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Mishra E, Majumder S, Varma S, Dowben PA. X-ray photoemission studies of the interaction of metals and metal ions with DNA. Z PHYS CHEM 2021. [DOI: 10.1515/zpch-2021-3037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.
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Affiliation(s)
- Esha Mishra
- Department of Physics and Astronomy , University of Nebraska–Lincoln , Jorgenson Hall, 855 North 16th Street , Lincoln , NE 68588-0299 , USA
| | - Subrata Majumder
- Department of Physics , National Institute of Technology , Patna , Bihar 800005 , India
| | - Shikha Varma
- Institute of Physics , Sachivalaya Marg , Bhubaneswar 751005 , India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar , Mumbai 400085 , India
| | - Peter A. Dowben
- Department of Physics and Astronomy , University of Nebraska–Lincoln , Jorgenson Hall, 855 North 16th Street , Lincoln , NE 68588-0299 , USA
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Pal C, Varma S, Majumder S. Oxygen vacancy assisted condensation of DNA molecule observed on ZnO thin film. Biophys Chem 2021; 277:106659. [PMID: 34340002 DOI: 10.1016/j.bpc.2021.106659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
An exotic condensation of DNA molecules is observed on the nanostructured ZnO surface. The ZnO nanostructures (NS) fabricated by thermal vapor deposition technique were associated with a large number of oxygen vacancies on the surface. These oxygen vacancies induced changes in the DNA conformation which further reflected through changes in the persistence length of the DNA molecules. This indicates a reinforcement of the bonds and binding in both the phosphate and the base regions of the DNA molecules with the positively charged core vacancy sites on the ZnO nanostructured surface through strong interaction mediated via long-range electrostatic forces which effectively reduced the end-to-end distance of the λ-DNA molecule. This strongly suggests a transition of the λ-DNA molecule through structural modification into a more compact higher-order fractal dimension from its native state.
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Affiliation(s)
| | - Shikha Varma
- Institute of Physics, Bhubaneswar, 751005, India
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BEDNARIKOVA Z, GAZOVA Z, VALLE F, BYSTRENOVA E. Atomic force microscopy as an imaging tool to study the bio/nonbio complexes. J Microsc 2020; 280:241-251. [DOI: 10.1111/jmi.12936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Z. BEDNARIKOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
| | - Z. GAZOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
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Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway. Mol Cell 2019; 75:982-995.e9. [PMID: 31444106 PMCID: PMC6739425 DOI: 10.1016/j.molcel.2019.07.025] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 01/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures ("kissing loops"). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation in vivo and disrupt MEG3 folding in vitro. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function.
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Valle F, Brucale M, Chiodini S, Bystrenova E, Albonetti C. Nanoscale morphological analysis of soft matter aggregates with fractal dimension ranging from 1 to 3. Micron 2017; 100:60-72. [DOI: 10.1016/j.micron.2017.04.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 11/25/2022]
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Multifrequency Force Microscopy of Helical Protein Assembly on a Virus. Sci Rep 2016; 6:21899. [PMID: 26915629 PMCID: PMC4768132 DOI: 10.1038/srep21899] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/09/2023] Open
Abstract
High-resolution microscopy techniques have been extensively used to investigate the structure of soft, biological matter at the nanoscale, from very thin membranes to small objects, like viruses. Electron microscopy techniques allow for obtaining extraordinary resolution by averaging signals from multiple identical structures. In contrast, atomic force microscopy (AFM) collects data from single entities. Here, it is possible to finely modulate the interaction with the samples, in order to be sensitive to their top surface, avoiding mechanical deformations. However, most biological surfaces are highly curved, such as fibers or tubes, and ultimate details of their surface are in the vicinity of steep height variations. This limits lateral resolution, even when sharp probes are used. We overcome this problem by using multifrequency force microscopy on a textbook example, the Tobacco Mosaic Virus (TMV). We achieved unprecedented resolution in local maps of amplitude and phase shift of the second excited mode, recorded together with sample topography. Our data, which combine multifrequency imaging and Fourier analysis, confirm the structure deduced from averaging techniques (XRD, cryoEM) for surface features of single virus particles, down to the helical pitch of the coat protein subunits, 2.3 nm. Remarkably, multifrequency AFM images do not require any image postprocessing.
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Cominato L, Valle F, Pierini G, Bonini P, Biscarini F, D'Elia M. Flattening mountains: micro-fabrication of planar replicas for bullet lateral striae analysis. Forensic Sci Int 2014; 247:97-104. [PMID: 25555234 DOI: 10.1016/j.forsciint.2014.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 11/26/2022]
Abstract
The application of replica molding has proven to be a valuable tool in the analysis of different forensic evidences in particular for its ability to extract the toolmarks from complex sample surfaces. A well known problem in the analysis of ballistic evidences is the accurate characterization of the lateral striae of real bullets seized on crime scenes after shots, due primarily to impact deformations and to unpredictable issues related to laboratory illumination setup. To overcome these problems a possible way is to confine over a flat surface all the features still preserving their three dimensionality. This can be achieved by a novel application of replica molding performed onto the relevant lateral portion of the bullet surface. A quasi-two-dimensional negative copy of the original tridimensional indented surface has been thus fabricated. It combines the real tridimensional topography of class characteristics (land and groove impressions) and of individual caracteristics (striae) impressed by rifled barrels on projectiles, moreover with the possibility of quantitative characterization of these features in a planar configuration, that will allow one-shot comparison of the "whole striae landscape" without the typical artifacts arising from the bullet shape and the illumination issue. A detailed analysis has been carried on at the morphological level by standard optical and scanning electron microscopy, while the 3D topography has been characterized by white light optical profilometry. A quantitative characterization of toolmarks of bullets derived from ammunitions shot by guns of large diffusion, as the Beretta 98 FS cal. 9×21 mm, has been performed and will be presented ranging between the whole landscape and the sub-μm resolution. To investigate the real potentiality of this technique, the experiment has been extended to highly impact-deformed projectiles.
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Affiliation(s)
- Laura Cominato
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Via Gobetti 101, I-40129 Bologna, Italy
| | - Francesco Valle
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Via Gobetti 101, I-40129 Bologna, Italy.
| | - Giovanni Pierini
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Università di Bologna, Via Irnerio 49, I-40126 Bologna, Italy
| | - Paolo Bonini
- Gabinetto Regionale di Polizia Scientifica per l'Emilia Romagna, Via Volto Santo 3, 40123 Bologna, Italy
| | - Fabio Biscarini
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Marcello D'Elia
- Gabinetto Regionale di Polizia Scientifica per l'Emilia Romagna, Via Volto Santo 3, 40123 Bologna, Italy
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Mazur AK, Maaloum M. Atomic force microscopy study of DNA flexibility on short length scales: smooth bending versus kinking. Nucleic Acids Res 2014; 42:14006-12. [PMID: 25414337 PMCID: PMC4267637 DOI: 10.1093/nar/gku1192] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The apparently anomalous flexibility of DNA on short length scales has attracted a lot of attention in recent years. We use atomic force microscopy (AFM) in solution to directly study the DNA bending statistics for small lengths down to one helical turn. The accuracy of experimental estimates could be improved due to a large data volume and a refined algorithm for image processing and measuring bend angles. It is found that, at length scales beyond two helical turns (7 nm), DNA is well described by the harmonic worm-like chain (WLC) model with the bending persistence length of 56 nm. Below this threshold, the AFM data are also described by the WLC model assuming that the accuracy of measured bend angles is limited by the physical width of the double helix. We conclude that the double helical DNA behaves as a uniform elastic rod even at very short length scales. Strong bends due to kinks, melting bubbles and other deviations from the WLC model are statistically negligible.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
| | - Mounir Maaloum
- Institut Charles Sadron, CNRS-University of Strasbourg, 23 rue du Loess, BP 84087, 67034 Strasbourg Cedex 2, France
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Biscarini F, Ong QK, Albonetti C, Liscio F, Longobardi M, Mali KS, Ciesielski A, Reguera J, Renner C, De Feyter S, Samorì P, Stellacci F. Quantitative analysis of scanning tunneling microscopy images of mixed-ligand-functionalized nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13723-13734. [PMID: 24083627 DOI: 10.1021/la403546c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ligand-protected gold nanoparticles exhibit large local curvatures, features rapidly varying over small scales, and chemical heterogeneity. Their imaging by scanning tunneling microscopy (STM) can, in principle, provide direct information on the architecture of their ligand shell, yet STM images require laborious analysis and are challenging to interpret. Here, we report a straightforward, robust, and rigorous method for the quantitative analysis of the multiscale features contained in STM images of samples consisting of functionalized Au nanoparticles deposited onto Au/mica. The method relies on the analysis of the topographical power spectral density (PSD) and allows us to extract the characteristic length scales of the features exhibited by nanoparticles in STM images. For the mixed-ligand-protected Au nanoparticles analyzed here, the characteristic length scale is 1.2 ± 0.1 nm, whereas for the homoligand Au NPs this scale is 0.75 ± 0.05 nm. These length scales represent spatial correlations independent of scanning parameters, and hence the features in the PSD can be ascribed to a fingerprint of the STM contrast of ligand-protected nanoparticles. PSD spectra from images recorded at different laboratories using different microscopes and operators can be overlapped across most of the frequency range, proving that the features in the STM images of nanoparticles can be compared and reproduced.
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Affiliation(s)
- Fabio Biscarini
- Dip. Scienze della Vita, Università di Modena e Reggio Emilia , Via Campi 183, 41125 Modena, Italy
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Morphology of polyaniline nanofibers synthesized under different conditions. RESEARCH ON CHEMICAL INTERMEDIATES 2013. [DOI: 10.1007/s11164-013-1035-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Valle F, Bianchi M, Tortorella S, Pierini G, Biscarini F, D’Elia M. Nanotechnology for forensic sciences: Analysis of PDMS replica of the case head of spent cartridges by optical microscopy, SEM and AFM for the ballistic identification of individual characteristic features of firearms. Forensic Sci Int 2012; 222:288-97. [DOI: 10.1016/j.forsciint.2012.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 06/30/2012] [Accepted: 07/04/2012] [Indexed: 11/16/2022]
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Shao Q, Wu P, Xu X, Zhang H, Cai C. Insight into the effects of graphene oxide sheets on the conformation and activity of glucose oxidase: towards developing a nanomaterial-based protein conformation assay. Phys Chem Chem Phys 2012; 14:9076-85. [PMID: 22641400 DOI: 10.1039/c2cp40654c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein conformation associates with particular properties of proteins and relates to protein-mediated diseases. Detailed elucidation of secondary and tertiary formation, stability, and the structural and dynamic properties of proteins has been one of the main topics studied in chemistry and biology. In this work, the conformation changes in glucose oxidase (GOx) induced by the graphene oxide (GO) sheets were studied in detail by various spectroscopic techniques including ultraviolet-visible (UV-vis) absorption, fluorescence, and circular dichroism (CD) spectroscopy. The results indicated that GOx underwent substantial conformation changes after assembling on the surface of GO. The interaction of GOx with GO could induce the exposure of the FAD (flavin adenine dinucleotide) moiety to solvent and transfer tryptophan (Trp) residues to a more hydrophobic environment. The calculation from CD spectra showed that GO could induce the conversion of α-helix to β-sheet structures, even unfolding of the protein. These alterations in the conformation of GOx resulted in a significant decrease in the catalytic activity of the enzyme in glucose oxidation. The possible reasons for these conformation changes in GOx are also discussed. This work not only provides insight into the interaction between atomically flat graphitic structures and various biological systems but also creates a framework for analyzing the biosafety of nanomaterials in terms of the biological behavior of biomacromolecules. The results obtained here can direct the further applications of the nanomaterials.
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Affiliation(s)
- Qian Shao
- Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, China
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Xu X, Wu P, Xu W, Shao Q, An L, Zhang H, Cai C, Zhao B. Effects of guanidinium ions on the conformational structure of glucose oxidase studied by electrochemistry, spectroscopy, and theoretical calculations: towards developing a chemical-induced protein conformation assay. Phys Chem Chem Phys 2012; 14:5824-36. [DOI: 10.1039/c2cp24121h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Gentili D, Foschi G, Valle F, Cavallini M, Biscarini F. Applications of dewetting in micro and nanotechnology. Chem Soc Rev 2012; 41:4430-43. [DOI: 10.1039/c2cs35040h] [Citation(s) in RCA: 203] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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