. [PMID: 25730484 PMCID: PMC4435138 DOI: 10.3390/s150304810] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/25/2014] [Accepted: 01/14/2015] [Indexed: 02/07/2023]
Abstract
Many types of materials such as inorganic semiconductors have been employed as detectors for nuclear radiation, the importance of which has increased significantly due to recent nuclear catastrophes. Despite the many advantages of this type of materials, the ability to measure direct cellular or biological responses to radiation might improve detector sensitivity. In this context, semiconducting organic materials such as deoxyribonucleic acid or DNA have been studied in recent years. This was established by studying the varying electronic properties of DNA-metal or semiconductor junctions when exposed to radiation. In this work, we investigated the electronics of aluminium (Al)/DNA/silicon (Si) rectifying junctions using their current-voltage (I-V) characteristics when exposed to alpha radiation. Diode parameters such as ideality factor, barrier height and series resistance were determined for different irradiation times. The observed results show significant changes with exposure time or total dosage received. An increased deviation from ideal diode conditions (7.2 to 18.0) was observed when they were bombarded with alpha particles for up to 40 min. Using the conventional technique, barrier height values were observed to generally increase after 2, 6, 10, 20 and 30 min of radiation. The same trend was seen in the values of the series resistance (0.5889–1.423 Ω for 2–8 min). These changes in the electronic properties of the DNA/Si junctions could therefore be utilized in the construction of sensitive alpha particle detectors.
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13
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Lai CY, Santos S, Chiesa M. General interpretation and theory of apparent height in dynamic atomic force microscopy. RSC Adv 2015. [DOI: 10.1039/c5ra16695k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We provide a general theory and interpretation behind the ubiquitous loss of apparent height of nanostructures in dynamic atomic force microscopy that occurs in the attractive regime irrespective of stiffness.
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Affiliation(s)
- Chia-Yun Lai
- Laboratory for Energy and NanoScience (LENS)
- Institute Center for Future Energy (iFES)
- Masdar Institute of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Sergio Santos
- Laboratory for Energy and NanoScience (LENS)
- Institute Center for Future Energy (iFES)
- Masdar Institute of Science and Technology
- Abu Dhabi
- United Arab Emirates
| | - Matteo Chiesa
- Laboratory for Energy and NanoScience (LENS)
- Institute Center for Future Energy (iFES)
- Masdar Institute of Science and Technology
- Abu Dhabi
- United Arab Emirates
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14
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