1
|
Dohi D, Hirano K, Terao K. Molecular ring toss of circular BAC DNA using micropillar array for single-molecule studies. BIOMICROFLUIDICS 2020; 14:014115. [PMID: 32128009 PMCID: PMC7039730 DOI: 10.1063/1.5142666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
This paper reports a method for trapping circular DNA molecules and imaging the dynamics with high spatial resolution using a micropillar-array device. We successfully trapped circular bacterial artificial chromosome DNA molecules at a micropillar-based "ring toss" in the laminar flow of a microchannel under a fluorescence microscope and demonstrated the imaging of their extension by flow and condensation process induced by spermine solution. DNA molecules were visualized in an extended loop conformation, allowing high spatial resolution, and the results showed that the dynamics is induced by the microfluidic control of the surrounding chemical environment. The method is expected to lead to the elucidation of the physical characteristics and the dynamics of circular DNA molecules.
Collapse
Affiliation(s)
- Daiki Dohi
- Department of Intelligent Mechanical Systems Engineering, Kagawa University, Takamatsu 761-0396, Japan
| | - Ken Hirano
- Authors to whom correspondence should be addressed:, Tel.: +81 (87) 869-3569 and , Tel.: +81 (87) 864-2346
| | - Kyohei Terao
- Authors to whom correspondence should be addressed:, Tel.: +81 (87) 869-3569 and , Tel.: +81 (87) 864-2346
| |
Collapse
|
2
|
Khan FA, Ali SO. Physiological Roles of DNA Double-Strand Breaks. J Nucleic Acids 2017; 2017:6439169. [PMID: 29181194 PMCID: PMC5664317 DOI: 10.1155/2017/6439169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/24/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.
Collapse
Affiliation(s)
- Farhaan A. Khan
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| | - Syed O. Ali
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| |
Collapse
|
3
|
Janockova J, Zilecka E, Kasparkova J, Brabec V, Soukup O, Kuca K, Kozurkova M. Assessment of DNA-binding affinity of cholinesterase reactivators and electrophoretic determination of their effect on topoisomerase I and II activity. MOLECULAR BIOSYSTEMS 2017; 12:2910-20. [PMID: 27412811 DOI: 10.1039/c6mb00332j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe the biochemical properties and biological activity of a series of cholinesterase reactivators (symmetrical bisquaternary xylene-linked compounds, K106-K114) with ctDNA. The interaction of the studied derivatives with ctDNA was investigated using UV-Vis, fluorescence, CD and LD spectrometry, and electrophoretic and viscometric methods. The binding constants K were estimated to be in the range 1.05 × 10(5)-5.14 × 10(6) M(-1) and the percentage of hypochromism was found to be 10.64-19.28% (from UV-Vis titration). The used methods indicate that the studied samples are groove binders. Electrophoretic methods proved that the studied compounds clearly influence calf thymus Topo I (at 5 μM concentration, except for compounds K107, K111 and K114 which were effective at higher concentrations) and human Topo II (K110 partially inhibited Topo II effects even at 5 μM concentration) activity.
Collapse
Affiliation(s)
- J Janockova
- Institute of Chemistry, Department of Biochemistry, Faculty of Science, P. J. Safarik University, Moyzesova 11, 040 01 Kosice, Slovak Republic. and Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - E Zilecka
- Institute of Chemistry, Department of Biochemistry, Faculty of Science, P. J. Safarik University, Moyzesova 11, 040 01 Kosice, Slovak Republic.
| | - J Kasparkova
- Department of Biophysics, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - V Brabec
- Department of Biophysics, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - O Soukup
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - K Kuca
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - M Kozurkova
- Institute of Chemistry, Department of Biochemistry, Faculty of Science, P. J. Safarik University, Moyzesova 11, 040 01 Kosice, Slovak Republic. and Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| |
Collapse
|
4
|
Marko D, Boege F. A possible link between nutritional uptake of ubiquitous topoisomerase inhibitors and autism? Int J Dev Neurosci 2016; 53:8-9. [DOI: 10.1016/j.ijdevneu.2016.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022] Open
Affiliation(s)
- Doris Marko
- University of ViennaFaculty of ChemistryDepartment of Food Chemistry and ToxicologyAustria
| | - Fritz Boege
- Central Institute of Clinical Chemistry and Laboratory DiagnosticsUniversity of DüsseldorfGermany
| |
Collapse
|