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Barinov NA, Ivanov DA, Dubrovin EV, Klinov DV. Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface. Int J Biol Macromol 2024; 267:131630. [PMID: 38631581 DOI: 10.1016/j.ijbiomac.2024.131630] [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: 01/14/2024] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.
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Affiliation(s)
- Nikolay A Barinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France
| | - Evgeniy V Dubrovin
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Dmitry V Klinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation.
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Dubrovin EV. Atomic force microscopy-based approaches for single-molecule investigation of nucleic acid- protein complexes. Biophys Rev 2023; 15:1015-1033. [PMID: 37974971 PMCID: PMC10643717 DOI: 10.1007/s12551-023-01111-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023] Open
Abstract
The interaction of nucleic acids with proteins plays an important role in many fundamental biological processes in living cells, including replication, transcription, and translation. Therefore, understanding nucleic acid-protein interaction is of high relevance in many areas of biology, medicine and technology. During almost four decades of its existence atomic force microscopy (AFM) accumulated a significant experience in investigation of biological molecules at a single-molecule level. AFM has become a powerful tool of molecular biology and biophysics providing unique information about properties, structure, and functioning of biomolecules. Despite a great variety of nucleic acid-protein systems under AFM investigations, there are a number of typical approaches for such studies. This review is devoted to the analysis of the typical AFM-based approaches of investigation of DNA (RNA)-protein complexes with a major focus on transcription studies. The basic strategies of AFM analysis of nucleic acid-protein complexes including investigation of the products of DNA-protein reactions and real-time dynamics of DNA-protein interaction are categorized and described by the example of the most relevant research studies. The described approaches and protocols have many universal features and, therefore, are applicable for future AFM studies of various nucleic acid-protein systems.
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Affiliation(s)
- Evgeniy V. Dubrovin
- Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny, 141700 Russian Federation
- Sirius University of Science and Technology, Olimpiyskiy Ave 1, Township Sirius, Krasnodar Region, 354349 Russia
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Dubrovin EV, Barinov NA, Klinov DV. Visualization of G-Quadruplexes, i-Motifs and Their Associates. Acta Naturae 2022; 14:4-18. [PMID: 36348720 PMCID: PMC9611856 DOI: 10.32607/actanaturae.11705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/13/2022] [Indexed: 09/07/2024] Open
Abstract
The non-canonical structures formed by G- or C-rich DNA regions, such as quadruplexes and i-motifs, as well as their associates, have recently been attracting increasing attention both because of the arguments in favor of their existence in vivo and their potential application in nanobiotechnology. When studying the structure and properties of non-canonical forms of DNA, as well as when controlling the artificially created architectures based on them, visualization plays an important role. This review analyzes the methods used to visualize quadruplexes, i-motifs, and their associates with high spatial resolution: fluorescence microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). The key approaches to preparing specimens for the visualization of this type of structures are presented. Examples of visualization of non-canonical DNA structures having various morphologies, such as G-wires, G-loops, as well as individual quadruplexes, i-motifs and their associates, are considered. The potential for using AFM for visualizing non-canonical DNA structures is demonstrated.
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Affiliation(s)
- E. V. Dubrovin
- M.V. Lomonosov Moscow State University, Faculty of Physics, Moscow, 119991 Russia
| | - N. A. Barinov
- M.V. Lomonosov Moscow State University, Faculty of Physics, Moscow, 119991 Russia
| | - D. V. Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435 Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, 117198 Russia
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Dubrovin EV, Klinov DV. Atomic Force Microscopy of Biopolymers on Graphite Surfaces. POLYMER SCIENCE SERIES A 2021. [DOI: 10.1134/s0965545x2106002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Barinov NA, Tolstova AP, Bersenev EA, Ivanov DA, Dubrovin EV, Klinov DV. Molecular patterns of oligopeptide hydrocarbons on graphite. Colloids Surf B Biointerfaces 2021; 206:111921. [PMID: 34157520 DOI: 10.1016/j.colsurfb.2021.111921] [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] [Received: 09/08/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Graphitic materials including graphene, carbon nanotubes and fullerenes, are promising for use in nanotechnology and biomedicine. Non-covalent functionalization by peptides and other organic molecules allows changing the properties of graphitic surfaces in a controlled manner and represents a big potential for fundamental research and applications. Recently described oligopeptide-hydrocarbon derivative N,N'-(decane-1,10-diyl)bis(tetraglycineamide) (GM) is highly prospective for the development of graphitic interfaces in biosensor application as well as in structural biology for improving the quality of high-resolution atomic force microscopy (AFM) visualization of individual biomacromolecules. However, molecular organization of GM on graphitic surfaces is still unknown. In this work, the molecular model of GM at the water/highly oriented pyrolytic graphite (HOPG) interface has been developed basing on the high-resolution AFM and full-atom molecular modeling data. This model explains two periodicities observed in AFM images by GM self-assembly on a HOPG surface with formation of the stacks with the lateral shifts. The obtained results reveal the particular patterns and dynamics of GM molecules adsorbed on graphite and unravel the puzzle of peptide self-assembly on graphitic surfaces.
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Affiliation(s)
- Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation
| | - Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Vavilova 32, 119991, Moscow, Russian Federation
| | - Egor A Bersenev
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse-IS2M, CNRS UMR 7361, 15, rue Jean Starcky, F-68057 Mulhouse, France
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation.
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Prokhorov VV, Barinov NA, Prusakov KA, Dubrovin EV, Frank-Kamenetskii MD, Klinov DV. Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations. NANO-MICRO LETTERS 2021; 13:130. [PMID: 34138333 PMCID: PMC8141082 DOI: 10.1007/s40820-021-00626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.
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Affiliation(s)
- Valery V Prokhorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russian Federation.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Kirill A Prusakov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Lomonosov Moscow State University, Leninskie gory, 1-2, Moscow, 119991, Russian Federation
| | | | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation.
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Dubrovin EV, Dadinova LA, Petoukhov MV, Soshinskaya EY, Mozhaev AA, Klinov DV, Schäffer TE, Shtykova EV, Batishchev OV. Spatial organization of Dps and DNA-Dps complexes. J Mol Biol 2021; 433:166930. [PMID: 33713674 DOI: 10.1016/j.jmb.2021.166930] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 02/04/2023]
Abstract
DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA-Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA-Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA-Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA-Dps complexes. Angle analysis has demonstrated that in DNA-Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.
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Affiliation(s)
- Evgeniy V Dubrovin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia; Lomonosov Moscow State University, Faculty of Physics, Leninskie Gory 1 bld 2, 119991 Moscow, Russia.
| | - Liubov A Dadinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Ekaterina Yu Soshinskaya
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Tilman E Schäffer
- University of Tübingen, Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, 119333 Moscow, Russia
| | - Oleg V Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
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Xiong X, Han J, Chen Y, Li S, Xiao W, Shi Q. DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment. NANOTECHNOLOGY 2021; 32:055601. [PMID: 33179606 DOI: 10.1088/1361-6528/abb507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The evolution of single-stranded DNA (ssDNA) assembly on octadecylamine (ODA) modified highly oriented pyrolytic graphite (HOPG) surface by heating and ultrasonic treatment has been studied for the first time. We have observed that DNA on the ODA coated HOPG surface underwent dramatic morphological changes as a function of heating and ultrasonic treatment. Ordered DNA firstly changed to random aggregates by heating and then changed to three-dimensional (3D) networks by ultrasonic treatment. This finding points to previously unknown factors that impact graphite-DNA interaction and opens new opportunities to control the deposition of DNA onto graphitic substrates. In this way, we built a cost-effective method to produce large-scale 3D ssDNA networks. All of these studies pave the way to understand the properties of DNA-solid interface, design novel nanomaterials, and improve the sensitivity of DNA biosensors.
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Affiliation(s)
- Xiaolu Xiong
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Junfeng Han
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yu Chen
- Institute of High Energy Physics, CAS. 19B Yuquan Road, Shijingshan District, Beijing 100081, People's Republic of China
| | - Shanshan Li
- Department of Rheumatology, China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Wende Xiao
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Qingfan Shi
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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Dubrovin EV, Schächtele M, Klinov DV, Schäffer TE. Time-Lapse Single-Biomolecule Atomic Force Microscopy Investigation on Modified Graphite in Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10027-10034. [PMID: 28850785 DOI: 10.1021/acs.langmuir.7b02220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Atomic force microscopy (AFM) of biomolecular processes at the single-molecule level can provide unique information for understanding molecular function. In AFM studies of biomolecular processes in solution, mica surfaces are predominantly used as substrates. However, owing to its high surface charge, mica may induce high local ionic strength in the vicinity of its surface, which may shift the equilibrium of studied biomolecular processes such as biopolymer adsorption or protein-DNA interaction. In the search for alternative substrates, we have investigated the behavior of adsorbed biomolecules, such as plasmid DNA and E. coli RNA polymerase σ70 subunit holoenzyme (RNAP), on highly oriented pyrolytic graphite (HOPG) surfaces modified with stearylamine and oligoglycine-hydrocarbon derivative (GM) monolayers using AFM in solution. We have demonstrated ionic-strength-dependent DNA mobility on GM HOPG and nativelike dimensions of RNAP molecules adsorbed on modified HOPG surfaces. We propose an approach to the real-time AFM investigation of transcription on stearylamine monolayers on graphite. We conclude that modified graphite allows us to study biomolecules and biomolecular processes on its surface at controlled ionic strength and may be used as a complement to mica in AFM investigations.
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Affiliation(s)
- Evgeniy V Dubrovin
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Federal Research and Clinical Center of Physical-Chemical Medicine , Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation
- Lomonosov Moscow State University , Leninskie gory 1-2, Moscow 119991, Russian Federation
| | - Marc Schächtele
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine , Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation
| | - Tilman E Schäffer
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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