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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 2024; 15:4178. [PMID: 38755200 PMCID: PMC11099156 DOI: 10.1038/s41467-024-48562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.
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Affiliation(s)
- Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Hosein Rostamian
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA.
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2
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Bairamukov VY, Kovalev RA, Ankudinov AV, Pantina RA, Fedorova ND, Bukatin AS, Grigoriev SV, Varfolomeeva EY. Alterations in the chromatin packaging, driven by transcriptional activity, revealed by AFM. Biochim Biophys Acta Gen Subj 2024; 1868:130568. [PMID: 38242181 DOI: 10.1016/j.bbagen.2024.130568] [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: 06/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND The gene expression differs in the nuclei of normal and malignant mammalian cells, and transcription is a critical initial step, which defines the difference. The mechanical properties of transcriptionally active chromatin are still poorly understood. Recently we have probed transcriptionally active chromatin of the nuclei subjected to mechanical stress, by Atomic Force Microscopy (AFM) [1]. Nonetheless, a systematic study of the phenomenon is needed. METHODS Nuclei were deformed and studied by AFM. Non-deformed nuclei were studied by fluorescence confocal microscopy. Their transcriptional activity was studied by RNA electrophoresis. RESULTS The malignant nuclei under the study were stable to deformation and assembled of 100-300 nm beads-like units, while normal cell nuclei were prone to deformation. The difference in stability to deformation of the nuclei correlated with DNA supercoiling, and transcription-depended units were responsive to supercoils breakage. The inhibitors of the topoisomerases I and II disrupted supercoiling and made the malignant nucleus prone to deformation. Cell nuclei treatment with histone deacetylase inhibitors (HDACIs) preserved the mechanical stability of deformed malignant nuclei and, at the same time, made it possible to observe chromatin decondensation up to 20-60 nm units. The AFM results were supplemented with confocal microscopy and RNA electrophoresis data. CONCLUSIONS Self-assembly of transcriptionally active chromatin and its decondensation, driven by DNA supercoiling-dependent rigidity, was visualized by AFM in the mechanically deformed nuclei. GENERAL SIGNIFICANCE We demonstrated that supercoiled DNA defines the transcription mechanics, and hypothesized the nuclear mechanics in vivo should depend on the chromatin architecture.
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Affiliation(s)
- V Yu Bairamukov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia.
| | - R A Kovalev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A V Ankudinov
- The Ioffe Physical-Technical Institute of the Russian Academy of Sciences, 26, Politekhnicheskaya, 194021 Saint Petersburg, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - N D Fedorova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A S Bukatin
- Alferov Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 8/3, Khlopina St., 194021 Saint Petersburg, Russia
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
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3
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566470. [PMID: 38014222 PMCID: PMC10680651 DOI: 10.1101/2023.11.09.566470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we developed an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrated that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacted nucleosome diffusive properties in a manner that was dependent on local chromatin density and supportive of a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Our results reveal that nuclear heterogeneity arises from both active and passive process and highlights the need to account for different organizational principals when modeling different chromatin environments.
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4
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Villaluenga JP, Cao-García FJ. Cooperative kinetics of ligand binding to linear polymers. Comput Struct Biotechnol J 2022; 20:521-533. [PMID: 35495112 PMCID: PMC9019704 DOI: 10.1016/j.csbj.2021.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022] Open
Abstract
Cooperative kinetic equation for large ligands binding to long polymers. Cooperativity in general affects binding and release rates. Appropriate counting of the available binding sites for a ligand to a linear polymer. Positive cooperativity increases polymer coverage by the ligand. Large ligand size reduces cooperativity effects.
Ligands change the chemical and mechanical properties of polymers. In particular, single strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA), modifying the ssDNA stiffness and the DNA replication rate, as recently measured with single-molecule techniques. SSB is a large ligand presenting cooperativity in some of its binding modes. We aim to develop an accurate kinetic model for the cooperative binding kinetics of large ligands. Cooperativity accounts for the changes in the affinity of a ligand to the polymer due to the presence of another bound ligand. Large ligands, attaching to several binding sites, require a detailed counting of the available binding possibilities. This counting has been done by McGhee and von Hippel to obtain the equilibrium state of the ligands-polymer complex. The same procedure allows to obtain the kinetic equations for the cooperative binding of ligands to long polymers, for all ligand sizes. Here, we also derive approximate cooperative kinetic equations in the large ligand limit, at the leading and next-to-leading orders. We found cooperativity is negligible at the leading-order, and appears at the next-to-leading order. Positive cooperativity (increased affinity) can be originated by increased binding affinity or by decreased release affinity, implying different kinetics. Nevertheless, the equilibrium state is independent of the origin of cooperativity and only depends on the overall increase in affinity. Next-to-leading approximation is found to be accurate, particularly for small cooperativity. These results allow to understand and characterize relevant ligand binding processes, as the binding kinetics of SSB to ssDNA, which has been reported to affect the DNA replication rate for several SSB-polymerase pairs.
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Affiliation(s)
- Juan P.G. Villaluenga
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Plaza de Ciencias, 1, 28040 Madrid, Spain
- Corresponding author.
| | - Francisco Javier Cao-García
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Plaza de Ciencias, 1, 28040 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Calle Faraday, 9, 28049 Madrid, Spain
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5
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Bazoni RF, Moura TA, Rocha MS. Hydroxychloroquine Exhibits a Strong Complex Interaction with DNA: Unraveling the Mechanism of Action. J Phys Chem Lett 2020; 11:9528-9534. [PMID: 33115235 DOI: 10.1021/acs.jpclett.0c02590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the past months, the use of the drug hydroxychloroquine has considerably increased in many countries, associated with a proposed treatment for the COVID-19 disease. Although there is no conclusive evidence about the efficacy of the drug for this purpose, surprisingly there are no conclusive studies in the literature concerning its mechanism of action inside cells, which is related to its interaction with nucleic acids. Here, we performed a robust characterization of the interaction between hydroxychloroquine and double-stranded DNA using single-molecule force spectroscopy and gel electrophoresis. Two different binding modes were identified, namely, minor groove binding for low drug concentrations and intercalation for high drug concentrations, and the sets of binding parameters were determined for each of these modes. Such results have unraveled in detail the molecular mechanism of action of the drug as a DNA ligand.
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Affiliation(s)
- R F Bazoni
- Departamento de Ciências Naturais, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo 29.932-540, Brazil
| | - T A Moura
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
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6
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Villaluenga JPG, Vidal J, Cao-García FJ. Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model. Phys Rev E 2020; 102:012407. [PMID: 32795076 DOI: 10.1103/physreve.102.012407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages.
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Affiliation(s)
- Juan P G Villaluenga
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Jules Vidal
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Francisco Javier Cao-García
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/Faraday, 9, 28049 Madrid, Spain
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7
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Understanding the role of hydrogen bonds in destruction of DNA by screening interactions of Flutamide anticancer drug with nucleotides bases: DFT perspective, MD simulation and free energy calculation. ADSORPTION 2019. [DOI: 10.1007/s10450-019-00179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Evaluating viscoelastic properties and membrane electrical charges of red blood cells with optical tweezers and cationic quantum dots - applications to β-thalassemia intermedia hemoglobinopathy. Colloids Surf B Biointerfaces 2019; 186:110671. [PMID: 31816460 DOI: 10.1016/j.colsurfb.2019.110671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/08/2019] [Accepted: 11/24/2019] [Indexed: 11/23/2022]
Abstract
Biomechanical and electrical properties are important to the performance and survival of red blood cells (RBCs) in the microcirculation. This study proposed and explored methodologies based on optical tweezers and cationic quantum dots (QDs) as biophotonic tools to characterize, in a complementary way, viscoelastic properties and membrane electrical charges of RBCs. The methodologies were applied to normal (HbA) and β-thalassemia intermedia (Hbβ) RBCs. The β-thalassemia intermedia disease is a hereditary hemoglobinopathy characterized by a reduction (or absence) of β-globin chains, which leads to α-globin chains precipitation. The apparent elasticity (μ) and membrane viscosity (ηm) of RBCs captured by optical tweezers were obtained in just a single experiment. Besides, the membrane electrical charges were evaluated by flow cytometry, exploring electrostatic interactions between cationic QDs, stabilized with cysteamine, with the negatively charged RBC surfaces. Results showed that Hbβ RBCs are less elastic, have a higher ηm, and presented a reduction in membrane electrical charges, when compared to HbA RBCs. Moreover, the methodologies based on optical tweezers and QDs, here proposed, showed to be capable of providing a deeper and integrated comprehension on RBC rheological and electrical changes, resulting from diverse biological conditions, such as the β-thalassemia intermedia hemoglobinopathy.
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Safari M, Parsaie H, Sameni HR, Aldaghi MR, Zarbakhsh S. Anti-Oxidative and Anti-Apoptotic Effects of Apigenin on Number of Viable and Apoptotic Blastomeres, Zona Pellucida Thickness and Hatching Rate of Mouse Embryos. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2018; 12:257-262. [PMID: 29935073 PMCID: PMC6018174 DOI: 10.22074/ijfs.2018.5392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/26/2017] [Indexed: 12/18/2022]
Abstract
Background Apigenin is a plant-derived compound belonging to the flavonoids category and bears protective effects on different cells. The aim of this study was to evaluate the effect of apigenin on the number of viable and
apoptotic blastomeres, the zona pellucida (ZP) thickness and hatching rate of pre-implantation mouse embryos exposed
to H2O2 and actinomycin D. Materials and Methods In this experimental study, 420 two-cell embryos were randomly divided into six groups:
i. Control, ii. Apigenin, iii. H2O2 , iv. Apigenin+H2O2 , v. Actinomycin D, and vi. Apigenin+Actinomycin D. The percentage of blastocysts and hatched blastocysts was calculated. Blastocyst ZP thickness was also measured. In addition, viable blastomeres quantity was counted by Hoechst and propidium iodide staining and the number of apoptotic
blastomeres was counted by TUNEL assay. Results The results of viable and apoptotic blastomeres quantity, the ZP thickness, and the percentage of blastocysts and hatched blastocysts were significantly
more favorable in the apigenin group, rather than the control
group (P<0.05). The results of the apigenin+H2O2 group were significantly more favorable than the H2O2 group
(P<0.05); and the results of apigenin+actinomycin D group were significantly more favorable than actinomycin D
group (P<0.05). Conclusion The results suggest that apigenin may protect mouse embryos against H2O2 and actinomycin D. So that
it increases the number of viable blastomeres and decreases the number of apoptotic blastomeres, which may cause
expanding the blastocysts, thinning of the ZP thickness and increasing the rate of hatching in mouse embryos.
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Affiliation(s)
- Manouchehr Safari
- Nervous System Stem Cells Research Center, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Houman Parsaie
- Nervous System Stem Cells Research Center, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamid Reza Sameni
- Nervous System Stem Cells Research Center, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohammad Reza Aldaghi
- Nervous System Stem Cells Research Center, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Sam Zarbakhsh
- Nervous System Stem Cells Research Center, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran. Electronic Address:
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10
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Sameni HR, Javadinia SS, Safari M, Tabrizi Amjad MH, Khanmohammadi N, Parsaie H, Zarbakhsh S. Effect of quercetin on the number of blastomeres, zona pellucida thickness, and hatching rate of mouse embryos exposed to actinomycin D: An experimental study. Int J Reprod Biomed 2018. [DOI: 10.29252/ijrm.16.2.101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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11
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Wang Y, van Merwyk L, Tönsing K, Walhorn V, Anselmetti D, Fernàndez-Busquets X. Biophysical characterization of the association of histones with single-stranded DNA. Biochim Biophys Acta Gen Subj 2017; 1861:2739-2749. [PMID: 28756274 DOI: 10.1016/j.bbagen.2017.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. METHODS Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. RESULTS Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. CONCLUSIONS At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. GENERAL SIGNIFICANCE In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin.
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Affiliation(s)
- Ying Wang
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Luis van Merwyk
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Katja Tönsing
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Volker Walhorn
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Barcelona Institute for Global Health (ISGlobal), Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, Barcelona 08036, Spain; Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona 08028, Spain.
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Azarhazin E, Izadyar M, Housaindokht MR. Molecular dynamic simulation and DFT study on the Drug-DNA interaction; Crocetin as an anti-cancer and DNA nanostructure model. J Biomol Struct Dyn 2017; 36:1063-1074. [PMID: 28330413 DOI: 10.1080/07391102.2017.1310060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In this research, the interaction of Crocetin as an anti-cancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of 12 base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA. Stabilizing interactions, obtained by ΔG calculations, showed that maximum and minimum interactions are related to the S1 and S3 regions, respectively. This means that the most probable van der Waals interaction site of the Dickerson B-DNA and Crocetin is located in the minor groove of DNA. Two sharp peaks at 2.55 and 1.75 Å in radial distribution functions of the PO⋯HO and NH⋯OC parts are related to new hydrogen bonds between the Crocetin and DNA in the complex which can be considered as the driving force of the anti-cancer mechanism of the Crocetin. Average values of 0.3 au and zero for the electron densities of the H⋯O bonds for DNA and complex, obtained by Quantum theory of atoms in molecules (QTAIM), means that the origin of DNA instability after complexation may be related to the H-bond denaturation by Crocetin. Finally, the evaluation of the dispersion interactions using the dispersion functional, -148.76 kcal.mol-1, confirmed the importance of the dispersion interaction in drug-DNA complex.
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Affiliation(s)
- Ebrahim Azarhazin
- a Faculty of Sciences, Department of Chemistry , Ferdowsi University of Mashhad , Mashhad , Iran
| | - Mohammad Izadyar
- a Faculty of Sciences, Department of Chemistry , Ferdowsi University of Mashhad , Mashhad , Iran
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13
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Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JPG, Ibarra B, Cao FJ. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLoS One 2017; 12:e0174830. [PMID: 28380044 PMCID: PMC5381885 DOI: 10.1371/journal.pone.0174830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/15/2017] [Indexed: 01/20/2023] Open
Abstract
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.
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Affiliation(s)
- Javier Jarillo
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - José A. Morín
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Elena Beltrán-Heredia
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Juan P. G. Villaluenga
- Departamento de Física Aplicada I. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Francisco J. Cao
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
- * E-mail:
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Silva EF, Bazoni RF, Ramos EB, Rocha MS. DNA-doxorubicin interaction: New insights and peculiarities. Biopolymers 2017; 107. [PMID: 27718222 DOI: 10.1002/bip.22998] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/25/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. This analysis has proven that the physical chemistry of such interaction can be modulated by changing the ionic strength of the surrounding buffer. In particular we have found that at low ionc strengths doxo interacts with DNA by simple intercalation (no aggregation) and/or by forming bound dimers. For high ionic strengths, otherwise, doxo-doxo self-association is enhanced, giving rise to the formation of bound doxo aggregates composed by 3 to 4 molecules along the double-helix. On the other hand, the results obtained for the persistence length of the DNA-doxo complexes is strongly force-dependent, presenting different behaviors when measured with stretching or non-stretching techniques.
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Affiliation(s)
- E F Silva
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E B Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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15
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Lima CHM, Rocha MS, Ramos EB. Unfolding DNA condensates produced by DNA-like charged depletants: A force spectroscopy study. J Chem Phys 2017; 146:054901. [DOI: 10.1063/1.4975103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Banerjee T, Banerjee S, Sett S, Ghosh S, Rakshit T, Mukhopadhyay R. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy. PLoS One 2016; 11:e0154666. [PMID: 27183010 PMCID: PMC4868319 DOI: 10.1371/journal.pone.0154666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.
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Affiliation(s)
- T. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - T. Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - R. Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
- * E-mail:
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Crisafuli FAP, da Silva LHM, Ferreira GMD, Ramos EB, Rocha MS. Depletion interactions and modulation of DNA-intercalators binding: Opposite behavior of the “neutral” polymer poly(ethylene-glycol). Biopolymers 2016; 105:227-33. [DOI: 10.1002/bip.22789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/17/2015] [Accepted: 11/22/2015] [Indexed: 11/11/2022]
Affiliation(s)
- F. A. P. Crisafuli
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - L. H. M. da Silva
- Departamento de Química; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - G. M. D. Ferreira
- Departamento de Química; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - E. B. Ramos
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - M. S. Rocha
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
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18
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Bernal WFP, Silva EF, Rocha MS. Unraveling the physical chemistry and the mixed binding modes of complex DNA ligands by single molecule stretching experiments. RSC Adv 2016. [DOI: 10.1039/c6ra22980h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this work we present a complete methodology to unravel the physical chemistry and the mixed binding modes of complex DNA ligands.
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Affiliation(s)
- W. F. P. Bernal
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - E. F. Silva
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
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19
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Wieczorek A, Rezaei N, Chan CK, Xu C, Panwar P, Brömme D, Merschrod S EF, Forde NR. Development and characterization of a eukaryotic expression system for human type II procollagen. BMC Biotechnol 2015; 15:112. [PMID: 26666739 PMCID: PMC4678704 DOI: 10.1186/s12896-015-0228-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Triple helical collagens are the most abundant structural protein in vertebrates and are widely used as biomaterials for a variety of applications including drug delivery and cellular and tissue engineering. In these applications, the mechanics of this hierarchically structured protein play a key role, as does its chemical composition. To facilitate investigation into how gene mutations of collagen lead to disease as well as the rational development of tunable mechanical and chemical properties of this full-length protein, production of recombinant expressed protein is required. Results Here, we present a human type II procollagen expression system that produces full-length procollagen utilizing a previously characterized human fibrosarcoma cell line for production. The system exploits a non-covalently linked fluorescence readout for gene expression to facilitate screening of cell lines. Biochemical and biophysical characterization of the secreted, purified protein are used to demonstrate the proper formation and function of the protein. Assays to demonstrate fidelity include proteolytic digestion, mass spectrometric sequence and posttranslational composition analysis, circular dichroism spectroscopy, single-molecule stretching with optical tweezers, atomic-force microscopy imaging of fibril assembly, and transmission electron microscopy imaging of self-assembled fibrils. Conclusions Using a mammalian expression system, we produced full-length recombinant human type II procollagen. The integrity of the collagen preparation was verified by various structural and degradation assays. This system provides a platform from which to explore new directions in collagen manipulation. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0228-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Wieczorek
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Naghmeh Rezaei
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Clara K Chan
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.,Present Address: Department of Bioengineering, University of California at Los Angeles, Los Angeles, USA
| | - Chuan Xu
- Department of Chemistry, Memorial University, St. John's, NL, A1B 3X7, Canada.,Present Address: Green Innovative Technologies R&D Centre Ltd, Vancouver, Canada
| | - Preety Panwar
- Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Dieter Brömme
- Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Biochemistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Erika F Merschrod S
- Department of Chemistry, Memorial University, St. John's, NL, A1B 3X7, Canada
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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20
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Abstract
We have investigated the interaction between the native neutral β-cyclodextrin (CD) and the DNA molecule by performing single-molecule stretching experiments with optical tweezers. In particular, we have monitored the changes of the mechanical properties of the CD-DNA complexes as a function of the CD concentration in the sample. By using a quenched disorder statistical model, we were also capable to extract important physicochemical information (equilibrium binding constants, cooperativity degree) of such interaction from the mechanical data. In addition, we have found that the interaction occurs by two different mechanisms, first with the formation of relatively large CD clusters along the double helix, which thereafter can locally denature the DNA molecule by forming hydrogen bonds with the base pairs that eventually flip out. A prediction of our quenched disorder model was that cooperativity could be controlled by adjusting the surface charge of β-CD molecules. This prediction is confirmed in the present work.
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Affiliation(s)
- P S Alves
- Departamento de Física, Universidade Federal de Minas Gerais , Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - O N Mesquita
- Departamento de Física, Universidade Federal de Minas Gerais , Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa , Av. P. H. Rolfs s/n, Viçosa, Minas Gerais 36570-900, Brazil
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21
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Suei S, Raudsepp A, Kent LM, Keen SAJ, Filichev VV, Williams MAK. DNA visualization in single molecule studies carried out with optical tweezers: Covalent versus non-covalent attachment of fluorophores. Biochem Biophys Res Commun 2015; 466:226-31. [PMID: 26362181 DOI: 10.1016/j.bbrc.2015.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022]
Abstract
In this study, we investigated the use of the covalent attachment of fluorescent dyes to double-stranded DNA (dsDNA) stretched between particles using optical tweezers (OT) and compared the mechanical properties of the covalently-functionalized chain to that of unmodified DNA and to DNA bound to a previously uncharacterized groove-binder, SYBR-gold. Modified DNA species were obtained by covalently linking azide-functionalized organic fluorophores onto the backbone of DNA chains via the alkyne moieties of modified bases that were incorporated during PCR. These DNA molecules were then constructed into dumbbells by attaching polystyrene particles to the respective chain ends via biotin or digoxigenin handles that had been pre-attached to the PCR primers which formed the ends of the synthesized molecule. Using the optical tweezers, the DNA was stretched by separating the two optically trapped polystyrene particles. Displacements of the particles were measured in 3D using an interpolation-based normalized cross-correlation method and force-extension curves were calculated and fitted to the worm-like chain model to parameterize the mechanical properties of the DNA. Results showed that both the contour and persistence length of the covalently-modified dsDNAs were indistinguishable from that of the unmodified dsDNA, whereas SYBR-gold binding perturbed the contour length of the chain in a force-dependent manner.
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Affiliation(s)
- Sandy Suei
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Allan Raudsepp
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Lisa M Kent
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; Riddet Institute, Massey University, Palmerston North 4442, New Zealand
| | - Stephen A J Keen
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Martin A K Williams
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand; Riddet Institute, Massey University, Palmerston North 4442, New Zealand.
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22
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Bazoni RF, Lima CHM, Ramos EB, Rocha MS. Force-dependent persistence length of DNA-intercalator complexes measured in single molecule stretching experiments. SOFT MATTER 2015; 11:4306-4314. [PMID: 25913936 DOI: 10.1039/c5sm00706b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
By using optical tweezers with an adjustable trap stiffness, we have performed systematic single molecule stretching experiments with two types of DNA-intercalator complexes, in order to investigate the effects of the maximum applied forces on the mechanical response of such complexes. We have explicitly shown that even in the low-force entropic regime the persistence length of the DNA-intercalator complexes is strongly force-dependent, although such behavior is not exhibited by bare DNA molecules. We discuss the possible physicochemical effects that can lead to such results. In particular, we propose that the stretching force can promote partial denaturation on the highly distorted double-helix of the DNA-intercalator complexes, which interfere strongly in the measured values of the persistence length.
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Affiliation(s)
- R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais, Brazil.
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23
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Rocha MS. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments. Integr Biol (Camb) 2015; 7:967-86. [DOI: 10.1039/c5ib00127g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review we focus on the idea of establishing connections between the mechanical properties of DNA–ligand complexes and the physical chemistry of DNA–ligand interactions.
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Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
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24
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Dubrovin EV, Speller S, Yaminsky IV. Statistical analysis of molecular nanotemplate driven DNA adsorption on graphite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15423-15432. [PMID: 25470069 DOI: 10.1021/la5041773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, we have studied the conformation of DNA molecules aligned on the nanotemplates of octadecylamine, stearyl alcohol, and stearic acid on highly oriented pyrolytic graphite (HOPG). For this purpose, fluctuations of contours of adsorbed biopolymers obtained from atomic force microscopy (AFM) images were analyzed using the wormlike chain model. Moreover, the conformations of adsorbed biopolymer molecules were characterized by the analysis of the scaling exponent ν, which relates the mean squared end-to-end distance and contour length of the polymer. During adsorption on octadecylamine and stearyl alcohol nanotemplates, DNA forms straight segments, which order along crystallographic axes of graphite. In this case, the conformation of DNA molecules can be described using two different length scales. On a large length scale (at contour lengths l > 200-400 nm), aligned DNA molecules have either 2D compact globule or partially relaxed 2D conformation, whereas on a short length scale (at l ≤ 200-400 nm) their conformation is close to that of rigid rods. The latter type of conformation can be also assigned to DNA adsorbed on a stearic acid nanotemplate. The different conformation of DNA molecules observed on the studied monolayers is connected with the different DNA-nanotemplate interactions associated with the nature of the functional group of the alkane derivative in the nanotemplate (amine, alcohol, or acid). The persistence length of λ-DNA adsorbed on octadecylamine nanotemplates is 31 ± 2 nm indicating the loss of DNA rigidity in comparison with its native state. Similar values of the persistence length (34 ± 2 nm) obtained for 24-times shorter DNA molecules adsorbed on an octadecylamine nanotemplate demonstrate that this rigidity change does not depend on biopolymer length. Possible reasons for the reduction of DNA persistence length are discussed in view of the internal DNA structure and DNA-surface interaction.
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Affiliation(s)
- E V Dubrovin
- Chair of Physics of Polymers and Crystals, Faculty of Physics, M. V. Lomonosov Moscow State University , Leninskie gory, 1/2, Moscow 119991, Russia
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25
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Characterizing the interaction between DNA and GelRed fluorescent stain. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 44:1-7. [DOI: 10.1007/s00249-014-0995-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/13/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
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Rocha MS, Cavalcante AG, Silva R, Ramos EB. On the effects of intercalators in DNA condensation: a force spectroscopy and gel electrophoresis study. J Phys Chem B 2014; 118:4832-9. [PMID: 24720756 DOI: 10.1021/jp501589d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we have characterized the effects of the intercalator ethidium bromide (EtBr) on the DNA condensation process by using force spectroscopy and gel electrophoresis. We have tested two condensing agents: spermine (spm(4+)), a tetravalent cationic amine which promotes cation-induced DNA condensation, and poly(ethylene glycol) (PEG), a neutral polymer which promotes DNA ψ-condensation. Two different types of experiments were performed. In the first type, bare DNA molecules disperse in solution are first treated with EtBr for intercalation, and then the condensing agent is added to the sample with the purpose of verifying the effects of the intercalator in hindering DNA condensation. In the second experiment type, the bare DNA molecules are first condensed, and then the intercalator is added to the sample in order to verify its influence on the previously condensed DNA. The results obtained with the two different experimental techniques used agree very well, indicating that previously intercalated EtBr can hinder both cation-induced and ψ-condensation, being more efficient in the first case. On the other hand, EtBr has little effect on the previously formed cation-induced condensates, but is efficient in unfolding the ψ-condensates.
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Affiliation(s)
- M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa , Viçosa, Minas Gerais, 36570-000, Brazil
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Reis LA, Ramos EB, Rocha MS. DNA Interaction with Diaminobenzidine Studied with Optical Tweezers and Dynamic Light Scattering. J Phys Chem B 2013; 117:14345-50. [DOI: 10.1021/jp409544e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. A. Reis
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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28
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Silva EF, Ramos EB, Rocha MS. DNA Interaction with Hoechst 33258: Stretching Experiments Decouple the Different Binding Modes. J Phys Chem B 2013; 117:7292-6. [DOI: 10.1021/jp403945e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. F. Silva
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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