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Ogawa H, Nishio T, Yoshikawa Y, Sadakane K, Kenmotsu T, Koga T, Yoshikawa K. Characteristic effect of hydroxyurea on the higher-order structure of DNA and gene expression. Sci Rep 2024; 14:13826. [PMID: 38879539 PMCID: PMC11180115 DOI: 10.1038/s41598-024-64538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024] Open
Abstract
Hydroxyurea (HU; hydroxycarbamide) is a chemotherapy medication used to treat various types of cancer and other diseases such as sickle cell anemia. HU inhibits DNA synthesis by targeting ribonucleotide reductase (RNR). Recent studies have suggested that HU also causes oxidative stress in living systems. In the present study, we investigated if HU could directly affect the activity and/or conformation of DNA. We measured in vitro gene expression in the presence of HU by adapting a cell-free luciferase assay. HU exhibited a bimodal effect on gene expression, where promotion or inhibition were observed at lower or higher concentrations (mM range), respectively. Using atomic force microscopy (AFM), the higher-order structure of DNA was revealed to be partially-thick with kinked-branching structures after HU was added. An elongated coil conformation was observed by AFM in the absence of HU. Single DNA molecules in bulk aqueous solution under fluctuating Brownian motion were imaged by fluorescence microscopy (FM). Both spring and damping constants, mechanical properties of DNA, increased when HU was added. These experimental investigations indicate that HU directly interacts with DNA and provide new insights into how HU acts as a chemotherapeutic agent and targets other diseases.
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Affiliation(s)
- Haruto Ogawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Tomoyuki Koga
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyoto, 610-0321, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan.
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, 606-8501, Japan.
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2
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Peng Y, Li D, Qiao B, Gao Z, Pu Q, Pang H, Lai X, Zhang R, Zhao X, Zhao G, Xu D, Han F, Wang Y, Ji Y, Pei H, Wu Q. Protonation-mediated DNA tile self-assembly with nuclease resistance characteristic for signal-amplified detection of microRNAs. Biosens Bioelectron 2024; 246:115869. [PMID: 38039736 DOI: 10.1016/j.bios.2023.115869] [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: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
DNA nanotechnology, developing rapidly in recent years, has unprecedented superiorities in biological application-oriented research including high programmability, convenient functionalization, reconfigurable structure, and intrinsic biocompatibility. However, the susceptibility to nucleases in the physiological environment has been an obstacle to applying DNA nanostructures in biological science research. In this study, a new DNA self-assembly strategy, mediated by double-protonated small molecules instead of classical metal ions, is developed to enhance the nuclease resistance of DNA nanostructures while retaining their integrality and functionality, and the relative application has been launched in the detection of microRNAs (miRNAs). Faced with low-abundance miRNAs, we integrate hybrid chain reaction (HCR) with DNA self-assembly in the presence of double-protonated small molecules to construct a chemiluminescence detection platform with nuclease resistance, which utilizes the significant difference of molecular weight between DNA arrays and false-positive products to effectively separate of reaction products and remove the detection background. This strategy attaches importance to the nucleic acid stability during the assay process via improving nuclease resistance while rendering the detection results for miRNAs more authentic and reliable, opening our eyes to more possibilities for the multiple applications of customized DNA nanostructures in biology, including bioassay, bioimaging, drug delivery, and cell modulation.
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Affiliation(s)
- Yanan Peng
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Dongxia Li
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Bin Qiao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China
| | - Zhijun Gao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Qiumei Pu
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Huajie Pang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Xiangde Lai
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Rui Zhang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Xuan Zhao
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Guangyuan Zhao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Dan Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, PR China
| | - Feng Han
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China
| | - Yuanyuan Wang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China
| | - Yuxiang Ji
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Hua Pei
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Qiang Wu
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China.
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Habibi A, Farhadian S, Shareghi B, Hashemi-Shahraki F. Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122264. [PMID: 36652806 DOI: 10.1016/j.saa.2022.122264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.
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Affiliation(s)
- Atefeh Habibi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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4
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Nishio T, Shimada Y, Yoshikawa Y, Kenmotsu T, Schiessel H, Yoshikawa K. The Anticancer Drug Daunomycin Directly Affects Gene Expression and DNA Structure. Int J Mol Sci 2023; 24:ijms24076631. [PMID: 37047603 PMCID: PMC10095590 DOI: 10.3390/ijms24076631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Daunomycin (DM), an anthracycline antibiotic, is frequently used to treat various cancers, but the direct effects of DM on gene expression and DNA structure are unclear. We used an in vitro cell-free system, optimized with spermine (SP), to study the effect of DM on gene expression. A bimodal effect of DM on gene expression, weak promotion followed by inhibition, was observed with increasing concentration of DM. We also performed atomic force microscopy observation to measure how DM affects the higher-order structure of DNA induced with SP. DM destroyed SP-induced flower-like conformations of DNA by generating double-strand breaks, and this destructive conformational change of DNA corresponded to the inhibitory effect on gene expression. Interestingly, the weakly enhanced cell-free gene expression occurred as DNA conformations were elongated or relaxed at lower DM concentrations. We expect these newly unveiled DM effects on gene expression and the higher-order structure of DNA will contribute further to the development and refinement of useful anticancer therapy chemicals.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Yohji Shimada
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
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Nishio T, Masaoka T, Yoshikawa Y, Sadakane K, Kenmotsu T, Schiessel H, Yoshikawa K. Markedly Different Effects of Monovalent Cations on the Efficiency of Gene Expression. Adv Biol (Weinh) 2023; 7:e2200164. [PMID: 36328593 DOI: 10.1002/adbi.202200164] [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: 06/15/2022] [Revised: 09/20/2022] [Indexed: 11/06/2022]
Abstract
The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system is examined using a luciferase assay. It is found that the potency for all ions analyzed here is in the order Rb+ > K+ > Cs+ > Na+ ≈ Li+ > (CH3 )4 N+ , where Rb+ is most efficient at promoting TX-TL and the ions of Li+ , Na+ , and (CH3 )4 N+ exhibit an inhibitory effect. Similar promotion/inhibition effects are observed for cell-free TL alone with an mRNA template.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Tomoya Masaoka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics Institute for Advanced Study, Kyoto University, Kyoto, 606-8501, Japan
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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Fujino K, Nishio T, Fujioka K, Yoshikawa Y, Kenmotsu T, Yoshikawa K. Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule. Polymers (Basel) 2022; 15:polym15010149. [PMID: 36616499 PMCID: PMC9823369 DOI: 10.3390/polym15010149] [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: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2-3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules.
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Affiliation(s)
- Kohei Fujino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307 Dresden, Germany
- Correspondence: (T.N.); (K.Y.)
| | - Keita Fujioka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Correspondence: (T.N.); (K.Y.)
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Yoshikawa K. Quantitative evaluation of DNA double-strand breaks (DSBs) through single-molecule observation. Enzymes 2022; 51:7-27. [PMID: 36336410 DOI: 10.1016/bs.enz.2022.08.002] [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] [Indexed: 06/16/2023]
Abstract
By adapting the method of single molecular observation for individual DNAs, it will be shown that reliable analysis of double-strand breaks, DSBs, becomes possible for various kinds of damage sources. Single DNA above the size of several-tens kilo base-pairs exhibits the length scale above several μm, indicating that their whole conformation is visible with fluorescence microscopy by adding suitable fluoresce dye to the solution. Various examples of the quantitative evaluation on DSBs are described, together with the evaluation of the protective effects of anti-oxidants.
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Affiliation(s)
- Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan; Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan.
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Vasiliu T, Mocci F, Laaksonen A, Engelbrecht LDV, Perepelytsya S. Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices. Front Chem 2022; 10:836994. [PMID: 35281557 PMCID: PMC8915389 DOI: 10.3389/fchem.2022.836994] [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: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine2+, spermidine3+, and spermine4+ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine3+ (Spd3+) cations were performed to study the structuring of Spd3+ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm3+ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd3+ interaction modes, with special attention given to Spd3+ conformational changes in the space between the two DNA molecules (caged Spd3+). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd3+ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.
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Affiliation(s)
- Tudor Vasiliu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Francesca Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- Division of Energy Science, Energy Engineering, Luleå University of Technology, Luleå, Sweden
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | | | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the NAS of Ukraine, Kyiv, Ukraine
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
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Higher-order structure of DNA determines its positioning in cell-size droplets under crowded conditions. PLoS One 2021; 16:e0261736. [PMID: 34937071 PMCID: PMC8694483 DOI: 10.1371/journal.pone.0261736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/08/2021] [Indexed: 11/19/2022] Open
Abstract
Background It is becoming clearer that living cells use water/water (w/w) phase separation to form membraneless organelles that exhibit various important biological functions. Currently, it is believed that the specific localization of biomacromolecules, including DNA, RNA and proteins in w/w microdroplets is closely related to their bio-activity. Despite the importance of this possible role of micro segregation, our understanding of the underlying physico-chemical mechanism is still unrefined. Further research to unveil the underlying mechanism of the localization of macromolecules in relation to their steric conformation in w/w microdroplets is needed. Principal findings Single-DNA observation of genome-size DNA (T4 GT7 bacteriophage DNA; 166kbp) by fluorescence microscopy revealed that DNAs are spontaneously incorporated into w/w microdroplets generated in a binary aqueous polymer solution with polyethylene glycol (PEG) and dextran (DEX). Interestingly, DNAs with elongated coil and shrunken conformations exhibit Brownian fluctuation inside the droplet. On the other hand, tightly packed compact globules, as well as assemblies of multiple condensed DNAs, tend to be located near the interface in the droplet. Conclusion and significance The specific localization of DNA molecules depending on their higher-order structure occurs in w/w microdroplet phase-separation solution under a binary aqueous polymer solution. Such an aqueous solution with polymers mimics the crowded conditions in living cells, where aqueous macromolecules exist at a level of 30–40 weight %. The specific positioning of DNA depending on its higher-order structure in w/w microdroplets is expected to provide novel insights into the mechanism and function of membraneless organelles and micro-segregated particles in living cells.
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