1
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Escalona-Rodriguez FA, Cruz-Leal Y, La O-Bonet J, Pérez-Erviti JA, Valdés-Tresanco ME, Rivero-Hernández AL, Sifontes-Niebla M, Manso-Vargas A, Sánchez B, Alvarez C, Barbosa LRS, Itri R, Lanio ME. Unveiling Sticholysin II and plasmid DNA interaction: Implications for developing non-viral vectors. Toxicon 2024; 238:107571. [PMID: 38141971 DOI: 10.1016/j.toxicon.2023.107571] [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: 08/16/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/25/2023]
Abstract
Non-viral gene delivery systems offer significant potential for gene therapy due to their versatility, safety, and cost advantages over viral vectors. However, their effectiveness can be hindered by the challenge of efficiently releasing the genetic cargo from endosomes to prevent degradation in lysosomes. To overcome this obstacle, functional components can be incorporated into these systems. Sticholysin II (StII) is one of the pore-forming proteins derived from the sea anemone Stichodactyla helianthus, known for its high ability to permeabilize cellular and model membranes. In this study, we aimed to investigate the interaction between StII, and a model plasmid (pDNA) as an initial step towards designing an improved vector with enhanced endosomal escape capability. The electrophoretic mobility shift assay (EMSA) confirmed the formation of complexes between StII and pDNA. Computational predictions identified specific residues involved in the StII-DNA interaction interface, highlighting the importance of electrostatic interactions and hydrogen bonds in mediating the binding. Atomic force microscopy (AFM) of StII-pDNA complexes revealed the presence of nodular fiber and toroid shapes. These complexes were found to have a predominantly micrometer size, as confirmed by dynamic light scattering (DLS) measurements. Despite increase in the overall charge, the complexes formed at the evaluated nitrogen-to-phosphorus (N/P) ratios still maintained a negative charge. Moreover, StII retained its pore-forming capacity regardless of its binding to the complexes. These findings suggest that the potential ability of StII to permeabilize endosomal membranes could be largely maintained when combined with nucleic acid delivery systems. Additionally, the still remaining negative charge of the complexes would enable the association of another positively charged component to compact pDNA. However, to minimize non-specific cytotoxic effects, it is advisable to explore methods to regulate the protein's activity in response to the microenvironment.
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Affiliation(s)
- Felipe A Escalona-Rodriguez
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Yoelys Cruz-Leal
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba.
| | - Javier La O-Bonet
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Julio A Pérez-Erviti
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba.
| | - Mario Ernesto Valdés-Tresanco
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba.
| | - Ada L Rivero-Hernández
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Maricary Sifontes-Niebla
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Alexis Manso-Vargas
- Immunology and Immunotherapy Direction, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Belinda Sánchez
- Immunology and Immunotherapy Direction, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Carlos Alvarez
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo, São Paulo, 05508-090, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, SP, Brazil.
| | - Rosangela Itri
- Institute of Physics, University of São Paulo, São Paulo, 05508-090, Brazil.
| | - María E Lanio
- Center for Protein Studies, Faculty of Biology, University of Havana (UH), 25th Street, Corner to J Street, Square of Revolution, Havana, 10400, Cuba; NanoCancer, Molecular Immunology Center (CIM), 216 Street, Corner to 15 Street, Playa, Havana, 11600, Cuba.
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2
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Chen C, Nie J, Ma M, Shi X. DNA Origami Nanostructure Detection and Yield Estimation Using Deep Learning. ACS Synth Biol 2023; 12:524-532. [PMID: 36696234 DOI: 10.1021/acssynbio.2c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA origami is a milestone in DNA nanotechnology. It is robust and efficient in constructing arbitrary two- and three-dimensional nanostructures. The shape and size of origami structures vary. To characterize them, an atomic force microscope, a transmission electron microscope, and other microscopes are utilized. However, the identification of various origami nanostructures heavily depends on the experience of researchers. In this study, we used the deep learning method (improved Yolox) to detect multiple DNA origami structures and estimate their yield. We designed a feature enhancement fusion network with the attention mechanism, and related parameters were researched. Experiments conducted to verify the proposed method showed that the detection accuracy was higher than that of other methods. This method can detect and estimate the DNA origami yield in complex environments, and the detection speed is in the millisecond range.
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Affiliation(s)
- Congzhou Chen
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
| | - Jinyan Nie
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing100094, China
| | - Mingyuan Ma
- School of Computer Science, Peking University, Beijing100871, China
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou510006, China
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3
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Xia F, Youcef-Toumi K. Review: Advanced Atomic Force Microscopy Modes for Biomedical Research. BIOSENSORS 2022; 12:1116. [PMID: 36551083 PMCID: PMC9775674 DOI: 10.3390/bios12121116] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Visualization of biomedical samples in their native environments at the microscopic scale is crucial for studying fundamental principles and discovering biomedical systems with complex interaction. The study of dynamic biological processes requires a microscope system with multiple modalities, high spatial/temporal resolution, large imaging ranges, versatile imaging environments and ideally in-situ manipulation capabilities. Recent development of new Atomic Force Microscopy (AFM) capabilities has made it such a powerful tool for biological and biomedical research. This review introduces novel AFM functionalities including high-speed imaging for dynamic process visualization, mechanobiology with force spectroscopy, molecular species characterization, and AFM nano-manipulation. These capabilities enable many new possibilities for novel scientific research and allow scientists to observe and explore processes at the nanoscale like never before. Selected application examples from recent studies are provided to demonstrate the effectiveness of these AFM techniques.
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4
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Abstract
Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometer resolution. For biological applications, one of its key advantages is its ability to visualize the substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine the secondary and tertiary structure of surface-bound DNA, and its interactions with proteins.
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Affiliation(s)
- Philip J Haynes
- London Centre for Nanotechnology, University College London, London, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Kavit H S Main
- London Centre for Nanotechnology, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Bernice Akpinar
- London Centre for Nanotechnology, University College London, London, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London, UK
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, London, UK.
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
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5
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Revealing DNA Structure at Liquid/Solid Interfaces by AFM-Based High-Resolution Imaging and Molecular Spectroscopy. Molecules 2021; 26:molecules26216476. [PMID: 34770895 PMCID: PMC8587808 DOI: 10.3390/molecules26216476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
DNA covers the genetic information in all living organisms. Numerous intrinsic and extrinsic factors may influence the local structure of the DNA molecule or compromise its integrity. Detailed understanding of structural modifications of DNA resulting from interactions with other molecules and surrounding environment is of central importance for the future development of medicine and pharmacology. In this paper, we review the recent achievements in research on DNA structure at nanoscale. In particular, we focused on the molecular structure of DNA revealed by high-resolution AFM (Atomic Force Microscopy) imaging at liquid/solid interfaces. Such detailed structural studies were driven by the technical developments made in SPM (Scanning Probe Microscopy) techniques. Therefore, we describe here the working principles of AFM modes allowing high-resolution visualization of DNA structure under native (liquid) environment. While AFM provides well-resolved structure of molecules at nanoscale, it does not reveal the chemical structure and composition of studied samples. The simultaneous information combining the structural and chemical details of studied analyte allows achieve a comprehensive picture of investigated phenomenon. Therefore, we also summarize recent molecular spectroscopy studies, including Tip-Enhanced Raman Spectroscopy (TERS), on the DNA structure and its structural rearrangements.
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6
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Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALB. Atomic force microscopy-A tool for structural and translational DNA research. APL Bioeng 2021; 5:031504. [PMID: 34286171 PMCID: PMC8272649 DOI: 10.1063/5.0054294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.
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Affiliation(s)
| | - James I. Provan
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - John A. Hartley
- UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
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7
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Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
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Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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8
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Shi L, Sun Y, Mi L, Li T. Target-Catalyzed Self-Growing Spherical Nucleic Acid Enzyme (SNAzyme) as a Double Amplifier for Ultrasensitive Chemiluminescence MicroRNA Detection. ACS Sens 2019; 4:3219-3226. [PMID: 31763826 DOI: 10.1021/acssensors.9b01655] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Portable chemiluminescence (CL) imaging with a smartphone has shown a great promise for point-of-care testing of diseases, especially for acute myocardial infarction (AMI), which may occur abruptly. A challenge remains how to improve the imaging sensitivity that usually is several orders of magnitude lower than those of counterpart methodologies using the sophisticated equipment. Toward this goal, here, we report the target-triggered in situ growth of AuNP@hairpin-DNA nanoprobes into spherical nucleic acid enzymes (SNAzymes), which serve as both nanolabels and amplifiers for portable CL imaging of microRNAs (miRNAs) with an ultrahigh sensitivity comparable to that of the instrumental measurement under same conditions. A G-quadruplex (G4) DNA dense layer is dynamically produced on the gold nanocore via a DNAzyme machine-driven hairpin cleaving and captures the cofactor hemin to form the SNAzymes with higher peroxidase activity and stronger nuclease resistance than the commonly used G4 DNAzymes. The matured SNAzymes are then utilized as catalytic labels in a luminol-artesunate CL system for miRNA imaging with a smartphone as the portable detector. In this way, two AMI-related miRNAs, miRNA-499 and miRNA-133a, are successfully detected in real patients' serum with a naked eye-visualized CL change at 10 fM, showing a 5 order of magnitude improvement on the sensitivity of visualizing the same disease markers in clinical circulating blood as compared to the reported strategy. In addition, a good selectivity of our developed CL imaging platform is demonstrated. These unique features make it promising to employ this portable imaging platform for clinical AMI diagnosis.
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Affiliation(s)
- Lin Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Yudie Sun
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lan Mi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
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9
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Nwokeoji AO, Kumar S, Kilby PM, Portwood DE, Hobbs JK, Dickman MJ. Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC. Analyst 2019; 144:4985-4994. [PMID: 31328735 DOI: 10.1039/c9an00954j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Long double-stranded (ds) RNA is emerging as a novel alternative to chemical and genetically-modified insect and fungal management strategies. The ability to produce large quantities of dsRNA in either bacterial systems, by in vitro transcription, in cell-free systems or in planta for RNA interference applications has generated significant demand for the development and application of analytical tools for analysis of dsRNA. We have utilised atomic force microscopy (AFM) in conjunction with ion-pair reverse-phase high performance liquid chromatography (IP-RP-HPLC) to provide novel insight into dsRNA for RNAi applications. The AFM analysis enabled direct structural characterisation of the A-form duplex dsRNA and accurate determination of the dsRNA duplex length. Moreover, further analysis under non-denaturing conditions revealed the presence of heterogeneous dsRNA species. IP-RP-HPLC fractionation and AFM analysis revealed that these alternative RNA species do not arise from different lengths of individual dsRNA molecules in the product, but represent misannealed RNA species that present as larger assemblies or multimeric forms of the RNA. These results for the first time provide direct structural insight into dsRNA produced both in vivo in bacterial systems and in vitro, highlighting the structural heterogeneity of RNA produced. These results are the first example of detailed characterisation of the different forms of dsRNA from two production systems and establish atomic force microscopy as an important tool for the characterisation of long dsRNA.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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10
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Akpinar B, Haynes PJ, Bell NAW, Brunner K, Pyne ALB, Hoogenboom BW. PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy. NANOSCALE 2019; 11:20072-20080. [PMID: 31612171 PMCID: PMC6964798 DOI: 10.1039/c9nr07104k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 09/22/2019] [Indexed: 05/20/2023]
Abstract
DNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working in biologically relevant protein concentrations, where proteins may be present in large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface for AFM studies. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/PLL1000-2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show - through the use of biotinylated DNA and streptavidin - that this selective adsorption extends to DNA-protein complexes and that DNA-bound streptavidin can be unambiguously distinguished in spite of an excess of unbound streptavidin in solution. Finally, we apply this to the nuclear enzyme PARP1, resolving the binding of individual PARP1 molecules to DNA by in-liquid AFM.
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Affiliation(s)
- Bernice Akpinar
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, UK. and Department of Chemistry, Imperial College London, SW7 2AZ, UK
| | - Philip J Haynes
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, UK. and Department of Chemistry, Imperial College London, SW7 2AZ, UK
| | | | - Katharina Brunner
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK and Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, UK. and Department of Materials Science and Engineering, University of Sheffield, S1 3JD, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, UK. and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
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11
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Papkov D, Delpouve N, Delbreilh L, Araujo S, Stockdale T, Mamedov S, Maleckis K, Zou Y, Andalib MN, Dargent E, Dravid VP, Holt MV, Pellerin C, Dzenis YA. Quantifying Polymer Chain Orientation in Strong and Tough Nanofibers with Low Crystallinity: Toward Next Generation Nanostructured Superfibers. ACS NANO 2019; 13:4893-4927. [PMID: 31038925 DOI: 10.1021/acsnano.8b08725] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Advanced fibers revolutionized structural materials in the second half of the 20th century. However, all high-strength fibers developed to date are brittle. Recently, pioneering simultaneous ultrahigh strength and toughness were discovered in fine (<250 nm) individual electrospun polymer nanofibers (NFs). This highly desirable combination of properties was attributed to high macromolecular chain alignment coupled with low crystallinity. Quantitative analysis of the degree of preferred chain orientation will be crucial for control of NF mechanical properties. However, quantification of supramolecular nanoarchitecture in NFs with low crystallinity in the ultrafine diameter range is highly challenging. Here, we discuss the applicability of traditional as well as emerging methods for quantification of polymer chain orientation in nanoscale one-dimensional samples. Advantages and limitations of different techniques are critically evaluated on experimental examples. It is shown that straightforward application of some of the techniques to sub-wavelength-diameter NFs can lead to severe quantitative and even qualitative artifacts. Sources of such size-related artifacts, stemming from instrumental, materials, and geometric phenomena at the nanoscale, are analyzed on the example of polarized Raman method but are relevant to other spectroscopic techniques. A proposed modified, artifact-free method is demonstrated. Outstanding issues and their proposed solutions are discussed. The results provide guidance for accurate nanofiber characterization to improve fundamental understanding and accelerate development of nanofibers and related nanostructured materials produced by electrospinning or other methods. We expect that the discussion in this review will also be useful to studies of many biological systems that exhibit nanofilamentary architectures and combinations of high strength and toughness.
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Affiliation(s)
- Dimitry Papkov
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
| | - Nicolas Delpouve
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Laurent Delbreilh
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Steven Araujo
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Taylor Stockdale
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Sergey Mamedov
- Division of HORIBA Instruments, Inc. , HORIBA Scientific , 20 Knightsbridge Road , Piscataway , New Jersey 08854 , United States
| | - Kaspars Maleckis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Yan Zou
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Mohammad Nahid Andalib
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Eric Dargent
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Vinayak P Dravid
- Department of Materials Science and Engineering , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martin V Holt
- Center for Nanoscale Materials , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Christian Pellerin
- Département de chimie , Université de Montréal , Montréal , QC H3C 3J7 , Canada
| | - Yuris A Dzenis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
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12
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Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS NANO 2019; 13:4220-4229. [PMID: 30938988 DOI: 10.1021/acsnano.8b09234] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl2 and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl2-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl2. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Physics , University of Colorado , Boulder , Colorado 80309 , United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Molecular, Cellular, and Developmental Biology , University of Colorado , Boulder , Colorado 80309 , United States
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13
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Li L, Zhang P, Li J, Wang Y, Wei Y, Hu J, Zhou X, Xu B, Li B. Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami. NANOSCALE 2019; 11:4707-4711. [PMID: 30834915 DOI: 10.1039/c8nr10354b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Characterization of the stiffness of thin DNA strands remains difficult. By constructing bilayer DNA molecules, we investigated their mechanical properties using AFM. Increased DNA thickness through DNA origami greatly reduced the substrate effect when measuring Young's modulus, thus providing a more accurate picture of the inherent nanomechanical properties of DNA.
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Affiliation(s)
- Lin Li
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China.
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14
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Terasaki K, Yokoyama T. Structural Modification of DNA Studied by Scanning Tunneling Microscopy. J Phys Chem B 2019; 123:1780-1783. [PMID: 30721062 DOI: 10.1021/acs.jpcb.8b12100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In addition to the well-known double-helix structure of deoxyribonucleic acid (DNA), theoretical simulations have predicted structural variants, such as cross and T-shaped formations. The direct visualization of individual DNA molecules by scanning probe microscopy should be able to identify these structures. In this study, we examine various structures of DNA deposited on Au(111) by using an electrospray method and analyzing with a low-temperature scanning tunneling microscope. We could identify in detail several interesting structures. In particular, we found that double-stranded DNAs are partially unraveled into single-stranded DNAs and we confirmed the presence of T-shaped DNA structures.
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Affiliation(s)
- Kohei Terasaki
- Department of Nanoscience and Technology , Yokohama City University , 22-2 Seto 236-0027 , Japan
| | - Takashi Yokoyama
- Department of Nanoscience and Technology , Yokohama City University , 22-2 Seto 236-0027 , Japan
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15
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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16
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Ares P, Fuentes-Perez ME, Herrero-Galán E, Valpuesta JM, Gil A, Gomez-Herrero J, Moreno-Herrero F. High resolution atomic force microscopy of double-stranded RNA. NANOSCALE 2016; 8:11818-11826. [PMID: 26876486 DOI: 10.1039/c5nr07445b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.
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Affiliation(s)
- Pablo Ares
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Maria Eugenia Fuentes-Perez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - Elías Herrero-Galán
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - José M Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - Adriana Gil
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - Julio Gomez-Herrero
- Department of Condensed Matter Physics, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
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17
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Hansma HG, Pietrasanta LI, Golan R, Sitko JC, Viani MB, Paloczi GT, Smith BL, Thrower D, Hansma PK. Recent highlights from atomic force microscopy of DNA. J Biomol Struct Dyn 2016; 17 Suppl 1:271-5. [PMID: 22607434 DOI: 10.1080/07391102.2000.10506631] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Seven recent highlights are presented from atomic force microscopy (AFM) of DNA in this lab. The first two involve advances in the observation of enzymatic reactions in near-physiological solutions. E. coli RNA polymerase was observed to process along its DNA template in a series of time-lapse images [S. Kasas, et al., Biochemistry 36, 461 (1997)], and a new small-cantilever atomic force microscope (AFM) imaged DNA degradation by DNase I at rates as fast as two seconds per image. The next five highlights involve structural observations of DNA and DNA-protein complexes, including DNA condensed for gene delivery, sequence-dependent DNA condensation, an AFM assay for RNA polymerase, and AFM evidence for a yeast kinetochore complex that may be involved in holding together sister chromatids during cell division.
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Affiliation(s)
- H G Hansma
- a Department of Physics , University of California , Santa Barbara , CA , 93106
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18
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Luque-Caballero G, Maldonado-Valderrama J, Quesada-Pérez M, Martín-Molina A. Atomic force microscopy as a tool to study the adsorption of DNA onto lipid interfaces. Microsc Res Tech 2016; 80:11-17. [PMID: 27014963 DOI: 10.1002/jemt.22654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/25/2016] [Accepted: 02/05/2016] [Indexed: 11/08/2022]
Abstract
The Atomic Force Microscopy (AFM) technique appears as a central tool for the characterization of DNA adsorption onto lipid interfaces. Regardless of the huge number of surveys devoted to this issue, there are still fascinating phenomena in this field that have not been explored in detail by AFM. For instance, adsorption of DNA onto like-charged lipid surfaces mediated by cations is still not fully understood even though it is gaining popularity nowadays in gene therapy and nanotechnology. Studies related to the complexation of DNA with anionic lipids as a non-viral gene delivery vehicle as well as the formation of self-assembled nanoscale DNA constructs (DNA origami) are two of the most attractive systems. Unfortunately, molecular mechanisms underlying the adsorption of DNA onto anionic lipid interfaces remain unclear so far. In view of that, AFM becomes an appropriate technique to provide valuable information to understand the adsorption of DNA to anionic lipid surfaces. As a second part of this review we provide an illustrative example of application of the AFM technique to probe the DNA adsorption onto a model lipid monolayer negatively charged. Microsc. Res. Tech. 80:11-17, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Germán Luque-Caballero
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
| | - Julia Maldonado-Valderrama
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
| | - Manuel Quesada-Pérez
- Departamento de Física, Escuela Politécnica Superior de Linares, Universidad de Jaén, Linares, Jaén, 23700, Spain
| | - Alberto Martín-Molina
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
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19
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Japaridze A, Vobornik D, Lipiec E, Cerreta A, Szczerbinski J, Zenobi R, Dietler G. Toward an Effective Control of DNA’s Submolecular Conformation on a Surface. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b01827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dusan Vobornik
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ewelina Lipiec
- The
Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland
| | - Andrea Cerreta
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacek Szczerbinski
- Laboratory
of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory
of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Giovanni Dietler
- Laboratory
of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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20
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Abstract
Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine superstructure and secondary structure of surface-bound DNA. The method is also readily applicable to probe DNA-DNA interactions and DNA-protein complexes.
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Affiliation(s)
- Alice L B Pyne
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, 17-19 Gordon Street, London, WC1H 0AH, UK.
| | - Bart W Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, 17-19 Gordon Street, London, WC1H 0AH, UK.
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21
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Abstract
This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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22
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Kim S, Faghihnejad A, Lee Y, Jho Y, Zeng H, Hwang DS. Cation–π interaction in DOPA-deficient mussel adhesive protein mfp-1. J Mater Chem B 2015; 3:738-743. [DOI: 10.1039/c4tb01646g] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Deployment of cation–π interactions can be a complementary strategy for the successful underwater adhesion of mussels.
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Affiliation(s)
- Sangsik Kim
- School of Environmental Science and Engineering
- Division of Integrative Biosciences and Biotechnology
- Pohang University of Science and Technology
- Pohang
- Korea
| | - Ali Faghihnejad
- Department of Chemical and Materials Engineering
- University of Alberta
- Edmonton
- Canada
| | - Yongjin Lee
- Department of Physics
- Pohang University of Science and Technology
- Asia Pacific Center for Theoretical Physics
- Pohang
- Korea
| | - YongSeok Jho
- Department of Physics
- Pohang University of Science and Technology
- Asia Pacific Center for Theoretical Physics
- Pohang
- Korea
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering
- University of Alberta
- Edmonton
- Canada
| | - Dong Soo Hwang
- School of Environmental Science and Engineering
- Division of Integrative Biosciences and Biotechnology
- Pohang University of Science and Technology
- Pohang
- Korea
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23
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Zhu X, Feng C, Zhang B, Tong H, Gao T, Li G. A netlike rolling circle nucleic acid amplification technique. Analyst 2015; 140:74-8. [DOI: 10.1039/c4an01711k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An isothermal nucleic acid amplification technique termed as netlike rolling circle amplification is proposed. Dense and uniform network morphology of amplified products is first observed, suggesting the ultrahigh amplification efficiency.
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Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P R China
| | - Chang Feng
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P R China
| | - Bin Zhang
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P R China
| | - Hui Tong
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P R China
| | - Tao Gao
- State Key Laboratory of Pharmaceutical Biotechnology
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P R China
| | - Genxi Li
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P R China
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24
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Pyne A, Thompson R, Leung C, Roy D, Hoogenboom BW. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3257-61. [PMID: 24740866 DOI: 10.1002/smll.201400265] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/20/2014] [Indexed: 05/23/2023]
Abstract
Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.
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Affiliation(s)
- Alice Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
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25
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Cerreta A, Vobornik D, Dietler G. Fine DNA structure revealed by constant height frequency modulation AFM imaging. Eur Polym J 2013. [DOI: 10.1016/j.eurpolymj.2013.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Ido S, Kimura K, Oyabu N, Kobayashi K, Tsukada M, Matsushige K, Yamada H. Beyond the helix pitch: direct visualization of native DNA in aqueous solution. ACS NANO 2013; 7:1817-22. [PMID: 23350676 DOI: 10.1021/nn400071n] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The DNA double helix was first elucidated by J.D. Watson and F.H.C. Crick over a half century ago. However, no one could actually "see" the well-known structure ever. Among all real-space observation methods, only atomic force microscopy (AFM) enables us to visualize the biologically active structure of natural DNA in water. However, conventional AFM measurements often caused the structural deformation of DNA because of the strong interaction forces acting on DNA. Moreover, large contact area between the AFM probe and DNA hindered us from imaging sub-molecular-scale features smaller than helical periodicity of DNA. Here, we show the direct observation of native plasmid DNA in water using an ultra-low-noise AFM with the highly sensitive force detection method (frequency modulation AFM: FM-AFM). Our micrographs of DNA vividly exhibited not only overall structure of the B-form double helix in water but also local structures which deviate from the crystallographic structures of DNA without any damage. Moreover, the interaction force area in the FM-AFM was small enough to clearly discern individual functional groups within DNA. The technique was also applied to explore the synthesized DNA nanostructures toward the current nanobiotechnology. This work will be essential for considering the structure-function relationship of biomolecular systems in vivo and for in situ analysis of DNA-based nanodevices.
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Affiliation(s)
- Shinichiro Ido
- Department of Electronic Science and Engineering, Kyoto University, Kyoto University Katsura, Nishikyo, Kyoto 615-8510, Japan
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27
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Park KH, Noh TH, Shim YB, Jung OS. Construction of right-handed-, left-handed-, and racemic helical coordination polymers. Enantioselective recognition using chiral helical crystals. Chem Commun (Camb) 2013; 49:4000-2. [DOI: 10.1039/c3cc00005b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Cerreta A, Vobornik D, Di Santo G, Tobenas S, Alonso-Sarduy L, Adamcik J, Dietler G. FM-AFM constant height imaging and force curves: high resolution study of DNA-tip interactions. J Mol Recognit 2012; 25:486-93. [PMID: 22899592 DOI: 10.1002/jmr.2212] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Interaction of the atomic force microscopy (AFM) tip with the sample can be invasive for soft samples. Frequency Modulation (FM) AFM is gentler because it allows scanning in the non-contact regime where only attractive forces exist between the tip and the sample, and there is no sample compression. Recently, FM-AFM was used to resolve the atomic structure of single molecules of pentacene and of carbon nanotubes. We are testing similar FM-AFM-based approaches to study biological samples. We present FM-AFM experiments on dsDNA deposited on 3-aminopropyltriethoxysilane modified mica in ultra high vacuum. With flexible samples such as DNA, the substrate flatness is a sub-molecular resolution limiting factor. Non-contact topographic images of DNA show variations that have the periodicity of the right handed helix of B-form DNA - this is an unexpected result as dehydrated DNA is thought to assume the A-form structure. Frequency shift maps at constant height allow working in the non-monotonic frequency shift range, show a rich contrast that changes significantly with the tip-sample separation, and show 0.2 to 0.4 nm size details on DNA. Frequency shift versus distance curves acquired on DNA molecules and converted in force curves show that for small molecules (height < 2.5 nm), there is a contribution to the interaction force from the substrate when the tip is on top of the molecules. Our data shine a new light on dehydrated and adsorbed DNA behavior. They show a longer tip-sample interaction distance. These experiments may have an impact on nanotechnological DNA applications in non-physiological environments such as DNA based nanoelectronics and nanotemplating.
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Affiliation(s)
- Andrea Cerreta
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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29
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The DNA–DNA spacing in gemini surfactants–DOPE–DNA complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2725-31. [DOI: 10.1016/j.bbamem.2012.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 05/10/2012] [Accepted: 05/18/2012] [Indexed: 12/27/2022]
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30
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Leung C, Bestembayeva A, Thorogate R, Stinson J, Pyne A, Marcovich C, Yang J, Drechsler U, Despont M, Jankowski T, Tschöpe M, Hoogenboom BW. Atomic force microscopy with nanoscale cantilevers resolves different structural conformations of the DNA double helix. NANO LETTERS 2012; 12:3846-50. [PMID: 22731615 DOI: 10.1021/nl301857p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural variability and flexibility are crucial factors for biomolecular function. Here we have reduced the invasiness and enhanced the spatial resolution of atomic force microscopy (AFM) to visualize, for the first time, different structural conformations of the two polynucleotide strands in the DNA double helix, for single molecules under near-physiological conditions. This is achieved by identifying and tracking the anomalous resonance behavior of nanoscale AFM cantilevers in the immediate vicinity of the sample.
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Affiliation(s)
- Carl Leung
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom.
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31
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Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy. Methods Mol Biol 2012; 931:295-312. [PMID: 23027008 DOI: 10.1007/978-1-62703-056-4_14] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface preparation is a key step for reliable and reproducible imaging of DNA and protein-DNA complexes with atomic force microscopy (AFM). This article describes the approaches for chemical functionalization of the mica surface. One approach utilizes 3-aminopropyl-trietoxy silane (APTES), enabling one to obtain a smooth surface termed AP-mica. This surface binds nucleic acids and nucleoprotein complexes in a wide range of ionic strengths, in the absence of divalent cations and in a broad range of pH. Another method utilizes aminopropyl silatrane (APS) to yield an APS-mica surface. The advantage of APS-mica compared with AP-mica is the ability to obtain reliable and reproducible time-lapse images in aqueous solutions. The chapter describes the methodologies for the preparation of AP-mica and APS-mica surfaces and the preparation of samples for AFM imaging. The protocol for synthesis and purification of APS is also provided. The applications are illustrated with a number of examples.
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32
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Lyubchenko YL, Shlyakhtenko LS, Ando T. Imaging of nucleic acids with atomic force microscopy. Methods 2011; 54:274-83. [PMID: 21310240 PMCID: PMC3114274 DOI: 10.1016/j.ymeth.2011.02.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 12/07/2010] [Accepted: 02/01/2011] [Indexed: 11/18/2022] Open
Abstract
Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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33
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Wang H, Wang X, Li H, Zhang X, Zhang Y, Hu J. Molecular expansion of an individual coiled DNA on a graphite surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2405-2410. [PMID: 21341704 DOI: 10.1021/la104776n] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Direct visualization and manipulation of a single polymer on a solid surface in fluid can greatly contribute to our understanding of polymer dynamics and physics relevant to many practical applications. In this paper, the authors report a novel phenomenon that a randomly coiled DNA molecule can be gradually expanded to form a spiral-like pattern by repeatedly rotating a water droplet on a graphite surface where the DNA molecule was deposited. The process of DNA expansion was traced using atomic force microscopy relocation imaging. A simple theoretical model based on the analysis of centrifugal and resistant forces exerted on the DNA molecule during the manipulation was presented to explain the formation of the spiral-like pattern. This study should provide us insight into the movement of polymers on a solid surface under fluid flow.
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Affiliation(s)
- Huabin Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, People's Republic of China
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34
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Josephs EA, Ye T. Nanoscale positioning of individual DNA molecules by an atomic force microscope. J Am Chem Soc 2010; 132:10236-8. [PMID: 20662500 DOI: 10.1021/ja1039677] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report a method to assemble nanoscale DNA structures with single-molecule precision. This assembly is accomplished by performing nanografting in the presence of short, thiolated DNA strands that have been diluted by a positively charged alkanethiol. The expected number of DNA molecules per patch can be modulated by the application of an electric potential to the surface during patterning. Our ability to position individual DNA within a controlled nanoscale environment and observe these molecules in situ will allow us to understand and potentially decouple the heterogeneity caused by the local environment from the intrinsic properties in single-molecule biophysical measurements. Additionally, our approach can potentially be extended to the molecule-by-molecule assembly of larger artificial test structures of nucleic acids or proteins.
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Affiliation(s)
- Eric A Josephs
- School of Engineering, 5200 North Lake Road, University of California, Merced, California 95343, USA
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35
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Lyubchenko YL. Preparation of DNA and nucleoprotein samples for AFM imaging. Micron 2010; 42:196-206. [PMID: 20864349 DOI: 10.1016/j.micron.2010.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/24/2010] [Accepted: 08/24/2010] [Indexed: 02/06/2023]
Abstract
Sample preparation techniques allowing reliable and reproducible imaging of DNA with various structures, topologies and complexes with proteins are reviewed. The major emphasis is given to methods utilizing chemical functionalization of mica, enabling preparation of the surfaces with required characteristics. The methods are illustrated by examples of imaging of different DNA structures. Special attention is given to the possibility of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time-lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein-DNA complexes is illustrated by a few examples of imaging site-specific complexes, as well as such systems as chromatin. The time-lapse AFM studies of protein-DNA complexes including very recent advances with the use of high-speed AFM are reviewed.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States.
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Shen XC, Bao L, Zhang ZL, Liu X, Pang DW, Xu J. A simple and effective sample preparation method for atomic force microscopy visualization of individual DNA molecules in situ. Mol Biol Rep 2010; 38:965-9. [PMID: 20535564 DOI: 10.1007/s11033-010-0190-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 05/21/2010] [Indexed: 10/19/2022]
Abstract
A simple, controllable and effective sample preparation method was established for atomic force microscopy (AFM) imaging of individual DNA molecules in aqueous solution. Firstly, magnesium ion (Mg(2+)) at a concentration of 5.0-10.0 mM as a positively charged bridge was transferred onto mica to immobilize DNA molecules. Then Mg(2+)-modified mica was used to investigate DNA molecules in any buffer without magnesium ion by AFM. AFM images demonstrated that DNA molecules can be successfully observed in solution with good resolution, reproducibility, and stability. Further, this DNA sample preparation method makes AFM successful to investigate DNA molecular interaction in situ and DNA/chitosan complex in gene delivery.
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Affiliation(s)
- Xin-Cheng Shen
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
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37
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Klinov DV, Neretina TV, Prokhorov VV, Dobrynina TV, Aldarov KG, Demin VV. High-resolution atomic force microscopy of DNA. BIOCHEMISTRY (MOSCOW) 2010; 74:1150-4. [PMID: 19916928 DOI: 10.1134/s0006297909100113] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A method using high resolution atomic force microscopy for imaging DNA has been elaborated. Using super-sharp probes and modified graphite as support for molecule adsorption, DNA molecule images were obtained whose resolution made possible the observation of their fine structure with repeated helical motifs. The method can be used to visualize individual spread molecules of single-stranded DNA.
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Affiliation(s)
- D V Klinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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38
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Yerkes S, Vesenka J, Kmiec EB. A stable G-quartet binds to a huntingtin protein fragment containing expanded polyglutamine tracks. J Neurosci Res 2010; 88:335-45. [DOI: 10.1002/jnr.22210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Truzzolillo D, Bordi F, Sciortino F, Cametti C. Kinetic arrest in polyion-induced inhomogeneously charged colloidal particle aggregation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2009; 29:229-237. [PMID: 19551418 DOI: 10.1140/epje/i2009-10471-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 05/07/2009] [Indexed: 05/28/2023]
Abstract
Polymer chains adsorbed onto oppositely charged colloidal particles can significantly modify the particle-particle interactions. For sufficient amounts of added polymers, the original electrostatic repulsion can even turn into an effective attraction and relatively large aggregates can form. The attractive interaction contribution between two particles arises from the correlated adsorption of polyions at the oppositely charged particle surfaces, resulting in a non-homogeneous surface charge distribution. Here, we investigate the aggregation kinetics of polyion-induced colloidal complexes through Monte Carlo simulation, in which the effect of charge anisotropy is taken into account by a DLVO-like inter-particle potential, as recently proposed by Velegol and Thwar (Langmuir 17, 7687 (2001)). The results reveal that the aggregation process slows down due to the progressive increase of the potential barrier height upon clustering. Within this framework, the experimentally observed cluster phases in polyelectrolyte-liposome solutions can be interpreted as a kinetic arrested state.
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Affiliation(s)
- D Truzzolillo
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale A. Moro 5, I-00185, Roma, Italy
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40
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Bordi F, Sennato S, Truzzolillo D. Polyelectrolyte-induced aggregation of liposomes: a new cluster phase with interesting applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:203102. [PMID: 21825508 DOI: 10.1088/0953-8984/21/20/203102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Different charged colloidal particles have been shown to be able to self-assemble, when mixed in an aqueous solvent with oppositely charged linear polyelectrolytes, forming long-lived finite-size mesoscopic aggregates. On increasing the polyelectrolyte content, with the progressive reduction of the net charge of the primary polyelectrolyte-decorated particles, larger and larger clusters are observed. Close to the isoelectric point, where the charge of the adsorbed polyelectrolytes neutralizes the original charge of the particles' surface, the aggregates reach their maximum size, while beyond this point any further increase of the polyelectrolyte-particle charge ratio causes the formation of aggregates whose size is progressively reduced. This re-entrant condensation behavior is accompanied by a significant overcharging. Overcharging, or charge inversion, occurs when more polyelectrolyte chains adsorb on a particle than are needed to neutralize its original charge so that, eventually, the sign of the net charge of the polymer-decorated particle is inverted. The stability of the finite-size long-lived clusters that this aggregation process yields results from a fine balance between long-range repulsive and short-range attractive interactions, both of electrostatic nature. For the latter, besides the ubiquitous dispersion forces, whose supply becomes relevant only at high ionic strength, the main contribution appears due to the non-uniform correlated distribution of the charge on the surface of the polyelectrolyte-decorated particles ('charge-patch' attraction). The interesting phenomenology shown by these system has a high potential for biotechnological applications, particularly when the primary colloidal particles are bio-compatible lipid vesicles. Possible applications of these systems as multi-compartment vectors for the simultaneous intra-cellular delivery of different pharmacologically active substances will be briefly discussed.
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Affiliation(s)
- F Bordi
- Dipartimento di Fisica, Università di Roma 'La Sapienza', Piazzale Aldo Moro 5, I-00185 Rome, Italy. CRS CNR-INFM 'SOFT', Università di Roma 'La Sapienza', Piazzale Aldo Moro 5, I-00185-Rome, Italy
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41
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Lyubchenko YL, Shlyakhtenko LS, Gall AA. Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry. Methods Mol Biol 2009; 543:337-351. [PMID: 19378175 DOI: 10.1007/978-1-60327-015-1_21] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Despite their rather recent invention, atomic force microscopes are widely available commercially. AFM and its special modifications (tapping mode and noncontact operation in solution) have been successfully used for topographic studies of a large number of biological objects including DNA, RNA, proteins, cell membranes, and even whole cells. AFM was also successfully applied to studies of nucleic acids and various protein DNA complexes. Part of this success is due to the development of reliable sample preparation procedures. This chapter describes one of the approaches based on chemical functionalization of mica surface with 1-(3-aminopropyl) silatrane (APS). One of the most important properties of APS-mica approach is that the sample can be deposited on the surface in a wide range of ionic strengths, in the absence of divalent cations and a broad range of pH. In addition to imaging of dried sample, APS-mica allows reliable and reproducible time lapse imaging in aqueous solutions. Finally, APS mica is terminated with reactive amino groups that can be used for covalent and ionic attachment of molecules for AFM force spectroscopy studies. The protocols for the preparation of APS, functionalization with APS mica and AFM probes, preparation of samples for imaging in air and in aqueous solutions, and force spectroscopy studies are outlined. All these applications are illustrated with a few examples.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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42
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Kumaki J, Sakurai SI, Yashima E. Visualization of synthetic helical polymers by high-resolution atomic force microscopy. Chem Soc Rev 2009; 38:737-46. [DOI: 10.1039/b718433f] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Sennato S, Truzzolillo D, Bordi F, Cametti C. Effect of temperature on the reentrant condensation in polyelectrolyte-liposome complexation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12181-12188. [PMID: 18831566 DOI: 10.1021/la8021563] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interactions of oppositely charged macroions in aqueous solution give rise to intriguing aggregation phenomena, resulting in finite-size, long-lived clusters, characterized by a quite narrow size distribution. Particularly, the adsorption of highly charged linear polyelectrolytes on oppositely charged colloidal particles is strongly correlated and some short-range order arises from competing electrostatic interactions between like-charged polymer chains (repulsion) and between polymer chains and particle surface (attraction). In these systems, in an interval of concentrations around the isoelectric point, relatively large clusters of polyelectrolyte-decorated particles form. However, the mechanisms that drive the aggregation and stabilize, at the different polymer/particle ratios, a well-defined size of the aggregates are not completely understood. Nor is clear the role that the correlated polyion adsorption plays in the aggregation, although the importance of "patchy interactions" has been stressed as the possible source of attractive interaction term between colloidal particles. Different models have been proposed to explain the formation of the observed cluster phase. However, a central question still remains unanswered, i.e., whether the clusters are true equilibrium or metastable aggregates. To elucidate this point, in this work, we have investigated the effect of the temperature on the cluster formation. We employed liposomes built up by DOTAP lipids interacting with a simple anionic polyion, polyacrylate sodium salt, over an extended concentration range below and above the isoelectric condition. Our results show that the aggregation process can be described by a thermally activated mechanism.
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Affiliation(s)
- S Sennato
- Dipartimento di Fisica, Università di Roma La Sapienza, Rome, Italy
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44
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Lyubchenko YL, Shlyakhtenko LS. AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods 2008; 47:206-13. [PMID: 18835446 DOI: 10.1016/j.ymeth.2008.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022] Open
Abstract
This paper describes protocols for studies of structure and dynamics of DNA and protein-DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach. The necessary specifics for the preparation of functionalized surfaces and AFM probes with the use of silanes and silatranes, including the protocols for synthesis of silatranes are provided. The methodology of studies of local and global conformations DNA with the major focus on the time-lapse imaging of DNA in aqueous solutions is illustrated by the study of dynamics of Holliday junctions including branch migration. The analysis of nucleosome dynamics is selected as an example to illustrate the application of the time-lapse AFM to studies of dynamics of protein-DNA complexes. The force spectroscopy is the modality of AFM with a great importance to various fields of biomedical studies. The AFM force spectroscopy approach for studies of specific protein-DNA complexes is illustrated by the data on analysis of dynamics of synaptic SfiI-DNA complexes. When necessary, additional specifics are added to the corresponding example.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, COP 1012, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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45
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Jung YK, Kim TW, Jung C, Cho DY, Park HG. A polydiacetylene microchip based on a biotin-streptavidin interaction for the diagnosis of pathogen infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:1778-1784. [PMID: 18819132 DOI: 10.1002/smll.200800947] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A micropatterned polydiacetylene (PDA) chip, utilizing the unique fluorogenic property of PDA and a specific biotin-streptavidin (STA) interaction, is constructed to detect pathogen infections. To construct the PDA chip, biotin-modified diacetylene liposomes are immobilized on aldehyde glass and conjugated with STA, followed by UV irradiation to polymerize the STA-functionalized diacetylene liposomes. Genomic DNA of a model pathogen, Chlamydia trachomatis, is isolated from human samples and biotin-labeled target DNA is obtained through PCR amplification using biotin-11-dUTP. Owing to the stimulus caused by the biotin-STA interaction, the biotinylated DNA induces an intense fluorescence signal on the immobilized PDA. By using this strategy, it is possible to diagnose Chlamydia infections by applying DNA samples from several nonhealthy humans to a single PDA chip. The results of this study serve as the basis for a new strategy for fluorogenic PDA microarray-based diagnosis of pathogen infections.
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Affiliation(s)
- Yun Kyung Jung
- Department of Chemical and Biomolecular Engineering (BK 21 Program), KAIST, Daejeon 305-701, Korea
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46
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Gromer A, Rawiso M, Maaloum M. Visualization of hydrophobic polyelectrolytes using atomic force microscopy in solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:8950-8953. [PMID: 18582135 DOI: 10.1021/la8009139] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have used atomic force microscopy to study the morphology of hydrophobic polyelectrolytes adsorbed on surfaces. The polyelectrolytes consisted of polystyrene sulfonate (PSS) chains made with three charge densities: 32%, 67%, and 92%. They were adsorbed on two types of surfaces: mica, and phospholipid bilayers made of mixed neutral and cationic lipids. We show that the chains with a low charge density (32%) are collapsed in spherical globules while highly charged chains (67% and 92%) are fully extended. End-to-end distances and contour lengths of the extended chains were measured. Statistical analysis shows that the persistence length of these chains depends on the surface where they adsorb. On lipid bilayers, highly ordered monolayers are formed upon increase of the proportion of cationic phospholipids. These results show that highly charged PSS chains behave in a similar manner than the stiffer, hydrophilic DNA when adsorbed on surfaces. It could lead to the design of new types of nanostructured surfaces using polyelectrolyte molecules synthesized with specific properties.
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Affiliation(s)
- Axel Gromer
- Institut Charles Sadron CNRS - UPR 22 23, rue du Loess BP 84047, 67034 Strasbourg Cedex 2, France
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47
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Bordi F, Cametti C, Sennato S, Truzzolillo D. Strong repulsive interactions in polyelectrolyte-liposome clusters close to the isoelectric point: a sign of an arrested state. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:061403. [PMID: 18233846 DOI: 10.1103/physreve.76.061403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 09/19/2007] [Indexed: 05/25/2023]
Abstract
Charged colloidal particles whose interacting potential is governed by a short-range attraction and a long-range screened electrostatic repulsion contributions form aggregates whose shape, size, and overall charge are sensitively dependent on the balance between attraction and repulsion. In some cases, this class of colloidal systems shows an equilibrium cluster phase, where particles associate and dissociate reversibly into clusters. When the aggregation of the charged particles is induced by adding an oppositely charged polyion, very close to the isoelectric condition, the interaggregate interactions become very strong and a dynamical arrested state seems to occur. We provide some experimental evidences of this structural arrest in a colloid system composed by vesicles built up by a cationic lipid stuck together by an oppositely charged linear polyion, by means of the combined use of static and dynamic light scattering technique complemented by laser Doppler electrophoretic measurements. Our results show that the second virial coefficient, which is related to the potential of mean force between two adjacent aggregates, markedly increases in the vicinity of the isoelectric point. We interpret this increase as a print of strong interparticle interactions, yielding to a dynamical arrested state via cluster growth.
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Affiliation(s)
- F Bordi
- Dipartimento di Fisica, Universita' di Roma La Sapienza, Piazzale A. Moro 2, Rome, Italy
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48
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Pastré D, Hamon L, Mechulam A, Sorel I, Baconnais S, Curmi PA, Le Cam E, Piétrement O. Atomic Force Microscopy Imaging of DNA under Macromolecular Crowding Conditions. Biomacromolecules 2007; 8:3712-7. [DOI: 10.1021/bm700856u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Pastré
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Loïc Hamon
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Alain Mechulam
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Isabelle Sorel
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Sonia Baconnais
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Patrick A. Curmi
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Eric Le Cam
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
| | - Olivier Piétrement
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM U829/Université d’Evry EA3637, Rue du Père Jarlan, 91025 Evry Cedex, France, CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, F-94805, France, and Université Paris Sud, Villejuif, F-94805, France
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49
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Rahman MM, Yasuda H, Katsura S, Mizuno A. Covalent Binding and Conformational Change of pUC19 DNA by Rhodium (II) Metal Complex. J Biomol Struct Dyn 2007; 24:553-60. [PMID: 17508777 DOI: 10.1080/07391102.2007.10507144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Binding of Rhodium (II) acetate [Rh(2)(O(2)CCH(3))(4)] (Rh1) compound with plasmid pUC19 DNA has been studied using different molar ratio of Rh1. After incubation for 24hr at 37 degrees C, binding of the Rh1 to pUC19 DNA was confirmed by agarose gel electrophoresis. The electrophoretic results indicated the slower migration speed for the linearized pUC19 DNA. Conformation change of the DNA after Rh1 binding was also indicated at higher molar ratio of Rh1. The atomic force microscopy images showed that the Rh1 induced the conformation change to unwind pUC19 DNA. The Rh1-DNA complexes are observed very stable due to covalent bond. This study clearly demonstrates that [Rh(2)(O(2)CCH(3))(4)] reacts with pUC19 DNA and covalently binds to be stable Rh1-pUC19 DNA as interstrand adducts.
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Affiliation(s)
- Md Masudur Rahman
- Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan
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50
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Jiang Y, Ke C, Mieczkowski PA, Marszalek PE. Detecting ultraviolet damage in single DNA molecules by atomic force microscopy. Biophys J 2007; 93:1758-67. [PMID: 17483180 PMCID: PMC1948057 DOI: 10.1529/biophysj.107.108209] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report detection and quantification of ultraviolet (UV) damage in DNA at a single molecule level by atomic force microscopy (AFM). By combining the supercoiled plasmid relaxation assay with AFM imaging, we find that high doses of medium wave ultraviolet (UVB) and short wave ultraviolet (UVC) light not only produce cyclobutane pyrimidine dimers (CPDs) as reported but also cause significant DNA degradation. Specifically, 12.5 kJ/m(2) of UVC and 165 kJ/m(2) of UVB directly relax 95% and 78% of pUC18 supercoiled plasmids, respectively. We also use a novel combination of the supercoiled plasmid assay with T4 Endonuclease V treatment of irradiated plasmids and AFM imaging of their relaxation to detect damage caused by low UVB doses, which on average produced approximately 0.5 CPD per single plasmid. We find that at very low UVB doses, the relationship between the number of CPDs and UVB dose is almost linear, with 4.4 CPDs produced per Mbp per J/m(2) of UVB radiation. We verified these AFM results by agarose gel electrophoresis separation of UV-irradiated and T4 Endonuclease V treated plasmids. Our AFM and gel electrophoresis results are consistent with the previous result obtained using other traditional DNA damage detection methods. We also show that damage detection assay sensitivity increases with plasmid size. In addition, we used photolyase to mark the sites of UV lesions in supercoiled plasmids for detection and quantification by AFM, and these results were found to be consistent with the results obtained by the plasmid relaxation assay. Our results suggest that AFM can supplement traditional methods for high resolution measurements of UV damage to DNA.
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Affiliation(s)
- Yong Jiang
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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