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Ghosh G, Mukherjee D, Ghosh R, Singh P, Pal U, Chattopadhyay A, Santra M, Ahn KH, Mosae Selvakumar P, Das R, Pal SK. A novel molecular reporter for probing protein DNA recognition: An optical spectroscopic and molecular modeling study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122313. [PMID: 36628863 DOI: 10.1016/j.saa.2022.122313] [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: 10/05/2022] [Revised: 12/11/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
A novel benzo[a]phenoxazine-based fluorescent dye LV2 has been employed as a molecular reporter to probe recognition of a linker histone protein H1 by calf-thymus DNA (DNA). Fluorescence lifetime of LV2 buried in the globular domain of H1 (∼2.1 ns) or in the minor groove of DNA (∼0.93 ns) increases significantly to 2.65 ns upon interaction of the cationic protein with DNA indicating formation of the H1-DNA complex. The rotational relaxation time of the fluorophore buried in the globular domain of H1 increases significantly from 2.2 ns to 8.54 ns in the presence of DNA manifesting the recognition of H1 by DNA leading to formation of the H1-DNA complex. Molecular docking and molecular dynamics (MD) simulations have shown that binding of LV2 is energetically most favourable in the interface of the H1-DNA complex than in the globular domain of H1 or in the minor groove of DNA. As a consequence, orientational relaxation of the LV2 is significantly hindered in the protein-DNA interface compared to H1 or DNA giving rise to a much longer rotational relaxation time (8.54 ns) in the H1-DNA complex relative to that in pure H1 (2.2 ns) or DNA (5.7 ns). Thus, via a significant change of fluorescence lifetime and rotational relaxation time, the benzo[a]phenoxazine-based fluorescent dye buried within the globular domain of the cationic protein, or within the minor groove of DNA, reports on recognition of H1 by DNA.
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Affiliation(s)
- Gourab Ghosh
- Dept. of Chemistry, West Bengal State University, Barasat, Kolkata 700126, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Priya Singh
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Arpita Chattopadhyay
- Department of Basic Science and Humanities, Techno International New Town, Rajarhat, Kolkata 700156, India
| | - Mithun Santra
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk 37673, Republic of Korea
| | - Kyo Han Ahn
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyungbuk 37673, Republic of Korea
| | - P Mosae Selvakumar
- Science and Math Program, Asian University for Women, Chittagong, Bangladesh
| | - Ranjan Das
- Dept. of Chemistry, West Bengal State University, Barasat, Kolkata 700126, India.
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, India.
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Qu J, Shi J, Wang Y, Tong H, Zhu Y, Xu L, Wang Y, Zhang B, Tao Y, Dai X, Zhang H, Zhang Y. Applications of functionalized magnetic biochar in environmental remediation: A review. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128841. [PMID: 35427975 DOI: 10.1016/j.jhazmat.2022.128841] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/14/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Magnetic biochar (MBC) is extensively applied on contaminants removal from environmental medium for achieving environmental-friendly remediation with reduction of secondary pollution owing to its easy recovery and separation. However, the summary of MBC synthesis methods is still lack of relevant information. Moreover, the adsorption performance for pollutants by MBC is limited, and thus it is imperative to adopt modification techniques to enhance the removal ability of MBC. Unfortunately, there are few reviews to present modification methods of MBC with applications for removing hazardous contaminants. Herein, we critically reviewed (i) MBC synthetic methods with corresponding advantages and limitations; (ii) adsorption mechanisms of MBC for heavy metals and organic pollutants; (iii) various modification methods for MBC such as functional groups grafting, nanoparticles loading and element doping; (iv) applications of modified MBC for hazardous contaminants adsorption with deep insight to relevant removal mechanisms; and (v) key influencing conditions like solution pH, temperature and interfering ions toward contaminants removal. Finally, some constructive suggestions were put forward for the practical applications of MBC in the near future. This review provided a comprehensive understanding of using functionalized MBC as effective adsorbent with low-cost and high-performance characteristics for contaminated environment remediation.
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Affiliation(s)
- Jianhua Qu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jiajia Shi
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yihui Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Hua Tong
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yujiao Zhu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lishu Xu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yifan Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Bo Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Tao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiao Dai
- Harbin ZENENG Environmental Technology Co. Ltd., China
| | - Hui Zhang
- Harbin ZENENG Environmental Technology Co. Ltd., China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China; Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Rd, Changchun 130102, China.
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Xiang H, Xie Y, Huang J. Study on the interaction of DNA with resveratrol by resonance light scattering technique and its analytical application. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934811040071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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