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Wang B, Dong J, Yang F, Ju T, Li J, Wang J, Wang Y, Crabbe MJC, Tian Y, Wang Z. Use of Atomic Force Microscopy in UVB-Induced Chromosome Damage Provides Important Bioinformation for Cell Damage Assessment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:13212-13221. [PMID: 37681704 DOI: 10.1021/acs.langmuir.3c01644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The chromosomal structure derived from UVB-stimulated HaCaT cells was detected by atomic force microscopy (AFM) to evaluate the effect of UVB irradiation. The results showed that the higher the UVB irradiation dose, the more the cells that had chromosome aberration. At the same time, different representative types of chromosome structural aberrations were investigated. We also revealed damage to both DNA and cells under the corresponding irradiation doses. It was found that the degree of DNA damage was directly proportional to the irradiation dose. The mechanical properties of cells were also changed after UVB irradiation, suggesting that cells experienced a series of chain reactions from inside to outside after irradiation. The high-resolution imaging of chromosome structures by AFM after UVB irradiation enables us to relate the damage between chromosomes, DNA, and cells caused by UVB irradiation and provides specific information on genetic effects.
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Affiliation(s)
- Bowei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jianjun Dong
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Fan Yang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Tuoyu Ju
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jiani Li
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Junxi Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Ying Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - M James C Crabbe
- Wolfson College, University of Oxford, Oxford OX2 6UD, U.K
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
| | - Yanling Tian
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
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2
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Gene-encoding DNA origami for mammalian cell expression. Nat Commun 2023; 14:1017. [PMID: 36823187 PMCID: PMC9950468 DOI: 10.1038/s41467-023-36601-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
DNA origami may enable more versatile gene delivery applications through its ability to create custom nanoscale objects with specific targeting, cell-invading, and intracellular effector functionalities. Toward this goal here we describe the expression of genes folded in DNA origami objects delivered to mammalian cells. Genes readily express from custom-sequence single-strand scaffolds folded within DNA origami objects, provided that the objects can denature in the cell. We demonstrate enhanced gene expression efficiency by including and tuning multiple functional sequences and structures, including virus-inspired inverted-terminal repeat-like (ITR) hairpin motifs upstream or flanking the expression cassette. We describe gene-encoding DNA origami bricks that assemble into multimeric objects to enable stoichiometrically controlled co-delivery and expression of multiple genes in the same cells. Our work provides a framework for exploiting DNA origami for gene delivery applications.
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Xiao D, Wang N, Chen S, Wang S, Yuan X, Fan W, Huo M. Synergism in sequential inactivation of Cryptosporidium parvum with trypsin and UV irradiation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:8354-8362. [PMID: 36445526 DOI: 10.1007/s11356-022-24408-4] [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: 07/11/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Cryptosporidium, a protozoan parasite, in wastewater presents a major public health concern for water safety. However, bactericidal efficiencies of conventional disinfection methods towards Cryptosporidium oocysts are still hampered owing to the presence of their thick outer wall. In this study, we present a novel UV inactivation process where the efficiency has been significantly enhanced by addition of a trypsin pretreatment stage. Notably, inactivation (log-reduction) of oocysts was noted to be 73.75-294.72% higher than that obtained by UV irradiation alone, under identical conditions. Experimental observations and supporting mechanistic analyses suggest that trypsin led to cleavage of the protein layers on the oocyst wall, facilitating penetration of UV radiation into the oocysts leading to degradation of their genomic DNA (gDNA). The dissociative effect of trypsin on the oocyst wall was indicated by the fact that 64.50% of oocysts displayed early apoptosis after trypsinization. Imaging by scanning electron microscopy indicated that this combined treatment led to substantial disruption of the oocyst coat, deforming their shape. This resulted in the release of cellular proteins and gDNA, their concentrations in bulk solution increasing by 1.22-8.60 times. As UV irradiation time was prolonged, gDNA was degraded into smaller fragments with lower molecular masses. Both laddering and diffuse smear patterns in gel analysis indicated significantly detrimental effects on gDNA and viability of oocysts. Overall, this study demonstrated enhancement of UV inactivation of Cryptosporidium oocysts by trypsin and explored the underlying mechanisms for the process.
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Affiliation(s)
- Dan Xiao
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Nan Wang
- Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun, 130062, China
| | - Shiheng Chen
- School of Chemical Engineering, Changchun University of Technology, Changchun, 130012, China
| | - Siyue Wang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xiangyi Yuan
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Wei Fan
- School of Environment, Northeast Normal University, Changchun, 130117, China.
| | - Mingxin Huo
- School of Environment, Northeast Normal University, Changchun, 130117, China
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Cheung E, Xia Y, Caporini MA, Gilmore JL. Tools shaping drug discovery and development. BIOPHYSICS REVIEWS 2022; 3:031301. [PMID: 38505278 PMCID: PMC10903431 DOI: 10.1063/5.0087583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 03/21/2024]
Abstract
Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.
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Affiliation(s)
- Eugene Cheung
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Yan Xia
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Marc A. Caporini
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jamie L. Gilmore
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
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Jabeen G, Ahmad MH, Aslam M, Riaz S, Hayat A, Nawaz MH. N-Doped graphene quantum dots (N-GQDs) as fluorescent probes for detection of UV induced DNA damage. RSC Adv 2022; 12:22458-22464. [PMID: 36105959 PMCID: PMC9366598 DOI: 10.1039/d2ra04462e] [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: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
UV induced DNA damage can lead to the development of skin cancer, skin aging and cell death. In this study, we fabricated a fluorescence-based biosensor that can be applied to the detection of DNA damage caused by UV radiation with the help of nitrogen doped graphene quantum dots (N-GQDs) as the probe material. In this paper, N-GQDs with good fluorescence efficiency have been synthesized by the hydrothermal method and were used as a fluorescent probe for the detection of UV damaged DNA. The fluorescence intensity of N-GQDs was quenched by the static quenching of UV damaged DNA through the formation of a N-GQD/UV damaged DNA complex. Moreover, the effects of different values of pH, NaCl and glucose on analytical performances of the sensor were also studied. Thus, using a fluorescence based approach, we demonstrated a quite simple, rapid, and inexpensive biosensor for the detection of DNA damage caused by UV radiation. UV induced DNA damage can lead to the development of skin cancer, skin aging and cell death.![]()
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Affiliation(s)
- Gulshan Jabeen
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Muhammad Hassan Ahmad
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Muhammad Aslam
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Sara Riaz
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Mian Hasnain Nawaz
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
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6
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Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALB. Atomic force microscopy-A tool for structural and translational DNA research. APL Bioeng 2021; 5:031504. [PMID: 34286171 PMCID: PMC8272649 DOI: 10.1063/5.0054294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.
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Affiliation(s)
| | - James I. Provan
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - John A. Hartley
- UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
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Barnett JT, Kuper J, Koelmel W, Kisker C, Kad NM. The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair. Nucleic Acids Res 2021; 48:12689-12696. [PMID: 33166411 PMCID: PMC7736792 DOI: 10.1093/nar/gkaa973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 09/17/2020] [Accepted: 10/13/2020] [Indexed: 01/09/2023] Open
Abstract
Nucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five ‘structural’ subunits, p62, p44, p34, p52 and p8. Recent cryo-EM structures show that p62 makes extensive contacts with p44 and in part occupies XPD’s DNA binding site. While p44 is known to regulate the helicase activity of XPD during NER, p62 is thought to be purely structural. Here, using helicase and adenosine triphosphatase assays we show that a complex containing p44 and p62 enhances XPD’s affinity for dsDNA 3-fold over p44 alone. Remarkably, the relative affinity is further increased to 60-fold by dsDNA damage. Direct binding studies show this preference derives from p44/p62’s high affinity (20 nM) for damaged ssDNA. Single molecule imaging of p44/p62 complexes without XPD reveals they bind to and randomly diffuse on DNA, however, in the presence of UV-induced DNA lesions these complexes stall. Combined with the analysis of a recent cryo-EM structure, we suggest that p44/p62 acts as a novel DNA-binding entity that enhances damage recognition in TFIIH. This revises our understanding of TFIIH and prompts investigation into the core subunits for an active role during DNA repair and/or transcription.
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Affiliation(s)
- Jamie T Barnett
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Wolfgang Koelmel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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Kolb T, Khalid U, Simović M, Ratnaparkhe M, Wong J, Jauch A, Schmezer P, Rode A, Sebban S, Haag D, Hergt M, Devens F, Buganim Y, Zapatka M, Lichter P, Ernst A. A versatile system to introduce clusters of genomic double‐strand breaks in large cell populations. Genes Chromosomes Cancer 2020; 60:303-313. [DOI: 10.1002/gcc.22890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 01/07/2023] Open
Affiliation(s)
- Thorsten Kolb
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Umar Khalid
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Milena Simović
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Manasi Ratnaparkhe
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - John Wong
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Anna Jauch
- Institute of Human Genetics University of Heidelberg Heidelberg Germany
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Agata Rode
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Shulamit Sebban
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel‐Canada The Hebrew University‐Hadassah Medical School Jerusalem Israel
| | - Daniel Haag
- Hopp Children's Cancer Center at the NCT (KiTZ) Heidelberg Germany
| | - Michaela Hergt
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Frauke Devens
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel‐Canada The Hebrew University‐Hadassah Medical School Jerusalem Israel
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors German Cancer Research Center (DKFZ) Heidelberg Germany
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Liu X, Hu JY. Effect of DNA sizes and reactive oxygen species on degradation of sulphonamide resistance sul1 genes by combined UV/free chlorine processes. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122283. [PMID: 32086093 DOI: 10.1016/j.jhazmat.2020.122283] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Nowadays, antibiotic resistance genes (ARGs) have been characterized as an emerging environmental contaminant, as the spread of ARGs may increase the difficulty of bacterial infection treatments. This study evaluates the combination of ultraviolet (UV) irradiation and chlorination, the two most commonly applied disinfection methods, on the degradation of sulphonamide resistance sul1 genes. The results revealed that although both of individual UV and chlorination processes were relatively less effective, two of the four combined processes, namely UV followed by chlorination (UV-Cl2) and simultaneous combination of UV and chlorination (UV/Cl2), delivered a better removal rate (up to 1.5 logs) with an observation of synergetic effects up to 0.609 log. The mechanisms analysis found that the difference of DNA size affected sul1 genes degradation by UV and chlorination; targeted genes on larger DNA fragments could be more effectively degraded by UV (1.09 logs for large fragments and 0.12 log for small fragments when UV dose reached 432 mJ/cm2), while to degrade ARGs on smaller DNA fragments required less free chlorine dosage (10 mg/L for small fragments and 40 mg/L for large fragments). The sequential combination of UV and chlorination (UV-Cl2) used the corresponding reactivity of both processes, which could be the reason for the synergetic effect. For UV/Cl2 process, the formation of reactive oxygen species (ROS) contributed to the synergetic effect. Scavenger analysis showed that the contribution of ROS to the sul1 gene reduction was 0.004 to 0.273 log (up to 45.5 % of the total synergy values), and among the two major reactive species in UV/Cl2 system, HO was the more important radical, while the contribution of Cl was negligible. Besides, UV/Cl2 process also used the corresponding reactivity of both processes to generate the remaining synergy values when excluding the contribution by reactive radicals. These findings provide a thorough understanding of the effects of UV and free chlorine on the degradation of ARGs and indicate the potential to utilize the combined processes of UV and free chlorine in water or wastewater treatment practice to control the dissemination of antibiotic resistance.
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Affiliation(s)
- Xiaochen Liu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Jiang Yong Hu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore.
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Fang W, Xie M, Hou X, Liu X, Zuo X, Chao J, Wang L, Fan C, Liu H, Wang L. DNA Origami Radiometers for Measuring Ultraviolet Exposure. J Am Chem Soc 2020; 142:8782-8789. [DOI: 10.1021/jacs.0c01254] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weina Fang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mo Xie
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Xiaoling Hou
- Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Dis-plays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210046, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huajie Liu
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai 200092, China
| | - Lihua Wang
- Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
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11
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Qiao H, Wei Z, Wang Y, Hu N, Sun S, Bai J, Fang L, Wang Z. Focused characteristics and effects of light reflected from spherical lipid membrane of giant unilamellar vesicles. Colloids Surf B Biointerfaces 2020; 189:110828. [PMID: 32028133 DOI: 10.1016/j.colsurfb.2020.110828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 10/25/2022]
Abstract
Lipid vesicle is spherical membranous structure with a concave surface on the inside. When a beam of light illuminates a lipid vesicle, the light reflected from the vesicular concave membrane can be focused to have higher intensity and generate enhanced effects. By observing and simulating light reflected from giant unilamellar vesicles (GUVs), the intensity distribution of the light reflected from a spherical concave lipid membrane was investigated. The reflected light had focused characteristics. Its intensity was concentrated 10,000 times and even exceeded the intensity of incident light in a confined region, creating another effective light source in the lipid vesicle. The fluorescence quenching of sulfo-Cy5 encapsulated in spherical GUVs was stronger than that of the outside solution when irradiated by a 632.8 nm laser. When irradiated with ultraviolet light C (UVC), the damage to plasmid DNA encapsulated with spherical GUVs was greater than that of pure plasmid DNA solution and plasmid DNA mixed with lipid membrane fragments. Therefore, in addition to the effects of incident light, the focused light reflected from GUVs could generate incremental effects on encapsulated photoreactive materials if the spherical structure of the lipid membrane was maintained. These results proved that concave lipid membranes of spherical vesicles can focus light and utilize it to generate enhanced effects. The capability of light focusing and its influence on DNA may provide new insights for understanding the function of lipid membranes in cellular life.
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Affiliation(s)
- Hai Qiao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Zixin Wei
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Yiting Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Na Hu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Sineng Sun
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Jin Bai
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Liaoqiong Fang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China.
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China.
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12
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Springall L, Hughes CD, Simons M, Azinas S, Van Houten B, Kad NM. Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival. Nucleic Acids Res 2019; 46:1256-1265. [PMID: 29240933 PMCID: PMC5814901 DOI: 10.1093/nar/gkx1244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.
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Affiliation(s)
- Luke Springall
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Stavros Azinas
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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13
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Jia T, Chen ZH, Guo P, Yu J. An insight into DNA binding properties of newly designed cationic δ,δ'‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:260-271. [PMID: 30557843 DOI: 10.1016/j.saa.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/19/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Two cationic δ,δ'‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH3 (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'‑diazacarbazoles and DNA were weakened, but δ,δ'‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.
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Affiliation(s)
- Tao Jia
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Zhi-Hang Chen
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peng Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, PR China.
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14
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Hwangbo M, Claycomb EC, Liu Y, Alivio TEG, Banerjee S, Chu KH. Effectiveness of zinc oxide-assisted photocatalysis for concerned constituents in reclaimed wastewater: 1,4-Dioxane, trihalomethanes, antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:1189-1197. [PMID: 30308890 PMCID: PMC7263876 DOI: 10.1016/j.scitotenv.2018.08.360] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/03/2018] [Accepted: 08/25/2018] [Indexed: 05/28/2023]
Abstract
Microbial and emerging chemical contaminants are unwanted constituents in reclaimed wastewater, due to the health concerns of using the water for agricultural irrigation, aquifer recharges, and potable water. Removal of these contaminants is required but it is currently challenging, given that there is no simple treatment technology to effectively remove the mixture of these contaminants. This study examined the effectiveness of ZnO-assisted photocatalytic degradation of several constituents, including 1,4-dioxane, trihalomethanes (THMs), triclosan (TCS), triclocarban (TCC), antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), under low intensity of UV exposure. E. coli with an ARGs-carrying circular plasmid (pUC19) was used as a model antibiotic resistant bacterium. Our results show that commercial zinc oxide (C-ZnO) assisted photodegradation of 1,4-dioxane, and dehalogenation of THMs, TCS, and TCC, while tetrapodal zinc oxide (T-ZnO) enhanced the dehalogenation of TCS and TCC. Additionally, T-ZnO assisted the photocatalytic inactivation of the E. coli within 6 h and caused structural changes in the plasmid DNA (pUC19) with additional UV exposure, resulting in non-functional AGR-containing plasmids. These results also suggest that higher UV dose is required not only to inactivate ARB but also to damage ARGs in the ARB in order to decrease risks in promoting ARB population in the environment. Overall, our results implicated that, under low UV intensity, ZnO-assisted photocatalysis is a promising alternative to simultaneously remove biological and emerging chemical contaminants in treated wastewater for safe reuse.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Everett Caleb Claycomb
- Department of Petroleum Engineering, Texas A&M University, College Station, TX 77843-3116, USA
| | - Yina Liu
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX 77843-3136, USA
| | - Theodore E G Alivio
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3012, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3003, USA
| | - Sarbajit Banerjee
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3012, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3003, USA
| | - Kung-Hui Chu
- Zachry Department of Civil Engineering, Texas A&M University, College Station, TX 77843-3136, USA.
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15
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Dai Z, Pomraning KR, Deng S, Hofstad BA, Panisko EA, Rodriguez D, Butcher MG, Culley DE, Magnuson JK. Deletion of the KU70 homologue facilitates gene targeting in Lipomyces starkeyi strain NRRL Y-11558. Curr Genet 2018; 65:269-282. [DOI: 10.1007/s00294-018-0875-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
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16
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Singh S, Singh MK, Das P. Visual detection of cyclobutane pyrimidine dimer DNA damage lesions by Hg 2+ and carbon dots. Anal Chim Acta 2018. [PMID: 29534804 DOI: 10.1016/j.aca.2018.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclobutane pyrimidine dimmers (CPDs) and 6-4-[pyrimidine-2'-one] pyrimidine (6-4 PP) are major UV induced DNA damage lesions formed from solar radiation and other sources. CPD lesions are presumably mutagenic and carcinogenic that inhibit polymerases and interfere in DNA replication. An easy and cost effective way for visual detection of these lesions by using fluorescence based method is shown here. Artificial UVA and UVB lights were used for the generation of CPD and 6-4 PPs in selected DNA samples. Binding of Hg2+ ions with DNA before and after induction of CPD and 6-4 PP lesions was evaluated in the presence of highly fluorescent blue emitting carbon dots (CDs). Induction of CPD and 6-4 PPs in DNA causes distortion of DNA structure which hinders the binding of Hg2+ ions to DNA nucleobases. Quenching of fluorescence intensity of CDs by unbound Hg2+ ions was found to be proportional to the amount of CPD and 6-4 PP lesions induced by UV irradiation of DNA samples that offer a biosensing platform for the sensitive detection of CPD lesions in DNA. The fluorescent quenching was visually detectable using hand held UV light without the intervention of any equipment.
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Affiliation(s)
- Seema Singh
- Department of Chemistry, Indian Institute of Technology Patna, Patna, 801106, Bihar, India
| | - Manoj K Singh
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna, 801106, Bihar, India.
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17
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Abstract
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways. Furthermore, unexpected discoveries have resulted from capabilities to resolve molecular heterogeneity and cell subpopulations, provoking new questions about the role of stochastic processes in DNA repair and mutagenesis. These studies are leading to new technologies that will find widespread use in basic research, biotechnology, and medicine.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
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18
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Chen H, Li R, Li S, Andréasson J, Choi JH. Conformational Effects of UV Light on DNA Origami. J Am Chem Soc 2017; 139:1380-1383. [DOI: 10.1021/jacs.6b10821] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haorong Chen
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shiming Li
- Department
of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Joakim Andréasson
- Department
of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jong Hyun Choi
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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19
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Synthesis of Modified Sterically Hindered Phenols and Investigation of Their Ability to Protect Bacterial DNA Against UVB Damage. Pharm Chem J 2015. [DOI: 10.1007/s11094-015-1196-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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D'Amico F, Cammisuli F, Addobbati R, Rizzardi C, Gessini A, Masciovecchio C, Rossi B, Pascolo L. Oxidative damage in DNA bases revealed by UV resonant Raman spectroscopy. Analyst 2015; 140:1477-85. [DOI: 10.1039/c4an02364a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report on the use of the UV Raman technique to monitor the oxidative damage of deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP) and DNA (plasmid vector) solutions.
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Affiliation(s)
| | - Francesca Cammisuli
- Institute for Maternal and Child Health
- Trieste
- Italy
- Department of Medical Science
- University of Trieste
| | | | | | | | | | - Barbara Rossi
- Department of Physics
- University of Trento
- Trento
- Italy
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21
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Berg F, Wilken J, Helm CA, Block S. AFM-Based Quantification of Conformational Changes in DNA Caused by Reactive Oxygen Species. J Phys Chem B 2014; 119:25-32. [DOI: 10.1021/jp507659x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Berg
- Institut
für Physik, Ernst-Moritz-Arndt Universität, Felix-Hausdorff-Strasse 6, D-17487 Greifswald, Germany
| | - Janine Wilken
- Institut
für Physik, Ernst-Moritz-Arndt Universität, Felix-Hausdorff-Strasse 6, D-17487 Greifswald, Germany
| | - Christiane A. Helm
- Institut
für Physik, Ernst-Moritz-Arndt Universität, Felix-Hausdorff-Strasse 6, D-17487 Greifswald, Germany
| | - Stephan Block
- Institut
für Physik, Ernst-Moritz-Arndt Universität, Felix-Hausdorff-Strasse 6, D-17487 Greifswald, Germany
- Department
of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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22
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Jia T, Wang J, Guo P, Yu J. Characterizations of cationic γ-carbolines binding with double-stranded DNA by spectroscopic methods and AFM imaging. Org Biomol Chem 2014; 13:1234-42. [PMID: 25434722 DOI: 10.1039/c4ob01905a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Two cationic γ-carbolines, 2-methyl-5H-pyrido[4,3-b]indolium iodide (MPII) and 2,5-dimethyl-5H-pyrido[4,3-b]indolium iodide (DPII), were synthesized, and the DNA-binding properties of the cationic γ-carbolines were elucidated. Through a series of experiments, we proved that the two cationic γ-carbolines could strongly interact with DNA by intercalative binding. However, DPII, with a methyl group substituting H atom of 5-NH, has shown a stronger intercalative interaction with DNA compared to MPII. The dissociation of H from the 5-NH of MPII resulted in better water solubility and less binding affinity to DNA. Atomic force microscopy (AFM) images of pBR322 showed that both MPII and DPII strongly interacted with DNA and induced conformational changes in DNA. Moreover, the CT-DNA circular dichroism (CD) spectra changes and the statistics of the node numbers of pBR322 in AFM images indicated that MPII had more profound effects on DNA conformations compared to DPII. Furthermore, our studies have shown that the interactions between cationic γ-carbolines and DNA were sensitive to ionic strength. Increased ionic strength in the buffer caused the DNA helix to shrink, and the base stacking would be more compact, which resulted in minimal intercalation of cationic γ-carbolines into DNA.
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Affiliation(s)
- Tao Jia
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China.
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23
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Detection of parametric changes in the Peyrard-Bishop- Dauxois model of DNA using nonlinear Kalman filtering. J Biol Phys 2014; 41:59-83. [PMID: 25294023 DOI: 10.1007/s10867-014-9366-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022] Open
Abstract
The derivative-free nonlinear Kalman filter is proposed for state estimation and fault diagnosis in distributed parameter systems of the wave-type and particularly in the Peyrard-Bishop-Dauxois model of DNA dynamics. At a first stage, a nonlinear filtering approach is introduced for estimating the dynamics of the Peyrard-Bishop-Dauxois 1D nonlinear wave equation, through the processing of a small number of measurements. It is shown that the numerical solution of the associated partial differential equation results in a set of nonlinear ordinary differential equations. With the application of a diffeomorphism that is based on differential flatness theory it is shown that an equivalent description of the system is obtained in the linear canonical (Brunovsky) form. This transformation enables to obtain local estimates about the state vector of the DNA model through the application us of the standard Kalman filter recursion. At a second stage, the local statistical approach to fault diagnosis is used to perform fault diagnosis for this distributed parameter system by processing with statistical tools the differences (residuals) between the output of the Kalman filter and the measurements obtained from the distributed parameter system. Optimal selection of the fault threshold is succeeded by using the local statistical approach to fault diagnosis. The efficiency of the proposed filtering approach in the problem of fault diagnosis for parametric change detection, in nonlinear wave-type models of DNA dynamics, is confirmed through simulation experiments.
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24
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Li YL, Meng YF, Zhang ZM, Jiang Y. Detecting the oligomeric state of Escherichia coli MutS from its geometric architecture observed by an atomic force microscope at a single molecular level. J Phys Chem B 2014; 118:9218-24. [PMID: 25029278 DOI: 10.1021/jp504644r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy (AFM), which provides true 3D surface topography, can also be used to determine the geometric parameters of proteins quantitatively at a single molecular level. In this paper, two different kinds of Escherichia coli MutS (MutS) protein were observed using AFM, and the geometric parameters of the proteins such as height, perimeter, area, and volume were measured. On the basis of these measurements, the molecular weight, association constant, oligomeric state, and orientation of MutS proteins on a mica surface were deduced. The oligomerization mechanism of MutS was analyzed in detail, and the results show that two different kinds of interactions between MutS protein may be involved in oligomerization. Our results also show that AFM imaging is an accurate method for analyzing the geometric structures of a single protein quantitatively at a single-molecule level.
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Affiliation(s)
- Yan-Li Li
- School of Chemistry and Chemical Engineering, Southeast University , No. 2 Dongnandaxue Road, Jiangning, Nanjing, Jiangsu 211189, China
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25
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Tian YZ, Li YL, Wang ZF, Jiang Y. Nuclease-responsive DNA–PEI hollow microcapsules for bio-stimuli controlled release. J Mater Chem B 2014; 2:1667-1672. [DOI: 10.1039/c3tb21191f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Marcélis L, Moucheron C, Kirsch-De Mesmaeker A. Ru-TAP complexes and DNA: from photo-induced electron transfer to gene photo-silencing in living cells. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120131. [PMID: 23776293 DOI: 10.1098/rsta.2012.0131] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this review, examples of applications of the photo-induced electron transfer (PET) process between photo-oxidizing Ru-TAP (TAP = 1,4,5,8-tetraazaphenanthrene) complexes and DNA or oligodeoxynucleotides (ODNs) are discussed. Applications using a free Ru-TAP complex (not chemically anchored to an ODN) are first considered. In this case, the PET gives rise to the production of an irreversible adduct of the Ru complex on a guanine (G) base, with formation of a covalent bond. After absorption of a second photon, this adduct can generate a bi-adduct, whereby the same complex binds to a second G moiety. These bi-adduct formations are responsible for photo-cross-linking between two strands of a duplex, each containing a G base, or between two G moieties of a single strand such as a telomeric sequence, as demonstrated by polyacrylamide gel electrophoresis analyses or mass spectrometry. Scanning force microscopy also allows the detection of such photobridgings with plasmid DNA. Other applications, for example with Ru-ODN, i.e. ODN with chemically anchored Ru-TAP complexes, are also discussed. It is shown that such Ru-ODN probes containing a G base in their own sequences are capable of photo-cross-linking selectively with their targeted complementary sequences, and, in the absence of such targets, they self-photo-inhibit. Such processes are applied successfully in gene photo-silencing of human papillomavirus cancer cells.
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Affiliation(s)
- Lionel Marcélis
- Chimie Organique et Photochimie, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, 1050 Bruxelles, Belgium
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27
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Lee J, Park HS, Lim S, Jo K. Visualization of UV-induced damage on single DNA molecules. Chem Commun (Camb) 2013; 49:4740-2. [DOI: 10.1039/c3cc38884k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Yin Y, Zhu WW, Guo LP, Yang R, Li XS, Jiang Y. RGDC Functionalized Titanium Dioxide Nanoparticles Induce Less Damage to Plasmid DNA but Higher Cytotoxicity to HeLa Cells. J Phys Chem B 2012; 117:125-31. [DOI: 10.1021/jp3092804] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuan Yin
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
| | - Wei-Wei Zhu
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
| | - Li-Ping Guo
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
| | - Ran Yang
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
| | - Xin-Song Li
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
| | - Yong Jiang
- School of Chemistry
and Chemical Engineering and ‡School of Materials Science and Engineering, Southeast University, Jiangning, Nanjing,
Jiangsu, 211189, People's Republic of China
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29
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Vanderlinden W, Blunt M, David CC, Moucheron C, Kirsch-De Mesmaeker A, De Feyter S. Mesoscale DNA Structural Changes on Binding and Photoreaction with Ru[(TAP)2PHEHAT]2+. J Am Chem Soc 2012; 134:10214-21. [DOI: 10.1021/ja303091q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Willem Vanderlinden
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Matthew Blunt
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Charlotte C. David
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Cécile Moucheron
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Andrée Kirsch-De Mesmaeker
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Steven De Feyter
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
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30
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31
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Kalle W, Strappe P. Atomic force microscopy on chromosomes, chromatin and DNA: a review. Micron 2012; 43:1224-31. [PMID: 22633852 DOI: 10.1016/j.micron.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/06/2012] [Accepted: 04/08/2012] [Indexed: 01/19/2023]
Abstract
The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.
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Affiliation(s)
- Wouter Kalle
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia.
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32
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33
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Trémezaygues L, Seifert M, Tilgen W, Reichrath J. 1,25-dihydroxyvitamin D(3) protects human keratinocytes against UV-B-induced damage: In vitro analysis of cell viability/proliferation, DNA-damage and -repair. DERMATO-ENDOCRINOLOGY 2011; 1:239-45. [PMID: 20592798 DOI: 10.4161/derm.1.4.9705] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Accepted: 08/04/2009] [Indexed: 11/19/2022]
Abstract
The skin is the only organ that has the capacity to photo-synthesize the biological active vitamin D metabolite 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] from 7-dehydocholesterol (7-DHC), following exposure to ultraviolet (UV)-B irradiation. The aim of the present work was to investigate the capacity of 1,25(OH)(2)D(3) to protect human keratinocytes (HaCaT) and squamous cell carcinoma cell lines (SCL-1) against the hazardous effects of UV-B irradiation. Human keratinocytes (HaCaT) and squamous cell carcinoma cell lines (SCL-1) were pretreated with 1,25(OH)(2)D(3) over 48 hours and then irradiated once with UVB-radiation. We evaluated the results of several assays (colony-forming-unit-culture assay, WST-1-assay and crystal violet assay), comparing viability/proliferation in 1,25(OH)(2)D(3)-pretreated cells with controls that were pretreated with the carrier substance ethanol alone. Additionally, we analyzed the effects of 1,25(OH)(2)D(3) on UV-induced DNA damage in HaCaT-keratinocytes by detection of cyclobutane pyrimidine dimers (CPDs) via dot blot analysis. We prove that 1,25(OH)(2)D(3), in a concentration of 10(-7) M, protects human keratinocytes (HaCaT) as well as squamous cell carcinoma cell lines (SCL-1) against the hazardous effects of UV-B-radiation (100 J/cm(2)-1,000 J/cm(2)) in vitro. Moreover, we demonstrate that the number of CPDs induced in HaCaT-keratinocytes after irradiation with UV-B (100 J/cm(2)-1,000 J/cm(2)) was decreased after pretreatment with 1,25(OH)(2)D(3), as compared to carrier-treated controls. Analysis of the time course revealed that the elimination of UV-B-induced DNA-damage in HaCaT-keratinocytes occurs quicker when cells are pretreated with 1,25(OH)(2)D(3) (as compared to controls). To put it in a nutshell, our data support the hypothesis that 1,25(OH)(2)D(3) protects cultured human keratinocytes against the hazardous effects of UV-B radiation.
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Affiliation(s)
- Lea Trémezaygues
- Department of Dermatology; The Saarland University Hospital; Homburg/Saar, Germany
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Pu T, Zhang XP, Liu F, Wang W. Coordination of the nuclear and cytoplasmic activities of p53 in response to DNA damage. Biophys J 2011; 99:1696-705. [PMID: 20858413 DOI: 10.1016/j.bpj.2010.07.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 07/19/2010] [Accepted: 07/22/2010] [Indexed: 01/28/2023] Open
Abstract
The tumor suppressor p53 plays a key role in the cellular response to various stresses. Most previous studies have focused on either the nuclear or cytoplasmic proapoptotic functions of p53, ignoring the combination of both functions. To explore how the two functions of p53 are coordinated in the DNA damage response via computer simulation, we construct a model for the p53 network comprising coupled positive and negative feedback loops involving p53, Mdm2, and Akt, as well as PUMA and Bax. In our model p53 is stabilized and accumulates in the nucleus and cytoplasm upon DNA damage. Nuclear p53 induces expression of Mdm2, PTEN, PUMA, and Bax. Cytoplasmic p53 is then released from the p53.Bcl-xL complex by PUMA to activate Bax directly. We find that the switching between low and high protein levels underlies the decision between cell survival and death. Moreover, a balance between the nuclear and cytoplasmic p53 levels and appropriate levels of Akt and PUMA are required for reliable cell fate decision. Our results indicate that coordination of the transcription-dependent and -independent activities of p53 is important in determining cellular outcomes. These findings advance our understanding of the mechanism for p53-mediated cellular responses and provide clues to p53-based cancer therapy.
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Affiliation(s)
- Tian Pu
- Department of Physics, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing, China
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Jiang Y, Rabbi M, Mieczkowski PA, Marszalek PE. Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis. J Phys Chem B 2010; 114:12162-5. [PMID: 20799746 DOI: 10.1021/jp105603k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy, which is normally used for DNA imaging to gain qualitative results, can also be used for quantitative DNA research, at a single-molecular level. Here, we evaluate the performance of AFM imaging specifically for quantifying supercoiled and relaxed plasmid DNA fractions within a mixture, and compare the results with the bulk material analysis method, gel electrophoresis. The advantages and shortcomings of both methods are discussed in detail. Gel electrophoresis is a quick and well-established quantification method. However, it requires a large amount of DNA, and needs to be carefully calibrated for even slightly different experimental conditions for accurate quantification. AFM imaging is accurate, in that single DNA molecules in different conformations can be seen and counted. When used carefully with necessary correction, both methods provide consistent results. Thus, AFM imaging can be used for DNA quantification, as an alternative to gel electrophoresis.
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Affiliation(s)
- Yong Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Jiangning, Nanjing, Jiangsu 211189, People's Republic of China.
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Yoshikawa Y, Mori T, Suzuki M, Imanaka T, Yoshikawa K. Comparative study of kinetics on DNA double-strand break induced by photo- and gamma-irradiation: Protective effect of water-soluble flavonoids. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The role of ultraviolet radiation (UV) in the pathogenesis has been discussed controversially for many decades. Studies in mice (SCID, HGF/SF, SV40T) which develop malignant melanoma, show a role of UVB in melanomagenesis. In contrast to this, the role of UVA is less clear. We will review the recent in vitro and in vivo data in support of the hypothesis that UVA is also involved in the development of malignant melanoma. The role of UVA in p53 activation, apoptosis, cell cycle arrest and photoproduct formation is discussed.
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El Kirat K, Bartkowski M, Haupt K. Probing the recognition specificity of a protein molecularly imprinted polymer using force spectroscopy. Biosens Bioelectron 2009; 24:2618-24. [DOI: 10.1016/j.bios.2009.01.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/27/2008] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
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Jiang Y, Rabbi M, Kim M, Ke C, Lee W, Clark RL, Mieczkowski PA, Marszalek PE. UVA generates pyrimidine dimers in DNA directly. Biophys J 2009; 96:1151-8. [PMID: 19186150 DOI: 10.1016/j.bpj.2008.10.030] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022] Open
Abstract
There is increasing evidence that UVA radiation, which makes up approximately 95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only approximately 60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA.
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Affiliation(s)
- Yong Jiang
- Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina, USA
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UV light-induced DNA damage detection in the unicellular green alga Chlamydomonas reinhardtii. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0149-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Liu CP, Wey MT, Chang CC, Kan LS. Direct observation of single molecule conformational change of tight-turn paperclip DNA triplex in solution. Appl Biochem Biotechnol 2008; 159:261-9. [PMID: 18931945 DOI: 10.1007/s12010-008-8390-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
DNA triplex modulates gene expression by forming stable conformation in physiological condition. However, it is not feasible to observe this unique molecular structure of large molecule with 54 oligodeoxynucleotides directly by conventional nuclear magnetic approach. In this study, we observed directly single molecular images of paperclip DNA triplexes formation in a buffer solution of pH 6.0 by atomic force microscopy (AFM). Meanwhile, a diffuse "tail" of unwound DNA was observed in pH 8.0 solution. This designable approach in visualizing the overall structures and shapes of oligo-DNAs at the single molecular level, by AFM, is applicable to other biopolymers as well.
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UV-C irradiation disrupts platelet surface disulfide bonds and activates the platelet integrin alphaIIbbeta3. Blood 2008; 112:4935-9. [PMID: 18796633 DOI: 10.1182/blood-2008-04-151043] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
UV-C irradiation has been shown to be effective for pathogen reduction in platelet concentrates, but preliminary work indicated that UV-C irradiation of platelets can induce platelet aggregation. In this study, the mechanism underlying this phenomenon was investigated. Irradiation of platelets with UV-C light (1500 J/m(2)) caused platelet aggregation, which was dependent on integrin alphaIIbbeta3 activation (GPIIb/IIIa). This activation occurred despite treatment with several signal transduction inhibitors known to block platelet activation. UV-C also induced activation of recombinant alphaIIbbeta3 in Chinese hamster ovary (CHO) cells, an environment in which physiologic agonists fail to activate. Activation of alphaIIbbeta3 requires talin binding to the beta3 tail, yet alphaIIbbeta3-Delta724 (lacking the talin binding site) was activated by UV-C irradiation, excluding a requirement for talin binding. The UV-C effect appears to be general in that beta(1) and beta(2) integrins are also activated by UV-C. To explain these findings, we investigated the possibility of UV-C-induced photolysis of disulfide bonds, in analogy with the activating effect of reducing agents on integrins. Indeed, UV-C induced a marked increase in free thiol groups in platelet surface proteins including alphaIIbbeta3. Thus, UV-C appears to activate alphaIIbbeta3 not by affecting intracellular signal transduction, but by reduction of disulfide bonds regulating integrin conformation.
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Li X, Ji T, Hu J, Sun J. Optimization of specimen preparation of thin cell section for AFM observation. Ultramicroscopy 2008; 108:826-31. [PMID: 18343583 DOI: 10.1016/j.ultramic.2008.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 01/08/2008] [Accepted: 01/23/2008] [Indexed: 11/24/2022]
Abstract
High resolution imaging of intracellular structures of ultrathin cell section samples is critical to the performance of precise manipulation by atomic force microscopy (AFM). Here, we test the effect of multiple factors during section sample preparation on the quality of the AFM image. These factors include the embedding materials, the annealing process of the specimen block, section thickness, and section side. We found that neither the embedding materials nor the temperature and speed of the annealing process has any effect on AFM image resolution. However, the section thickness and section side significantly affect the surface topography and AFM image resolution. By systematically testing the image quality of both sides of cell sections over a wide range of thickness (40-1000 nm), we found that the best resolution was obtained with upper-side sections approximately 50-100 nm thick. With these samples, we could observe precise structure details of the cell, including its membrane, nucleoli, and other organelles. Similar results were obtained for other cell types, including Tca8113, C6, and ECV-304. In brief, by optimizing the condition of ultrathin cell section preparation, we were able to obtain high resolution intracellular AFM images, which provide an essential basis for further AFM manipulation.
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Affiliation(s)
- Xinhui Li
- Nanobiology Laboratory, Bio-X Life Science Research Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
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Ke C, Jiang Y, Mieczkowski PA, Muramoto GG, Chute JP, Marszalek PE. Nanoscale detection of ionizing radiation damage to DNA by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:288-294. [PMID: 18247386 DOI: 10.1002/smll.200700527] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The detection and quantification of ionizing radiation damage to DNA at a single-molecule level by atomic force microscopy (AFM) is reported. The DNA damage-detection technique combining supercoiled plasmid relaxation assay with AFM imaging is a direct and quantitative approach to detect gamma-ray-induced single- and double-strand breaks in DNA, and its accuracy and reliability are validated through a comparison with traditional agarose gel electrophoresis. In addition, the dependence of radiation-induced single-strand breaks on plasmid size and concentration at a single-molecule level in a low-dose (1 Gy) and low-concentration range (0.01 ng microL(-1)-10 ng microL(-1)) is investigated using the AFM-based damage-detection assay. The results clearly show that the number of single-strand breaks per DNA molecule is linearly proportional to the plasmid size and inversely correlated to the DNA concentration. This assay can also efficiently detect DNA damage in highly dilute samples (0.01 ng microL(-1)), which is beyond the capability of traditional techniques. AFM imaging can uniquely supplement traditional techniques for sensitive measurements of damage to DNA by ionizing radiation.
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Affiliation(s)
- Changhong Ke
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical, Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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