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Kariyawasam NL, Wereszczynski J. The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600666. [PMID: 38979319 PMCID: PMC11230366 DOI: 10.1101/2024.06.25.600666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mica serves as a crucial substrate in Atomic Force Microscopy (AFM) studies for visualizing and characterizing nucleosomes. Nucleosomes interact with the negatively charged mica surface via adsorbed cations. However, the specific influences of monovalent and divalent cations on nucleosome adsorption to the mica surface remain unclear. In this study, we investigated the binding of nucleosomes to the mica surface in the presence of monovalent potassium ions and divalent magnesium ions using molecular dynamics simulations. We also explored the impact of pre-treated mica surfaces on nucleosome binding and structure. Our findings reveal that nucleosome-mica interactions vary depending on the cations present, resulting in distinct effects on nucleosome structure. Notably, nucleosomes bind effectively to a mica surface in the presence of potassium ions with minimal structural perturbations.
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Affiliation(s)
- Nilusha L Kariyawasam
- Department of Physics, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
| | - Jeff Wereszczynski
- Departments of Physics and Biology, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
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2
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Neyra K, Everson HR, Mathur D. Dominant Analytical Techniques in DNA Nanotechnology for Various Applications. Anal Chem 2024; 96:3687-3697. [PMID: 38353660 PMCID: PMC11261746 DOI: 10.1021/acs.analchem.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
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3
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Shahjin F, Patel M, Machhi J, Cohen JD, Nayan MU, Yeapuri P, Zhang C, Waight E, Hasan M, Abdelmoaty MM, Dash PK, Zhou Y, Andreu I, Gendelman HE, Kevadiya BD. Multipolymer microsphere delivery of SARS-CoV-2 antigens. Acta Biomater 2023; 158:493-509. [PMID: 36581007 PMCID: PMC9791794 DOI: 10.1016/j.actbio.2022.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Effective antigen delivery facilitates antiviral vaccine success defined by effective immune protective responses against viral exposures. To improve severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigen delivery, a controlled biodegradable, stable, biocompatible, and nontoxic polymeric microsphere system was developed for chemically inactivated viral proteins. SARS-CoV-2 proteins encapsulated in polymeric microspheres induced robust antiviral immunity. The viral antigen-loaded microsphere system can preclude the need for repeat administrations, highlighting its potential as an effective vaccine. STATEMENT OF SIGNIFICANCE: Successful SARS-CoV-2 vaccines were developed and quickly approved by the US Food and Drug Administration (FDA). However, each of the vaccines requires boosting as new variants arise. We posit that injectable biodegradable polymers represent a means for the sustained release of emerging viral antigens. The approach offers a means to reduce immunization frequency by predicting viral genomic variability. This strategy could lead to longer-lasting antiviral protective immunity. The current proof-of-concept multipolymer study for SARS-CoV-2 achieve these metrics.
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Affiliation(s)
- Farah Shahjin
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Jacob D Cohen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Mohammad Ullah Nayan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Pravin Yeapuri
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Chen Zhang
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Emiko Waight
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mai Mohamed Abdelmoaty
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Prasanta K Dash
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - You Zhou
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Irene Andreu
- RI Consortium of Nanoscience and Nanotechnology and Department of Chemical Engineering University of Rhode Island, RI, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA.
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
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Azadmanesh J, Seleem MA, Struble L, Wood NA, Fisher DJ, Lovelace JJ, Artigues A, Fenton AW, Borgstahl GEO, Ouellette SP, Conda-Sheridan M. The structure of caseinolytic protease subunit ClpP2 reveals a functional model of the caseinolytic protease system from Chlamydia trachomatis. J Biol Chem 2023; 299:102762. [PMID: 36463962 PMCID: PMC9823225 DOI: 10.1016/j.jbc.2022.102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Chlamydia trachomatis (ct) is the most reported bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Caseinolytic proteases (ClpP) from pathogenic bacteria are attractive antibiotic targets, particularly for bacterial species that form persister colonies with phenotypic resistance against common antibiotics. ClpP functions as a multisubunit proteolytic complex, and bacteria are eradicated when ClpP is disrupted. Although crucial for chlamydial development and the design of agents to treat chlamydia, the structures of ctClpP1 and ctClpP2 have yet to be solved. Here, we report the first crystal structure of full-length ClpP2 as an inactive homotetradecamer in a complex with a candidate antibiotic at 2.66 Å resolution. The structure details the functional domains of the ClpP2 protein subunit and includes the handle domain, which is integral to proteolytic activation. In addition, hydrogen-deuterium exchange mass spectroscopy probed the dynamics of ClpP2, and molecular modeling of ClpP1 predicted an assembly with ClpP2. By leveraging previous enzymatic experiments, we constructed a model of ClpP2 activation and its interaction with the protease subunits ClpP1 and ClpX. The structural information presented will be relevant for future rational drug design against these targets and will lead to a better understanding of ClpP complex formation and activation within this important human pathogen.
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Affiliation(s)
- Jahaun Azadmanesh
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mohamed A Seleem
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lucas Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nicholas A Wood
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Derek J Fisher
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Scot P Ouellette
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska, USA.
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5
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Lushnikov AJ, Avila YI, Afonin KA, Krasnoslobodtsev AV. Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy. Methods Mol Biol 2023; 2709:191-202. [PMID: 37572281 PMCID: PMC10483931 DOI: 10.1007/978-1-0716-3417-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
The protocol described in this chapter allows for acquiring topography images of RNA-based nanoring structures and assessing their dynamic properties using atomic force microscopy (AFM) imaging. AFM is an indispensable tool for characterization of nucleic acid-based nanostructures with the exceptional capability of observing complexes in the range of a few nanometers. This method can visualize structural characteristics and evaluate differences between individual structurally different RNA nanorings. Due to the highly resolved AFM topography images, we introduce an approach that allows to distinguish the differences in the dynamic behavior of RNA nanoparticles not amenable to other experimental techniques. This protocol describes in detail the preparation procedures of RNA nanostructures, AFM imaging, and data analysis.
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Affiliation(s)
- Alexander J Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, USA
| | - Yelixza I Avila
- Department of Chemistry, Nanoscale Science Program, University of North Carolina, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, University of North Carolina, Charlotte, NC, USA
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6
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3-Aminopropylsilatrane and Its Derivatives: A Variety of Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113549. [PMID: 35684486 PMCID: PMC9182167 DOI: 10.3390/molecules27113549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/26/2022]
Abstract
Silatranes arouse much research interest owing to their unique structure, unusual physical–chemical properties, and diverse biological activity. The application of some silatranes and their analogues has been discussed in several works. Meanwhile, a comprehensive review of the wide practical usage of silatranes is still absent in the literature. The ability of silatranes to mildly control hydrolysis allows them to form extremely stable and smooth siloxane monolayers almost on any surface. The high physiological activity of silatranes makes them prospective drug candidates. In the present review, based on the results of numerous previous studies, using the commercially available 3-aminopropylsilatrane and its hybrid derivatives, we have demonstrated the high potential of 1-organylsilatranes in various fields, including chemistry, biology, pharmaceuticals, medicine, agriculture, and industry. For example, these compounds can be employed as plant growth biostimulants, drugs, optical, catalytic, sorption, and special polymeric materials, as well as modern high-tech devices.
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Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. ACS NANO 2021; 15:16957-16973. [PMID: 34677049 PMCID: PMC9023608 DOI: 10.1021/acsnano.0c10240] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) hosts an annual meeting series focused on presenting the latest research achievements involving RNA-based therapeutics and strategies, aiming to expand their current biomedical applications while overcoming the remaining challenges of the burgeoning field of RNA nanotechnology. The most recent online meeting hosted a series of engaging talks and discussions from an international cohort of leading nanotechnologists that focused on RNA modifications and modulation, dynamic RNA structures, overcoming delivery limitations using a variety of innovative platforms and approaches, and addressing the newly explored potential for immunomodulation with programmable nucleic acid nanoparticles. In this Nano Focus, we summarize the main discussion points, conclusions, and future directions identified during this two-day webinar as well as more recent advances to highlight and to accelerate this exciting field.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47304, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Rouse Life Sciences Building, Auburn, Alabama 36849, United States
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa 52242, United States
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachussets 02114, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de São Paulo - ICESP, Faculdade de Medicina da Universidade de São Paulo - FMUSP, Avenida Dr. Arnaldo 251, Cerqueira César, São Paulo 01246-000, São Paulo, Brazil
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering and Department of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78714, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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Okimune K, Hataya S, Matsumoto K, Ushirogata K, Banko P, Takeda S, Takasuka TE. Histone chaperone-mediated co-expression assembly of tetrasomes and nucleosomes. FEBS Open Bio 2021; 11:2912-2920. [PMID: 34614293 PMCID: PMC8564334 DOI: 10.1002/2211-5463.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022] Open
Abstract
The nucleosome, a basic unit of chromatin found in all eukaryotes, is thought to be assembled through the orchestrated activity of several histone chaperones and chromatin assembly factors in a stepwise manner, proceeding from tetrasome assembly, to H2A/H2B deposition, and finally to formation of the mature nucleosome. In this study, we demonstrate chaperone-mediated assembly of both tetrasomes and nucleosomes on the well-defined Widom 601 positioning sequence using a co-expression/reconstitution wheat germ cell-free system. The purified tetrasomes and nucleosomes were positioned around the center of a given sequence. The heights and diameters were measured by atomic force microscopy. Together with the reported unmodified native histones produced by the wheat germ cell-free platform, our method is expected to be useful for downstream applications in the field of chromatin research.
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Affiliation(s)
- Kei‐ichi Okimune
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Shogo Hataya
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kazuki Matsumoto
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kanako Ushirogata
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Petra Banko
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | - Seiji Takeda
- Faculty of Pharmaceutical SciencesHokkaido University of ScienceSapporoJapan
| | - Taichi E. Takasuka
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
- Global Institute for Collaborative Research and EducationHokkaido UniversitySapporoJapan
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9
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Chhunchha B, Kubo E, Kompella UB, Singh DP. Engineered Sumoylation-Deficient Prdx6 Mutant Protein-Loaded Nanoparticles Provide Increased Cellular Defense and Prevent Lens Opacity. Antioxidants (Basel) 2021; 10:antiox10081245. [PMID: 34439493 PMCID: PMC8389307 DOI: 10.3390/antiox10081245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant Sumoylation-mediated protein dysfunction is involved in a variety of oxidative and aging pathologies. We previously reported that Sumoylation-deficient Prdx6K(lysine)122/142R(Arginine) linked to the TAT-transduction domain gained stability and protective efficacy. In the present study, we formulated wild-type TAT-HA-Prdx6WT and Sumoylation-deficient Prdx6-loaded poly-lactic-co-glycolic acid (PLGA) nanoparticles (NPs) to further enhance stability, protective activities, and sustained delivery. We found that in vitro and subconjuctival delivery of Sumoylation-deficient Prdx6-NPs provided a greater protection of lens epithelial cells (LECs) derived from human and Prdx6-/--deficient mouse lenses against oxidative stress, and it also delayed the lens opacity in Shumiya cataract rats (SCRs) than TAT-HA-Prdx6WT-NPs. The encapsulation efficiencies of TAT-HA-Prdx6-NPs were ≈56%-62%. Dynamic light scattering (DLS) and atomic force microscopy (AFM) analyses showed that the NPs were spherical, with a size of 50-250 nm and a negative zeta potential (≈23 mV). TAT-HA-Prdx6 analog-NPs released bioactive TAT-HA-Prdx6 (6%-7%) within 24 h. Sumoylation-deficient TAT-HA-Prdx6-NPs provided 35% more protection by reducing the oxidative load of LECs exposed to H2O2 compared to TAT-HA-Prdx6WT-NPs. A subconjuctival delivery of TAT-HA-Prdx6 analog-NPs demonstrated that released TAT-HA-Prdx6K122/142R could reduce lens opacity by ≈60% in SCRs. Collectively, our results demonstrate for the first time that the subconjuctival delivery of Sumoylation-deficient Prdx6-NPs is efficiently cytoprotective and provide a proof of concept for potential use to delay cataract and oxidative-related pathobiology in general.
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Affiliation(s)
- Bhavana Chhunchha
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (B.C.); (D.P.S.)
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Kanazawa 9200265, Ishikawa, Japan;
| | - Uday B. Kompella
- Departments of Pharmaceutical Sciences, Ophthalmology, and Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Dhirendra P. Singh
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (B.C.); (D.P.S.)
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10
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Spakman D, Bakx JAM, Biebricher AS, Peterman EJG, Wuite GJL, King GA. Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches. Nucleic Acids Res 2021; 49:5470-5492. [PMID: 33963870 PMCID: PMC8191776 DOI: 10.1093/nar/gkab239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
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Affiliation(s)
- Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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11
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Mohammed Khalid AA, Parisse P, Medagli B, Onesti S, Casalis L. Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA. MATERIALS 2021; 14:ma14030687. [PMID: 33540751 PMCID: PMC7867263 DOI: 10.3390/ma14030687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022]
Abstract
The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.
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Affiliation(s)
- Amna Abdalla Mohammed Khalid
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (IOM-CNR), 34149 Trieste, Italy
- Correspondence: (P.P.); (S.O.); (L.C.)
| | - Barbara Medagli
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy
| | - Silvia Onesti
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Correspondence: (P.P.); (S.O.); (L.C.)
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste, 34149 Trieste, Italy; (A.A.M.K.); (B.M.)
- Correspondence: (P.P.); (S.O.); (L.C.)
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12
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Bashiri S, Lucidi M, Visaggio D, Capecchi G, Persichetti L, Cincotti G, Visca P, Capellini G. Growth Phase- and Desiccation-Dependent Acinetobacter baumannii Morphology: An Atomic Force Microscopy Investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1110-1119. [PMID: 33433226 DOI: 10.1021/acs.langmuir.0c02980] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Acinetobacter baumannii has emerged as a major bacterial pathogen during the past three decades. The majority of the A. baumannii infections occur in hospitals and are caused by strains endowed with high desiccation tolerance, which represents an essential feature for the adaptation to the nosocomial environment. This work aims at investigating the desiccation response of the multidrug-resistant A. baumannii strain ACICU as a function of the bacterial growth phase and oxygen availability, by correlating bacterial survival with shape alterations. The three-dimensional morphological analysis of bacteria was carried out by atomic force microscopy (AFM), following the evolution of bacterial shape descriptors, such as the area, volume, roughness of individual cell membranes, and the cell cluster roughness, which exhibited peculiar and distinctive behavior as a function of the growth conditions. AFM images of A. baumannii ACICU cells revealed the prevalence of the coccoid morphology at all growth stages, with a tendency to reduce their size in the stationary phase, accompanied by a higher survival rate to air-drying. Moreover, cells harvested from the logarithmic phase featured a larger volume and resulted to be more sensitive to desiccation compared to the cells harvested at later growth stages. In addition, oxygen deprivation caused a significant decrease in cellular size and was associated with the formation of pores in the cell membrane, accompanied by a relative reduction in culturability after desiccation. Morphological plasticity and multidrug resistance may contribute to desiccation tolerance and therefore to persistence in the hospital setting.
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Affiliation(s)
- Shadi Bashiri
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Massimiliano Lucidi
- Department of Engineering, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Daniela Visaggio
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Giulia Capecchi
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Luca Persichetti
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Gabriella Cincotti
- Department of Engineering, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Giovanni Capellini
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
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13
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Yourston L, Rolband L, West C, Lushnikov A, Afonin KA, Krasnoslobodtsev AV. Tuning properties of silver nanoclusters with RNA nanoring assemblies. NANOSCALE 2020; 12:16189-16200. [PMID: 32705105 DOI: 10.1039/d0nr03589k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Combining atomically resolved DNA-templated silver nanoclusters (AgNCs) with nucleic acid nanotechnology opens new exciting possibilities for engineering bioinorganic nanomaterials with uniquely tunable properties. In this unforeseen cooperation, nucleic acids not only drive the formation of AgNCs but also promote their spatial organization in supra-assemblies. In this work, we confirm the feasibility of this approach using programmable RNA rings to control formation and optical properteis of six individual AgNCs. "Red" (λEXC/λEM = 565/623 nm) and "green" (λEXC/λEM = 440/523 nm) emitting AgNCs are templated on cytosine-rich DNA fragments embedded into the RNA rings. Optical properties of the AgNCs formed on the RNA rings are characterized in detail. While all "red" species passively transition to "green" emitters with time, the initial fluorescent properties and relative stabilities of "red" AgNCs can be regulated by altering the relative orientation of AgNCs within the RNA rings. As such, the oxidative stability increases dramatically for AgNC positioned towards the center of the RNA rings rather than facing outward. Overall, our findings expand the existing AgNC fluorescent toolkit while uncovering the complexity of the AgNC electronic structures with the abundance of possibilities for controlling de-excitation processes.
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Affiliation(s)
- Liam Yourston
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Caroline West
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V Krasnoslobodtsev
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA. and Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
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14
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Pan Y, Banerjee S, Zagorski K, Shlyakhtenko LS, Kolomeisky AB, Lyubchenko YL. Molecular Model for the Surface-Catalyzed Protein Self-Assembly. J Phys Chem B 2020; 124:366-372. [PMID: 31867969 DOI: 10.1021/acs.jpcb.9b10052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimer's and Parkinson's diseases. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting that interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind the on-surface aggregation process remain unclear. Here, we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This physical-chemical theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic α-synuclein protein and non-amyloidogenic cytosine deaminase APOBEC3G.
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Affiliation(s)
- Yangang Pan
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha , Nebraska 68198-6025 , United States
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha , Nebraska 68198-6025 , United States
| | - Karen Zagorski
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha , Nebraska 68198-6025 , United States
| | - Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha , Nebraska 68198-6025 , United States
| | - Anatoly B Kolomeisky
- Department of Chemistry-MS 60 , Rice University , 6100 Main Street , Houston , Texas 77005-1892 , Unites States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha , Nebraska 68198-6025 , United States
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15
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Abstract
Atomic force and transmission electron microscopies (AFM/TEM) are powerful tools to analyze RNA-based nanostructures. While cryo-TEM analysis allows the determination of near-atomic resolution structures of large RNA complexes, this chapter intends to present how RNA nanostructures can be analyzed at room temperature on surfaces. Indeed, TEM and AFM analyses permit the conformation of a large population of individual molecular structures to be observed, providing a statistical basis for the variability of these nanostructures within the population. Nevertheless, if double-stranded DNA molecular imaging has been described extensively, only a few investigations of single-stranded DNA and RNA filaments have been conducted so far. Indeed, technique for spreading and adsorption of ss-molecules on AFM surfaces or TEM grids is a crucial step to avoid disturbing RNA conformation on the surface. In this chapter, we present a specific method to analyze RNA assemblies and RNA-protein complexes for molecular microscopies.
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Affiliation(s)
- Olivier Piétrement
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne, Dijon Cedex, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-Sur-Yvette, France
- Université de Paris, Paris, France
| | - Christophe Lavelle
- Museum National d'Histoire Naturelle, CNRS UMR 7196/INSERM U1154, Paris, France.
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16
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Lushnikov A, Hooy R, Sohn J, Krasnoslobodtsev A. Characterization of DNA bound cyclic GMP-AMP synthase using atomic force microscopy imaging. Methods Enzymol 2019; 625:157-166. [PMID: 31455525 DOI: 10.1016/bs.mie.2019.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The protocol described herein allows for acquiring topography images of DNA-protein complexes using Atomic Force Microscopy imaging. Since the very beginning of this method, AFM has been an indispensable tool for characterization of biomolecular complexes with exceptional capability of observing single complexes. This method can visualize structural characteristics of DNA-protein assemblies and evaluate differences between individual complexes. Although this protocol is generally applicable to a large number of various proteins complexed with DNA, we use cyclic G/AMP synthase (cGAS) enzyme as a case study for the protocol description.
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Affiliation(s)
- Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, United States
| | - Richard Hooy
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD, United States
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD, United States
| | - Alexey Krasnoslobodtsev
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, United States; Department of Physics, University of Nebraska Omaha, Omaha, NE, United States.
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17
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Yourston LE, Lushnikov AY, Shevchenko OA, Afonin KA, Krasnoslobodtsev AV. First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E613. [PMID: 31013933 PMCID: PMC6523636 DOI: 10.3390/nano9040613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022]
Abstract
Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence-an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence-twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single "basic" templating element, (dC)12, emit in "red". The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in "green". A new population of "blue" emitting clusters forms only when ssDNA templating sequence is placed on the 5' end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure-a first step towards a larger assembly.
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Affiliation(s)
- Liam E Yourston
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Alexander Y Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Oleg A Shevchenko
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Alexey V Krasnoslobodtsev
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA.
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18
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Ultra selective label free electrochemical detection of cancer prognostic p53-antibody at DNA functionalized graphene. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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19
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Stumme-Diers MP, Stormberg T, Sun Z, Lyubchenko YL. Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging. J Vis Exp 2019. [PMID: 30774135 DOI: 10.3791/58820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.
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Affiliation(s)
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center;
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20
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Wasilewski T, Szulczyński B, Kamysz W, Gębicki J, Namieśnik J. Evaluation of Three Peptide Immobilization Techniques on a QCM Surface Related to Acetaldehyde Responses in the Gas Phase. SENSORS 2018; 18:s18113942. [PMID: 30441858 PMCID: PMC6264005 DOI: 10.3390/s18113942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022]
Abstract
The quartz-crystal microbalance is a sensitive and universal tool for measuring concentrations of various gases in the air. Biochemical functionalization of the QCM electrode allows a label-free detection of specific molecular interactions with high sensitivity and specificity. In addition, it enables a real-time determination of its kinetic rates and affinity constants. This makes QCM a versatile bioanalytical screening tool for various applications, with surface modifications ranging from the detection of single molecular monolayers to whole cells. Various types of biomaterials, including peptides mapping the binding sites of olfactory receptors, can be deposited as a sensitive element on the surface of the electrodes. One of key ways to ensure the sensitivity and accuracy of the sensor is provided by application of an optimal and repeatable method of immobilization. Therefore, effective sensors operation requires development of an optimal method of deposition. This paper reviews popular techniques (drop-casting, spin-coating, dip-coating) for coating peptides on piezoelectric crystals surface. Peptide (LEKKKKDC-NH₂) derived from an aldehyde binding site in the HarmOBP7 protein was synthesized and used as a sensing material for the biosensor. The degree of deposition of the sensitive layer was monitoring by variations in the sensors frequency. The highest mass threshold for QCM measurements for peptides was approximately 16.43 µg·mm-2 for spin coating method. Developed sensor exhibited repeatable response to acetaldehyde. Moreover, responses to toluene was observed to evaluate sensors specificity. Calibration curves of the three sensors showed good determination coefficients (R² > 0.99) for drop casting and dip coating and 0.97 for the spin-coating method. Sensors sensitivity vs. acetaldehyde were significantly higher for the dip-coating and drop-casting methods and lower for spin-coating one.
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Affiliation(s)
- Tomasz Wasilewski
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland.
| | - Bartosz Szulczyński
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland.
| | - Jacek Gębicki
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Jacek Namieśnik
- Department of Analytical Chemistry, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland.
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21
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Eisenbeis J, Saffarzadeh M, Peisker H, Jung P, Thewes N, Preissner KT, Herrmann M, Molle V, Geisbrecht BV, Jacobs K, Bischoff M. The Staphylococcus aureus Extracellular Adherence Protein Eap Is a DNA Binding Protein Capable of Blocking Neutrophil Extracellular Trap Formation. Front Cell Infect Microbiol 2018; 8:235. [PMID: 30038902 PMCID: PMC6047304 DOI: 10.3389/fcimb.2018.00235] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
The extracellular adherence protein (Eap) of Staphylococcus aureus is a secreted protein known to exert a number of adhesive and immunomodulatory properties. Here we describe the intrinsic DNA binding activity of this multifunctional secretory factor. By using atomic force microscopy, we provide evidence that Eap can bind and aggregate DNA. While the origin of the DNA substrate (e.g., eukaryotic, bacterial, phage, and artificial DNA) seems to not be of major importance, the DNA structure (e.g., linear or circular) plays a critical role with respect to the ability of Eap to bind and condense DNA. Further functional assays corroborated the nature of Eap as a DNA binding protein, since Eap suppressed the formation of "neutrophil extracellular traps" (NETs), composed of DNA-histone scaffolds, which are thought to function as a neutrophil-mediated extracellular trapping mechanism. The DNA binding and aggregation activity of Eap may thereby protect S. aureus against a specific anti-microbial defense reaction from the host.
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Affiliation(s)
- Janina Eisenbeis
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Mona Saffarzadeh
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Henrik Peisker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Nicolas Thewes
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Klaus T. Preissner
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Virginie Molle
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Centre National de la Recherche Scientifique, UMR 5235, Université de Montpellier, Montpellier, France
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Karin Jacobs
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
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22
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Zhang Y, Hashemi M, Lv Z, Williams B, Popov KI, Dokholyan NV, Lyubchenko YL. High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. J Chem Phys 2018; 148:123322. [PMID: 29604892 PMCID: PMC5764752 DOI: 10.1063/1.5008874] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/26/2017] [Indexed: 11/14/2022] Open
Abstract
α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson's disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a "hinge". Monomers within dimers have a large interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Furthermore, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.
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Affiliation(s)
- Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Benfeard Williams
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
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23
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Murugesapillai D, Bouaziz S, Maher LJ, Israeloff NE, Cameron CE, Williams MC. Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid. NANOSCALE 2017; 9:11327-11337. [PMID: 28762410 PMCID: PMC5597049 DOI: 10.1039/c7nr04231k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model. This often results in a persistence length measurement that is different from the value determined using bulk and single molecule methods. We describe a method for obtaining accurate three-dimensional (3D) persistence length measurements for DNA and DNA-protein complexes by using a previously developed liquid AFM imaging method and then applying the 3D WLC model. To demonstrate the method, we image in both air and liquid several different dsDNA constructs and DNA-protein complexes that both increase (HIV-1 Vpr) and decrease (yeast HMO1) dsDNA persistence length. Fitting the liquid AFM-imaging contour to the 3D WLC model results in a value in agreement with measurements obtained in optical tweezers experiments. Because AFM also allows characterization of local DNA properties, the ability to correctly measure global flexibility will strongly increase the impact of measurements that use AFM imaging.
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Affiliation(s)
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - L James Maher
- Mayo Clinic College of Medicine and Science, Department of Biochemistry and Molecular Biology, Rochester, MN 55905, USA
| | | | - Craig E Cameron
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, PA 16802, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA.
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24
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Igarashi C, Murata A, Itoh Y, Subekti DRG, Takahashi S, Kamagata K. DNA Garden: A Simple Method for Producing Arrays of Stretchable DNA for Single-Molecule Fluorescence Imaging of DNA-Binding Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160298] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chihiro Igarashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Agato Murata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Yuji Itoh
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Dwiky Rendra Graha Subekti
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Satoshi Takahashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Kiyoto Kamagata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
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25
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Sukhanova MV, Abrakhi S, Joshi V, Pastre D, Kutuzov MM, Anarbaev RO, Curmi PA, Hamon L, Lavrik OI. Single molecule detection of PARP1 and PARP2 interaction with DNA strand breaks and their poly(ADP-ribosyl)ation using high-resolution AFM imaging. Nucleic Acids Res 2015; 44:e60. [PMID: 26673720 PMCID: PMC4824093 DOI: 10.1093/nar/gkv1476] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 12/05/2015] [Indexed: 12/31/2022] Open
Abstract
PARP1 and PARP2 are implicated in the synthesis of poly(ADP-ribose) (PAR) after detection of DNA damage. The specificity of PARP1 and PARP2 interaction with long DNA fragments containing single- and/or double-strand breaks (SSBs and DSBs) have been studied using atomic force microscopy (AFM) imaging in combination with biochemical approaches. Our data show that PARP1 localizes mainly on DNA breaks and exhibits a slight preference for nicks over DSBs, although the protein has a moderately high affinity for undamaged DNA. In contrast to PARP1, PARP2 is mainly detected at a single DNA nick site, exhibiting a low level of binding to undamaged DNA and DSBs. The enhancement of binding affinity of PARP2 for DNA containing a single nick was also observed using fluorescence titration. AFM studies reveal that activation of both PARPs leads to the synthesis of highly branched PAR whose size depends strongly on the presence of SSBs and DSBs for PARP1 and of SSBs for PARP2. The initial affinity between the PARP1, PARP2 and the DNA damaged site appears to influence both the size of the PAR synthesized and the time of residence of PARylated PARP1 and PARP2 on DNA damages.
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Affiliation(s)
- Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Russian Federation INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - Sanae Abrakhi
- INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - Vandana Joshi
- INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - David Pastre
- INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Russian Federation
| | - Rashid O Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Russian Federation Novosibirsk State University, 630090, Novosibirsk, Russian Federation
| | - Patrick A Curmi
- INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - Loic Hamon
- INSERM, U1204, Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne, F-91025 Evry, France
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, 630090, Novosibirsk, Russian Federation Novosibirsk State University, 630090, Novosibirsk, Russian Federation
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26
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Rehman SU, Sarwar T, Husain MA, Ishqi HM, Tabish M. Studying non-covalent drug-DNA interactions. Arch Biochem Biophys 2015; 576:49-60. [PMID: 25951786 DOI: 10.1016/j.abb.2015.03.024] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/09/2015] [Accepted: 03/28/2015] [Indexed: 12/14/2022]
Abstract
Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.
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Affiliation(s)
- Sayeed Ur Rehman
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Tarique Sarwar
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammed Amir Husain
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Hassan Mubarak Ishqi
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India.
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27
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Pang D, Thierry AR, Dritschilo A. DNA studies using atomic force microscopy: capabilities for measurement of short DNA fragments. Front Mol Biosci 2015; 2:1. [PMID: 25988169 PMCID: PMC4429637 DOI: 10.3389/fmolb.2015.00001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/02/2015] [Indexed: 01/05/2023] Open
Abstract
Short DNA fragments, resulting from ionizing radiation induced DNA double strand breaks (DSBs), or released from cells as a result of physiological processes and circulating in the blood stream, may play important roles in cellular function and potentially in disease diagnosis and early intervention. The size distribution of DNA fragments contribute to knowledge of underlining biological processes. Traditional techniques used in radiation biology for DNA fragment size measurements lack the resolution to quantify short DNA fragments. For the measurement of cell-free circulating DNA (ccfDNA), real time quantitative Polymerase Chain Reaction (q-PCR) provides quantification of DNA fragment sizes, concentration and specific gene mutation. A complementary approach, the imaging-based technique using Atomic Force Microscopy (AFM) provides direct visualization and measurement of individual DNA fragments. In this review, we summarize and discuss the application of AFM-based measurements of DNA fragment sizes. Imaging of broken plasmid DNA, as a result of exposure to ionizing radiation, as well as ccfDNA in clinical specimens offer an innovative approach for studies of short DNA fragments and their biological functions.
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Affiliation(s)
- Dalong Pang
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherche Médicale U896 Montpellier, France
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
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28
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Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy. Methods Mol Biol 2015; 1262:119-53. [PMID: 25555579 DOI: 10.1007/978-1-4939-2253-6_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Since the inception of atomic force microscopy (AFM) in 1986, the value of this technology for exploring the structure and biophysical properties of a variety of biological samples has been increasingly recognized. AFM provides the opportunity to both image samples at nanometer resolution and also measure the forces on the surface of the sample. Here, we describe a variety of methods for studying nuclear samples including single nucleic acid molecules, higher-order chromatin structures, the nucleolus, and the nucleus. Protocols to prepare nucleic acids, nucleic acid-protein complexes, reconstituted chromatin, the cell nucleus, and the nucleolus are included, as well as protocols describing how to prepare the AFM substrate and the AFM tip. Finally, we describe how to perform conventional imaging, high-speed imaging, recognition imaging, force spectroscopy, and nanoindentation experiments.
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