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Cristofalo M, Marrano CA, Salerno D, Corti R, Cassina V, Mammola A, Gherardi M, Sclavi B, Cosentino Lagomarsino M, Mantegazza F. Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers. Biochim Biophys Acta Gen Subj 2020; 1864:129725. [PMID: 32891648 DOI: 10.1016/j.bbagen.2020.129725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment. METHODS We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding. RESULTS In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively. CONCLUSIONS We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG. GENERAL SIGNIFICANCE Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.
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Affiliation(s)
- M Cristofalo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - C A Marrano
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - D Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - R Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - V Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - A Mammola
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - M Gherardi
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - B Sclavi
- Université Pierre et Marie Curie, Institut de Biologie Paris Seine, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - M Cosentino Lagomarsino
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - F Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy.
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Suzuki H, Fujiyoshi K, Kaji N, Tokeshi M, Baba Y. Observation of Ethanol-Induced Condensation and Decondensation Processes at a Single-DNA Molecular Level in Microfluidic Devices Equipped with a Rapid Solution Exchange System. Anal Chem 2020; 92:9132-9137. [PMID: 32483963 DOI: 10.1021/acs.analchem.0c01417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational transitions from secondary (e.g., B- to A-form DNA) to higher-order (e.g., coil to globule) transitions play important roles in genome expression and maintenance. Several single-molecule approaches using microfluidic devices have been used to determine the kinetics of DNA chromatin assembly because microfluidic devices can afford stretched DNA molecules through laminar flow and rapid solution exchange. However, some issues, particularly the uncertainty of time 0 in the solution exchange process, are encountered. In such kinetic experiments, it is critical to determine when the target solution front approaches the target DNA molecules. Therefore, a new design for a microfluidic device is developed that enables the instantaneous exchange of solutions in the observation channel, allowing accurate measurements of DNA conformational transitions; stepwise, ethanol-induced conformational transitions are revealed. Although full DNA contraction from coil to globule is observed with >50% ethanol, no outstanding change is observed at concentrations <40% in 10 min. With 50% ethanol solution, the DNA conformational transition passes through two steps: (i) fast and constant-velocity contraction and (ii) relatively slow contraction from the free end. The first process is attributed to the B to A conformational transition by gradual dehydration. The second process is due to the coil-globule transition as the free end of DNA starts the contraction. This globular structure formation counteracts the shear force from the microfluids and decelerates the contraction velocity. This real-time observation system can be applied to the kinetic analysis of DNA conformational transitions such as kinetics of chromatin assembly and gene expression.
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Affiliation(s)
- Hiroshi Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kentaro Fujiyoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Manabu Tokeshi
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita-13, Nishi-8, Kita-Ku, Sapporo 060-8628, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shih-Chuan First Road, Kaohsiung 807, Taiwan, R.O.C
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Lima CHM, de Paula HMC, da Silva LHM, Rocha MS. Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA). Biopolymers 2017; 107. [DOI: 10.1002/bip.23071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 02/02/2023]
Affiliation(s)
- C. H. M. Lima
- Departamento de Física, Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - H. M. C. de Paula
- Departamento de Química, Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - L. H. M. da Silva
- Departamento de Química, 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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