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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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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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Abstract
Atomic force and transmission electron microscopies (AFM/TEM) are powerful tools to analyze RNA-based nanostructures. While cryo-TEM analysis allows the determination of near-atomic resolution structures of large RNA complexes, this chapter intends to present how RNA nanostructures can be analyzed at room temperature on surfaces. Indeed, TEM and AFM analyses permit the conformation of a large population of individual molecular structures to be observed, providing a statistical basis for the variability of these nanostructures within the population. Nevertheless, if double-stranded DNA molecular imaging has been described extensively, only a few investigations of single-stranded DNA and RNA filaments have been conducted so far. Indeed, technique for spreading and adsorption of ss-molecules on AFM surfaces or TEM grids is a crucial step to avoid disturbing RNA conformation on the surface. In this chapter, we present a specific method to analyze RNA assemblies and RNA-protein complexes for molecular microscopies.
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Affiliation(s)
- Olivier Piétrement
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne, Dijon Cedex, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-Sur-Yvette, France
- Université de Paris, Paris, France
| | - Christophe Lavelle
- Museum National d'Histoire Naturelle, CNRS UMR 7196/INSERM U1154, Paris, France.
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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: 38] [Impact Index Per Article: 7.6] [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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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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Nie H, Huang H, Li W, Yang T. A Label-free Time-resolved Luminescent Platform for Sensitive Endonuclease V Detection Based on Exonuclease III Regulated DNA-Tb 3+ Luminescence. ANAL SCI 2016; 32:1245-1250. [PMID: 27829633 DOI: 10.2116/analsci.32.1245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Endonuclease V (EndoV) plays the important role of nucleotide excision repair (NER) in the maintenance of genomic stability. Highly sensitive detection of EndoV was achieved through an oligonucleotides sensitizing Tb3+ luminescent technique. We found that although both guanine-rich (G-rich) single-stranded DNA and dGMP could enhance the time-resolved luminescence of Tb3+, their efficiencies of enhancement were considerably different. Employing such interesting phenomenon, a label-free and time-resolved luminescent strategy for the sensitive detection of EndoV activity was developed based on DNA-enhanced time-resolved luminescence (TRL) of Tb3+. The EndoV was used to cut off the deoxyinosine site (dI) and convert the 3'-protruding termini to a recessed end, and Exonuclease III (Exo III) was used to enhance the signal contrast via digestion of G-rich DNA to dNTP. Combining with the natural advantages of the TRL, the proposed method exhibited a good linear response to EndoV ranging from 0.005 to 0.4 U/mL, with a low limit of detection of 0.005 U/mL.
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Affiliation(s)
- Huaijun Nie
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Key Laboratory of Drinking Water Source Safety Control, Shenzhen Research Academy of Environmental Sciences
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Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M, Salomé L, Tardin C. Probing a label-free local bend in DNA by single molecule tethered particle motion. Nucleic Acids Res 2015; 43:e72. [PMID: 25765645 PMCID: PMC4477641 DOI: 10.1093/nar/gkv201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/01/2015] [Indexed: 02/07/2023] Open
Abstract
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
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Affiliation(s)
- Annaël Brunet
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Sébastien Chevalier
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Nicolas Destainville
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Manoel Manghi
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Philippe Rousseau
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Maya Salhi
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Laurence Salomé
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Catherine Tardin
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
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Pang D, Thierry AR, Dritschilo A. DNA studies using atomic force microscopy: capabilities for measurement of short DNA fragments. Front Mol Biosci 2015; 2:1. [PMID: 25988169 PMCID: PMC4429637 DOI: 10.3389/fmolb.2015.00001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/02/2015] [Indexed: 01/05/2023] Open
Abstract
Short DNA fragments, resulting from ionizing radiation induced DNA double strand breaks (DSBs), or released from cells as a result of physiological processes and circulating in the blood stream, may play important roles in cellular function and potentially in disease diagnosis and early intervention. The size distribution of DNA fragments contribute to knowledge of underlining biological processes. Traditional techniques used in radiation biology for DNA fragment size measurements lack the resolution to quantify short DNA fragments. For the measurement of cell-free circulating DNA (ccfDNA), real time quantitative Polymerase Chain Reaction (q-PCR) provides quantification of DNA fragment sizes, concentration and specific gene mutation. A complementary approach, the imaging-based technique using Atomic Force Microscopy (AFM) provides direct visualization and measurement of individual DNA fragments. In this review, we summarize and discuss the application of AFM-based measurements of DNA fragment sizes. Imaging of broken plasmid DNA, as a result of exposure to ionizing radiation, as well as ccfDNA in clinical specimens offer an innovative approach for studies of short DNA fragments and their biological functions.
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Affiliation(s)
- Dalong Pang
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherche Médicale U896 Montpellier, France
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
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Jiang XQ, Guo SM, Zhang M, Zhou M, Ye BC. DNA-hosted Hoechst dyes: application for label-free fluorescent monitoring of endonuclease activity and inhibition. Analyst 2014; 139:5682-5. [DOI: 10.1039/c4an01373e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI. Sci Rep 2014; 4:5897. [PMID: 25077775 PMCID: PMC4116625 DOI: 10.1038/srep05897] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 11/09/2022] Open
Abstract
DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic force microscopy (AFM) and magnetic tweezers (MT). With Ca(2+) substituted for the normal enzyme cofactor Mg(2+) and enzyme concentration below the critical concentration of 6 units/mL, AFM images of DNA-BspMI complex show that the number of binding and looping events increases with enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation concentration represents more than 8% of the total BspMI-DNA complexes directly observed in AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme concentration is higher than its saturation valueand the complex is incubated for a long time (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at less than saturation concentration has a peak at about 3 pN, which is lower than the force required to open additional loops due to enzyme aggregation at higher than saturation concentration (>6 pN).
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Yamazaki T, Aiba Y, Yasuda K, Sakai Y, Yamanaka Y, Kuzuya A, Ohya Y, Komiyama M. Clear-cut observation of PNA invasion using nanomechanical DNA origami devices. Chem Commun (Camb) 2013; 48:11361-3. [PMID: 23073563 DOI: 10.1039/c2cc36358e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Invasive binding event of PNA into DNA duplex was clearly observed both by atomic force microscope (AFM) imaging and electrophoretic mobility shift assay (EMSA) with the aid of nanomechanical DNA origami devices as 'single-molecule' visual probes, showing their potential as universal platform for the analysis of PNA invasion.
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Affiliation(s)
- Takahiro Yamazaki
- RCAST, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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Ahmadi F, Jamali N. Study of DNA-Deltamethrin Binding by Voltammetry, Competitive Fluorescence, Thermal Denaturation, Circular Dichroism, and Atomic Force Microscopy Techniques. DNA Cell Biol 2012; 31:811-9. [DOI: 10.1089/dna.2011.1442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Farhad Ahmadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
| | - Nasibeh Jamali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
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15
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Deng J, Jin Y, Wang L, Chen G, Zhang C. Sensitive detection of endonuclease activity and inhibition using gold nanorods. Biosens Bioelectron 2012; 34:144-50. [DOI: 10.1016/j.bios.2012.01.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/22/2012] [Accepted: 01/27/2012] [Indexed: 12/30/2022]
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16
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Deng J, Jin Y, Chen G, Wang L. Label-free fluorescent assay for real-time monitoring site-specific DNA cleavage by EcoRI endonuclease. Analyst 2012; 137:1713-7. [PMID: 22354164 DOI: 10.1039/c2an16287c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA cleavage reaction catalyzed by nucleases is essential in many important biological processes and medicinal chemistry. Therefore, it is important to develop reliable and facile methods to assay nuclease activity. With this goal in mind, we report a fluorescent assay for label-free, facile, and real-time monitoring of DNA cleavage by EcoRI endonuclease using SYBR Green I (SGI) as a signal probe. The fluorescence of SGI dramatically increased when the free SGI was mixed with double-stranded DNA (dsDNA) substrate. Upon interacting with EcoRI, which cleaves the dsDNA into small fragments, the weakened interaction between SGI and the shortened DNA fragments caused a decrease in fluorescence of SGI. EcoRI-DNA interaction was real-time studied by monitoring fluorescence change with the prolonging of interaction time. The important kinetic parameters, including Michaelis-Menten constant (K(M)) and maximum initial velocity (V(max)), were accurately calculated, which is consistent with previously reported studies. Site-specific DNA cleavage by EcoRI endonuclease has also been verified by gel electrophoresis analysis, which indicated that this method is a simple and effective approach to assay DNA cleavage reaction. Specificity investigation demonstrated that EcoRI-DNA interactions can be studied with high selectivity. Compared with previously reported methods, this approach is selective, simple, convenient and cost-efficient without any labeling of the probe or of the target.
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Affiliation(s)
- Jing Deng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemistry Engineering, Shaanxi Normal University, Xi'an, 710062, China
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Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012; 135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A 2012; 109:1856-61. [PMID: 22308447 DOI: 10.1073/pnas.1120063109] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. We have proposed a model where repair proteins containing redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in finding lesions. In this model, the population of sites to search is reduced by a localization of protein in the vicinity of lesions. Here, we examine this model using single-molecule atomic force microscopy (AFM). XPD, a 5'-3' helicase involved in nucleotide excision repair, contains a [4Fe-4S] cluster and exhibits a DNA-bound redox potential that is physiologically relevant. In AFM studies, we observe the redistribution of XPD onto kilobase DNA strands containing a single base mismatch, which is not a specific substrate for XPD but, like a lesion, inhibits CT. We further provide evidence for DNA-mediated signaling between XPD and Endonuclease III (EndoIII), a base excision repair glycosylase that also contains a [4Fe-4S] cluster. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto the mismatched strand. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between different repair proteins in their search for damage in the genome.
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19
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Romano CA, Sontz PA, Barton JK. Mutants of the base excision repair glycosylase, endonuclease III: DNA charge transport as a first step in lesion detection. Biochemistry 2011; 50:6133-45. [PMID: 21651304 DOI: 10.1021/bi2003179] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Endonuclease III (EndoIII) is a base excision repair glycosylase that targets damaged pyrimidines and contains a [4Fe-4S] cluster. We have proposed a model where BER proteins that contain redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in the detection of DNA lesions. Here, several mutants of EndoIII were prepared to probe their efficiency of DNA/protein charge transport. Cyclic voltammetry experiments on DNA-modified electrodes show that aromatic residues F30, Y55, Y75, and Y82 help mediate charge transport between DNA and the [4Fe-4S] cluster. On the basis of circular dichroism studies to measure protein stability, mutations at residues W178 and Y185 are found to destabilize the protein; these residues may function to protect the [4Fe-4S] cluster. Atomic force microscopy studies furthermore reveal a correlation in the ability of mutants to carry out protein/DNA CT and their ability to relocalize onto DNA strands containing a single base mismatch; EndoIII mutants that are defective in carrying out DNA/protein CT do not redistribute onto mismatch-containing strands, consistent with our model. These results demonstrate a link between the ability of the repair protein to carry out DNA CT and its ability to relocalize near lesions, thus pointing to DNA CT as a key first step in the detection of base damage in the genome.
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Affiliation(s)
- Christine A Romano
- Division of Chemistry and Chemical Engineering, California Institute of Technolog, Pasadena, California 91125, USA
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20
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Wu N, Zhou X, Czajkowsky DM, Ye M, Zeng D, Fu Y, Fan C, Hu J, Li B. In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami. NANOSCALE 2011; 3:2481-2484. [PMID: 21526259 DOI: 10.1039/c1nr10181a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Individual biomolecular binding events were recorded in situ by combining time-lapse atomic force microscopy and DNA origami. Single streptavidin molecules bound to specifically biotinyated DNA origami were simply counted as a function of time to obtain a direct measure of the binding rate.
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Affiliation(s)
- Na Wu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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21
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Xiao Z, Cao L, Zhu D, Lu Z. Atomic force microscopy studies on circular DNA structural changes by vincristine and aspirin. Methods Mol Biol 2011; 736:425-435. [PMID: 21660742 DOI: 10.1007/978-1-61779-105-5_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this chapter, we have presented materials and methods to study the interaction between DNA and small molecule drugs by AFM. The detailed AFM imaging of the circular DNA after incubation with -various concentrations of vincristine and aspirin have been demonstrated. The immobilization of DNA fragments on mica surface as well as the force between tip and sample plays an important role for successful imaging of DNA-drug complexes. How to quantitatively describe the conformations and structures of circular DNA molecules and their changes is also introduced. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.
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Affiliation(s)
- Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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22
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Liu Z, Tan S, Zu Y, Fu Y, Meng R, Xing Z. The interactions of cisplatin and DNA studied by atomic force microscopy. Micron 2010; 41:833-9. [DOI: 10.1016/j.micron.2010.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
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23
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Camacho A, Salas M. DNA bending and looping in the transcriptional control of bacteriophage phi29. FEMS Microbiol Rev 2010; 34:828-41. [PMID: 20412311 DOI: 10.1111/j.1574-6976.2010.00219.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Recent studies on the regulation of phage phi29 gene expression reveal new ways to accomplish the processes required for the orderly gene expression in prokaryotic systems. These studies revealed a novel DNA-binding domain in the phage main transcriptional regulator and the nature and dynamics of the multimeric DNA-protein complex responsible for the switch from early to late gene expression. This review describes the features of the regulatory mechanism that leads to the simultaneous activation and repression of transcription, and discusses it in the context of the role of the topological modification of the DNA carried out by two phage-encoded proteins working synergistically with the DNA.
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Affiliation(s)
- Ana Camacho
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
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24
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Pastré D, Hamon L, Sorel I, Le Cam E, Curmi PA, Piétrement O. Specific DNA-protein interactions on mica investigated by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:2618-2623. [PMID: 19791748 DOI: 10.1021/la902727b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA processing by site-specific proteins on surface remains a challenging issue for nanobioscience applications and, in particular, for high-resolution imaging by atomic force microscopy (AFM). To obtain high-resolution conditions, mica, an atomically flat and negatively charged surface, is generally used. However, even though many specific DNA/protein interactions have already been observed by AFM, little is known about DNA accessibility to specific enzymes on mica. Here we measured the accessibility of adsorbed DNA to restriction endonucleases (EcoRI and EcoRV) using AFM. By increasing the concentration of divalent or multivalent salts, DNA adsorption on mica switches from weak to strong binding. Interestingly, while the accessibility of strongly bound DNA was inhibited, loosely adsorbed DNA was efficiently cleaved on mica. This result opens new perspective to study DNA/protein interaction by AFM or to modify specifically DNA on surface.
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Affiliation(s)
- David Pastré
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM/UEVE U829, Université d'Evry val d'Essonne, Evry F-91025, France.
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25
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Hamon L, Curmi PA, Pastré D. High-resolution imaging of microtubules and cytoskeleton structures by atomic force microscopy. Methods Cell Biol 2010; 95:157-74. [PMID: 20466134 DOI: 10.1016/s0091-679x(10)95009-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Atomic force microscopy (AFM), which combines a nanometer-scale resolution and a unique capacity to image biomolecular interactions in liquid environment, is a promising tool for the investigation of biological samples. In contrast with nucleic acids and nucleoprotein complexes, for which AFM is now of common use and participates in the recent advances in the knowledge of DNA-related biomolecular processes, AFM investigations of cytoskeleton structures and especially microtubules remain rare. The most critical step to observe biomolecules using AFM is the spreading of the biological material on a flat surface. This issue is now better documented concerning DNA but a lot remains to be done concerning microtubules. This is a prerequisite to further document this issue for a proper and large use of AFM to study cytoskeleton structures. We present here an overview of the various procedures previously used to spread microtubules on a flat surface and advance an easy-to-use and efficient experimental protocol for microtubule imaging by AFM in air. We show application of this protocol to observe intermediate structures of microtubule assembly without using any stabilizing agent and the observation of more complex systems like proteins or messenger ribonucleoprotein particles in interaction with microtubules.
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Affiliation(s)
- Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM - UEVE UMR U829, Evry 91025, France
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26
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Destainville N, Manghi M, Palmeri J. Microscopic mechanism for experimentally observed anomalous elasticity of DNA in two dimensions. Biophys J 2009; 96:4464-9. [PMID: 19486670 DOI: 10.1016/j.bpj.2009.03.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 02/26/2009] [Accepted: 03/10/2009] [Indexed: 11/27/2022] Open
Abstract
By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair denaturation, we demonstrate that small denaturation bubbles lead to anomalies in the flexibility of DNA at the nanometric scale, when confined in two dimensions (2D), as reported in atomic-force microscopy experiments. Our model yields very good fits to experimental data and quantitative predictions that can be tested experimentally. Although such anomalies exist when DNA fluctuates freely in three dimensions (3D), they are too weak to be detected. Interactions between bases in the helical double-stranded DNA are modified by electrostatic adsorption on a 2D substrate, which facilitates local denaturation. This work reconciles the apparent discrepancy between observed 2D and 3D DNA elastic properties and points out that conclusions about the 3D properties of DNA (and its companion proteins and enzymes) do not directly follow from 2D experiments by atomic-force microscopy.
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Affiliation(s)
- Nicolas Destainville
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Physique Théorique (Institut de Recherche sur Systèmes Atomiques et Moléculaires Complexes), Toulouse, France.
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27
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van Vugt JJFA, de Jager M, Murawska M, Brehm A, van Noort J, Logie C. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS One 2009; 4:e6345. [PMID: 19626125 PMCID: PMC2710519 DOI: 10.1371/journal.pone.0006345] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 06/25/2009] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.
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Affiliation(s)
- Joke J. F. A. van Vugt
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Martijn de Jager
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Magdalena Murawska
- Institut für Molekularbiologie und Tumorforschung, University of Marburg, Marburg, Germany
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, University of Marburg, Marburg, Germany
| | - John van Noort
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Colin Logie
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands
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28
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Dorvel B, Sigalov G, Zhao Q, Comer J, Dimitrov V, Mirsaidov U, Aksimentiev A, Timp G. Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore. Nucleic Acids Res 2009; 37:4170-9. [PMID: 19433506 PMCID: PMC2709577 DOI: 10.1093/nar/gkp317] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/17/2009] [Accepted: 04/19/2009] [Indexed: 11/14/2022] Open
Abstract
Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.
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Affiliation(s)
| | | | | | | | | | | | | | - G. Timp
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA
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29
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SONG Y, WANG L, ZHAO S, LIAN W, LI Z. Disassembly of DNA-ligand on mica surface: atomic force microscopy studies. J Microsc 2009; 234:130-6. [DOI: 10.1111/j.1365-2818.2009.03154.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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30
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Hamon L, Panda D, Savarin P, Joshi V, Bernhard J, Mucher E, Mechulam A, Curmi PA, Pastré D. Mica surface promotes the assembly of cytoskeletal proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3331-3335. [PMID: 19275176 DOI: 10.1021/la8035743] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the surface-mediated polymerization of FtsZ protein, the prokaryote homologue of tubulin, by AFM. FtsZ protein can form filaments on mica whereas the bulk FtsZ concentration is orders of magnitude lower than the critical concentration. Surface polymerization is favored by a local increase in protein concentration and requires a high mobility of proteins on the surface. To generalize to other cytoskeleton protein, we also show that mica can initiate the formation of tubulin protofilaments. This study is of particular interest for studying cytoskeletal protein dynamics by AFM but also for the surface autoassembly of nanostructures.
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Affiliation(s)
- Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM/UEVE U829, Evry 91025 France.
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31
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Atomic force microscopy reveals binding of mRNA to microtubules mediated by two major mRNP proteins YB-1 and PABP. FEBS Lett 2008; 582:2875-81. [PMID: 18652827 DOI: 10.1016/j.febslet.2008.07.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 06/25/2008] [Accepted: 07/11/2008] [Indexed: 01/16/2023]
Abstract
A significant fraction of mRNAs is known to be associated in the form of mRNPs with microtubules for active transport. However, little is known about the interaction between mRNPs and microtubules and most of previous works were focused on molecular motor:microtubule interactions. Here, we have identified, via high resolution atomic force microscopy imaging, a significant binding of mRNA to microtubules mediated by two major mRNP proteins, YB-1 and PABP. This interaction with microtubules could be of critical importance for active mRNP traffic and for mRNP granule formation. A similar role may be fulfilled by other cationic mRNA partners.
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32
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Guo C, Song Y, Wang L, Sun L, Sun Y, Peng C, Liu Z, Yang T, Li Z. Atomic Force Microscopic Study of Low Temperature Induced Disassembly of RecA−dsDNA Filaments. J Phys Chem B 2008; 112:1022-7. [DOI: 10.1021/jp077233y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cunlan Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Yonghai Song
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Li Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Lanlan Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Yujing Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Chongyang Peng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Zhelin Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Tao Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
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Xiong XF, Li H, Cao EH. PIG11 protein binds to DNA in sequence-independent manner in vitro. Biochem Biophys Res Commun 2007; 358:29-34. [PMID: 17482569 DOI: 10.1016/j.bbrc.2007.04.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/17/2022]
Abstract
PIG11 (p53-induced protein 11), one of early transcriptional targets of tumor suppressor p53, was up-regulated in the induction of apoptosis or cell growth inhibition by multiple chemopreventive agents. However, its biological role remains unclear. Here, we expressed His(6)-tagged PIG11 protein in Escherichia coli and demonstrated the recombinant His(6)-tagged PIG11 protein could bind to supercoiled and relaxed closed circular plasmid DNA or linear DNA with different length using gel retardation assays in vitro. The interaction between DNA and PIG11 protein was sequence-independent and related to charge effect. The reducing thiol group in PIG11 protein was involved in the binding activity of PIG11 to DNA. Furthermore, the images of atomic force microscopy directly confirmed the binding of DNA and PIG11 protein and showed the PIG11-DNA complex formed a beads-on-a-string appearance in which PIG11 protein associated with DNA as polymer. These findings suggest that PIG11 protein may play an important role by interaction with other biological molecules in the regulation of apoptosis and provided us a novel angel of view to explore the possible function of PIG11 in vivo.
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Affiliation(s)
- Xiu-Fang Xiong
- Institute of Biophysics, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 15 Datum Road, Chaoyang District, Beijing 100101, PR China
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