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Verebová V, Bedlovičová Z, Bednáriková Z, Staničová J. Monitoring of DNA structural changes after incorporation of the phenylpyrazole insecticide fipronil. Arch Biochem Biophys 2024; 756:110001. [PMID: 38636692 DOI: 10.1016/j.abb.2024.110001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
The use of insecticides presents a risk to the environment because they can accumulate in the water, soil, air, and organisms, endangering human and animal health. It is therefore essential to investigate the effects of different groups of insecticides on individual biomacromolecules such as DNA. We studied fipronil, which belongs to the group of phenylpyrazole insecticides. The interaction of fipronil with calf thymus DNA was investigated using spectroscopic methods (absorption and fluorescence spectroscopy) complemented with infrared spectroscopy and viscosity measurement. Fluorescence emission spectroscopy showed the formation of a fipronil/DNA complex with a combined static and dynamic type of quenching. The binding constant was 4.15 × 103 L/mol. Viscosity changes were recorded to confirm/disconfirm the intercalation mode of interaction. A slight change in DNA viscosity in the presence of fipronil was observed. The phenylpyrazole insecticide does not cause significant conformational changes in DNA structure or increase of its chain length. We hypothesize that fipronil is incorporated into the minor groove of the DNA macromolecule via hydrogen interactions as indicated by FT-IR and CD measurements.
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Affiliation(s)
- Valéria Verebová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zdenka Bedlovičová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zuzana Bednáriková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Science, Watsonova 1935/47, 040 01, Košice, Slovakia
| | - Jana Staničová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia; Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, Kateřinská 1, Prague, Czech Republic.
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2
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Coatrini-Soares A, Soares JC, Popolin-Neto M, de Mello SS, Sanches EA, Paulovich FV, Oliveira ON, Mattoso LHC. Multidimensional calibration spaces in Staphylococcus Aureus detection using chitosan-based genosensors and electronic tongue. Int J Biol Macromol 2024; 271:132460. [PMID: 38772468 DOI: 10.1016/j.ijbiomac.2024.132460] [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: 03/06/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Mastitis diagnosis can be made by detecting Staphylococcus aureus (S. aureus), which requires high sensitivity and selectivity. Here, we report on microfluidic genosensors and electronic tongues to detect S. aureus DNA using impedance spectroscopy with data analysis employing visual analytics and machine learning techniques. The genosensors were made with layer-by-layer films containing either 10 bilayers of chitosan/chondroitin sulfate or 8 bilayers of chitosan/sericin functionalized with an active layer of cpDNA S. aureus. The specific interactions leading to hybridization in these genosensors allowed for a low limit of detection of 5.90 × 10-19 mol/L. The electronic tongue had four sensing units made with 6-bilayer chitosan/chondroitin sulfate films, 10-bilayer chitosan/chondroitin sulfate, 8-bilayer chitosan/sericin, and 8-bilayer chitosan/gold nanoparticles modified with sericin. Despite the absence of specific interactions, various concentrations of DNA S. aureus could be distinguished when the impedance data were plotted using a dimensionality reduction technique. Selectivity of S. aureus DNA was confirmed using multidimensional calibration spaces, based on machine learning, with accuracy up to 89 % for the genosensors and 66 % for the electronic tongue. Hence, with these computational methods one may opt for the more expensive genosensors or the simpler and cheaper electronic tongue, depending on the sensitivity level required to diagnose mastitis.
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Affiliation(s)
- Andrey Coatrini-Soares
- Embrapa Instrumentação, Nanotechnology National Laboratory for Agriculture (LNNA), São Carlos, Brazil.
| | - Juliana Coatrini Soares
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), 13566-590 São Carlos, Brazil
| | - Mario Popolin-Neto
- Institute of Mathematics and Computer Sciences (ICMC), University of São Paulo (USP), 13566-590 São Carlos, Brazil; Federal Institute of São Paulo (IFSP), 14804-296 Araraquara, Brazil
| | | | | | - Fernando V Paulovich
- Department of Mathematics and Computer Science, Eindhoven University of Technology (TU/e), 5600 MB Eindhoven, the Netherlands
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), 13566-590 São Carlos, Brazil.
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3
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Shaldam M, Tawfik H, Elmansi H, Belal F, Yamaguchi K, Sugiura M, Magdy G. Synthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent. J Biomol Struct Dyn 2023; 41:8876-8890. [PMID: 36310097 DOI: 10.1080/07391102.2022.2138551] [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: 07/13/2022] [Accepted: 10/15/2022] [Indexed: 10/31/2022]
Abstract
In the present study, a drug-like molecular hybrid structure between chalcone and sulfonamide moieties was synthesized and characterized. The structural peculiarities of the synthesized hybrid were further verified by means of single crystal X-ray crystallography. Furthermore, its biological activity as an anticancer agent was evaluated. The synthesized model of chalcone-sulfonamide hybrid 3 was found to have potent anticancer properties against the studied cancer cell lines. Hence, the in vitro binding interaction of hybrid 3 with Calf thymus DNA (CT-DNA) was studied at a simulated physiological pH to confirm its anticancer activity for the first time. This was investigated by applying different spectroscopic techniques, ionic strength measurements, viscosity measurements, thermodynamics, molecular dynamic simulation and molecular docking studies. The obtained results showed a clear binding interaction between hybrid 3 and CT-DNA with a moderate affinity via a minor groove binding mechanism. The binding constant (Kb) at 298 K calculated from the Benesi-Hildebrand equation was found to be 3.49 × 104 M-1. The entropy and enthalpy changes (ΔS0 and ΔH0) were 204.65 J mol-1 K-1 and 35.08 KJ mol-1, respectively, indicating that hydrophobic interactions constituted the major binding forces. The results obtained from molecular docking and dynamic simulation studies confirmed the minor groove binding interaction and the stability of the formed complex. This study can contribute to further understanding of the molecular mechanism of hybrid 3 as a potential antitumor agent and can also guide future clinical and pharmacological studies for rational drug design with enhanced or more selective activity and greater efficacy.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Moataz Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Haytham Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Heba Elmansi
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fathalla Belal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Koki Yamaguchi
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Masaharu Sugiura
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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4
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Peng B, Liao P, Jiang Y. Preferential interactions of surface-bound engineered single stranded DNA with highly aromatic natural organic matter: Mechanistic insights and implications for optimizing practical aquatic applications. WATER RESEARCH 2022; 223:119015. [PMID: 36044796 DOI: 10.1016/j.watres.2022.119015] [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: 05/30/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Engineered short-chain single stranded DNA (ssDNA) are emerging materials with various environmental applications, such as aptasensor, selective adsorbent, and hydrological tracer. However, the lack of fundamental understanding on the interactions of such materials with natural organic matter (NOM) hinders the improvement of their application performance in terms of sensitivity, selectivity, and stability. In this study, we investigated the interactions of ssDNA (four strands with systematically varied length and sequence) with two humic acids (Suwannee River humic acid (SRHA) and Aldrich humic acid (AHA)) and two humic-like NOM present in local aquatic matrices (ROM in river water and WOM in wastewater). Detailed, molecular level interaction mechanisms were obtained by probing the colloidal stability of the ssDNA-coated gold nanoparticles, coupled with product characterization using a suite of microscopic and spectroscopic techniques. Our study revealed that π-π interactions and divalent cation bridging were the major mechanisms for ssDNA-NOM interactions. ssDNA preferentially interacted with NOM with high aromaticity (AHA > SRHA/WOM/ROM). With divalent cations present (especially Ca2+), even a small amount of AHA could completely shield ssDNA, whereas the extent of shielding by SRHA/WOM/ROM depended on the relative content of ssDNA and NOM and whether bridges formed. The extent of shielding of ssDNA by NOM provides a potential answer to the reported conflicting effects of natural water matrices on the performance of DNA-based sensors. Taken together, our findings provide insights into the transformations of engineered ssDNA under environmentally relevant conditions as well as implications for their performance optimization in practical aquatic applications (e.g., from DNA design to pretreatment strategy).
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Affiliation(s)
- Bo Peng
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Peng Liao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 99 Lingcheng West Road, Guiyang 550081, China
| | - Yi Jiang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.
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5
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Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib. Sci Rep 2022; 12:14723. [PMID: 36042232 PMCID: PMC9427788 DOI: 10.1038/s41598-022-19015-9] [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: 06/21/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 103 M−1. The enthalpy and entropy changes (∆H0 and ∆S0) were − 33.09 kJ mol−1 and 61.78 J mol−1 K−1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.
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Aminipoya H, Bagheri GH A. Ciprofloxacin: Binding Efficacy with DNA and Enhanced Photocatalytic Degradation by ZrO 2 Synthesized Using Coffee Extract. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Hana Aminipoya
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Azar Bagheri GH
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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7
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Chanphai P, Tajmir-Riahi HA. DNA acidification by citric acid and gallic acid: acid binding site and DNA structural dynamics. J Biomol Struct Dyn 2022; 40:2389-2394. [DOI: 10.1080/07391102.2020.1835730] [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]
Affiliation(s)
- P. Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois, Rivières, Trois-Rivières (Québec), Canada
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois, Rivières, Trois-Rivières (Québec), Canada
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8
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Peng T, Liao W, Gu G, Qiu G, Wu X, Yang F, Zeng W. Insights into the role of extracellular DNA in heavy metal adsorption. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152067. [PMID: 34863749 DOI: 10.1016/j.scitotenv.2021.152067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Extracellular polymeric substances (EPS) participate in heavy metal adsorption in the aquatic environments. Extracellular DNA (eDNA) is an essential component of EPS, but its involvement in metal binding remains ambiguous. Herein, the role of eDNA in Cd(II) and Ni(II) adsorption was described using a combination of semi-quantitative and qualitative approaches. EPS were extracted from Burkholderia sp. MBR-1 and eDNA accounted for 6.9% of the total mass of EPS. The eDNA in the extracted EPS was digested using the DNase II to prepare an eDNA-free EPS sample. Potentiometric titration unveiled that the number of total binding sites of the eDNA-free EPS was 19% lower than the untreated EPS. The Cd(II) and Ni(II) adsorption capacity of the eDNA-free EPS was lower than the untreated EPS at the pH range of 4-7. At pH 7, the results of batch adsorption experiments showed that removing eDNA from EPS resulted in declines of 12.6% and 15.7% in the adsorption capacities for Cd(II) and Ni(II), respectively. Furthermore, Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy unraveled that the phosphoryl groups and purines of eDNA are responsible for Cd(II) and Ni(II) complexation. The results demonstrated that eDNA plays an essential role in heavy metal adsorption.
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Affiliation(s)
- Tangjian Peng
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, China; School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Wanqing Liao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Guohua Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Fei Yang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, China; Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; CSIRO Process Science and Engineering, Clayton, Victoria 3168, Australia.
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9
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Ali SB, Oshido AB, Houlton A, Horrocks BR. Models for sensing by nanowire networks: application to organic vapour detection by multiwall carbon nanotube-DNA films. NANOTECHNOLOGY 2021; 33:045502. [PMID: 34624883 DOI: 10.1088/1361-6528/ac2e20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Electronic sensors for volatile organic compounds have been prepared by drop-casting dispersions of multi-wall carbon nanotubes (MWCNTs) in aqueous solutions ofλ-DNA onto Pt microband electrodes. The MWCNTs themselves show a metal-like temperature dependence of the conductance, but the conductance of DNA/MWCNT composites has an activated component that corresponds to inter-tube tunneling. The resistance of the composite was modelled by a series combination of a term linear in temperature for the nanotubes and a stretched exponential form for the inter-tube junctions. The resistance may increase or decrease with temperature according to the composition and may be tuned to be almost temperature-independent at 67% by mass of DNA. Upon exposure to organic vapours, the resistance of the composites increases and the time-dependence of this signal is consistent with diffusion of the vapour into the composite. The fractional change in resistance at steady-state provides an analytical signal with a linear calibration and the presence of DNA enhances the signal and adjusts the selectivity in favour of polar analytes. The temperature dependence of the signal is determined by the enthalpy of adsorption of the analyte in the inter-tube junctions and may be satisfactorily modelled using the Langmuir isotherm. Temperature and pressure-dependent studies indicate that neither charge injection by oxidation/reduction of the analyte nor condensation of analyte on the device is responsible for the signal. We suggest that the origin of the sensing response is an adsorption of the analyte in the inter-tube regions that modulates the tunneling barriers. This suggests a general route to tuning the selectivity of MWCNT gas sensors using non-conductive polymers of varying chemical functionality.
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Affiliation(s)
- Shams B Ali
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Laser and Optoelectronics Engineering, University of Technology, Baghdad, 10066, Iraq
| | - Atsinafe B Oshido
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Chemistry, Benue State University, Makurdi, 970222, Nigeria
| | - Andrew Houlton
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Benjamin R Horrocks
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
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Magdy G, Belal F, Abdel Hakiem AF, Abdel-Megied AM. Salmon sperm DNA binding study to cabozantinib, a tyrosine kinase inhibitor: Multi-spectroscopic and molecular docking approaches. Int J Biol Macromol 2021; 182:1852-1862. [PMID: 34062156 DOI: 10.1016/j.ijbiomac.2021.05.164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022]
Abstract
In the current work, the binding interaction of cabozantinib with salmon sperm DNA (SS-DNA) was studied under simulated physiological conditions (pH 7.4) using fluorescence emission spectroscopy, UV-Vis absorption spectroscopy, viscosity measurement, ionic strength measurement, FT-IR spectroscopy, and molecular modeling methods. The obtained experimental data demonstrated an apparent binding interaction of cabozantinib with SS-DNA. The binding constant (Kb) of cabozantinib with SS-DNA evaluated from the Benesi-Hildebrand plot was equal to 5.79 × 105 at 298 K. The entropy and enthalpy changes (∆S0 and ∆H0) in the binding interaction of SS-DNA with cabozantinib were 44.13 J mol-1 K-1 and -19.72 KJ mol-1, respectively, demonstrating that the basic binding interaction forces are hydrophobic and hydrogen bonding interactions. Results from UV-Vis absorption spectroscopy, competitive binding interaction with rhodamine B or ethidium bromide, and viscosity measurements revealed that cabozantinib binds to SS-DNA via minor groove binding. The molecular docking results revealed that cabozantinib fits into the AT-rich region of the B-DNA minor groove and the binding site of cabozantinib was 4 base pairs long. Moreover, cabozantinib has eight active torsions, implying a high degree of flexibility in its structure, which played a significant role in the formation of a stable cabozantinib-DNA complex.
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Affiliation(s)
- Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt.
| | - Fathalla Belal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, P.O. Box 35516, Egypt
| | - Ahmed Faried Abdel Hakiem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt
| | - Ahmed M Abdel-Megied
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine Street, Baltimore, MD 21201, USA
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11
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Mohammadkhani A, Bagheri Gh A. Cephalexin: DNA minor groove binders and enhanced photocatalytic degradation by Tl 2O 3 synthesized using basil seed. INORG NANO-MET CHEM 2021. [DOI: 10.1080/24701556.2020.1764972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Arezo Mohammadkhani
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Azar Bagheri Gh
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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12
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Ray B, Mehrotra R. Nucleic acid binding mechanism of flavone derivative, riviciclib: Structural analysis to unveil anticancer potential. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 211:111990. [PMID: 32858336 DOI: 10.1016/j.jphotobiol.2020.111990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/17/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
Despite burgeoned knowledge about the origin, growth, tissue interactions, and spread of cancer in recent years, the functional complexity and unique survival ability of cancer cells still make it difficult to target them. Riviciclib is a semi-synthetic derivative of rohitukine and possesses anticancer potential. Inhibition of nucleic acid activity in an uncontrolled dividing cell can form the basis for the development of new-age cancer therapeutics. The present study reports the molecular interaction between riviciclib and nucleic acid (DNA/tRNA) using spectroscopic and molecular docking studies in an attempt to comprehend its cellular toxicity as well as the nature and mode of binding between them. Vibrational spectroscopic results suggest that riviciclib intercalates DNA duplex and primarily binds with guanine, adenine, and thymine nucleobases. While in the case of riviciclib-tRNA complexation, riviciclib interacts mostly with uracil residues of the tRNA molecule. Besides nucleobases, riviciclib interacts with the sugar-phosphate backbone of both biomacromolecules. Conformationally, DNA alters from B-form to C-form, whereas tRNA shows no change in its native A-form. The order (104 M-1) of binding constant for riviciclib-nucleic acid complexation infer moderate to strong affinity of riviciclib with DNA and tRNA, respectively. Molecular docking explorations are further in corroboration with our spectroscopic outcomes.
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Affiliation(s)
- Bhumika Ray
- CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ranjana Mehrotra
- CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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13
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Chanphai P, Cloutier F, Reyes-Moreno C, Bérubé G, Tajmir-Riahi HA. Locating the binding sites of two aminobenzoic acid derivatives on tRNA: drug binding efficacy and RNA structure. J Biomol Struct Dyn 2020; 40:130-135. [PMID: 32811341 DOI: 10.1080/07391102.2020.1808076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The binding of tRNA to aminobenzoic acid derivatives DAB-0 (N'-[4-(2,5-dioxo-pyrrolidin-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) and DAB-1 (N'-[4-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) was investigated in aqueous solution at physiological pH. Thermodynamic parameters ΔH0 -4.8 to -4.30 (kJ mol-1), ΔS0 24.20 to 22 (J mol-1K-1) and ΔG0 -12 to -11.40 (kJ mol-1) showed that DAB-0 and DAB-1 readily bind tRNA via ionic interactions with DAB-1 forming stronger tRNA adducts. Similar binding sites to A-T and G-C bases were located with DAB-0 and DAB-1. The binding efficacy ranged from 40% to 50%. No alteration of tRNA conformation was detected upon drug complexation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Penparapa Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Francis Cloutier
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Carlos Reyes-Moreno
- Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Department of Medical Biology, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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14
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Xue Y, Wang Y, Wang S, Yan M, Huang J, Yang X. Label-Free and Regenerable Aptasensor for Real-Time Detection of Cadmium(II) by Dual Polarization Interferometry. Anal Chem 2020; 92:10007-10015. [PMID: 32618180 DOI: 10.1021/acs.analchem.0c01710] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, numerous aptamer-based biosensors have been developed to detect heavy metal ions. Most of aptamer-based biosensors only can be used to get some quantitative information. The mechanism of the interaction between aptamer and metal ions, however, is rarely studied. In this work, a label-free and regenerable aptamer-based biosensor was constructed using dual polarization interferometry (DPI). This aptasensor was used to investigate the real-time interaction process between cadmium(II) and its aptamer. According to the information on mass, thickness, and density obtained by DPI, a Cd2+ concentration-dependent interaction mechanism and conformation of aptamer was proposed. At low Cd2+ concentration, Cd2+ mainly interacted with phosphate groups on aptamer, resulting in the stretched ssDNA and a few vertical hairpin structures. When adding the high concentration of Cd2+, Cd2+ primarily bound with bases of DNA by coordination interaction and the conformation of aptamer transferred to a tight and short hairpin structure. In addition, the association rate constant (ka), dissociation rate constant (kd) and disassociation constant (KD) between Cd2+ and its aptamer were calculated to be 96 M-1 S-1, 2.11 × 10-5 S-1, and 220 nM, respectively. The proposed aptasensor showed high sensitivity for Cd2+ detection with the detection limit of 0.61 μg/L, which was far below the 5.0 μg/L ranked by the U.S. Environmental Protection Agency. The biosensor also exhibited excellent regenerability and could be used for three cycles without obvious change in response signal. Therefore, the developed method could not only provide quantitative information, but also offered the information on conformation and kinetics for molecular interaction. This method can facilely extend to study the interaction of DNA with other ions, small molecules, or biomacromolecules.
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Affiliation(s)
- Yu Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yu Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Mengxia Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
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15
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de Campos Vidal B, Mello MLS. Sodium valproate (VPA) interactions with DNA and histones. Int J Biol Macromol 2020; 163:219-231. [PMID: 32619665 DOI: 10.1016/j.ijbiomac.2020.06.265] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023]
Abstract
Valproic acid/sodium valproate (VPA) constitutes a widely prescribed drug for the treatment of seizure disorders and is a well-known epigenetic agent, inducing the acetylation of histones and affecting the methylation status of DNA and histones, with consequences on gene expression. Because this drug has been recently reported to exert affinity for histone H1, and to a minor degree for DNA, in this work, we investigated a possible interaction of sodium valproate with DNA and histones H1 and H3 using high-performance polarization microscopy and Fourier-transform infrared (FTIR) microspectroscopy. The preparations under examination consisted of hemispheres resulting from drop-casting samples containing VPA-DNA and VPA-histone mixtures. The results indicated that VPA may interact with DNA and histones, inducing changes in the textural superstructure and molecular order of the DNA possibly through van der Waals forces, and in histone H1 and H3 conformations, probably as a result of electrostatic binding between the drug and protein amino acid residues. These results contribute to a better understanding of the pharmacological potential of VPA. The precise sites and mechanisms involved in these interactions would certainly benefit from investigations provided by complementary methodologies.
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Affiliation(s)
- Benedicto de Campos Vidal
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), 13083-862 Campinas, SP, Brazil
| | - Maria Luiza S Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), 13083-862 Campinas, SP, Brazil.
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16
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Maurya N, Imtiyaz K, Alam Rizvi MM, Khedher KM, Singh P, Patel R. Comparative in vitro cytotoxicity and binding investigation of artemisinin and its biogenetic precursors with ctDNA. RSC Adv 2020; 10:24203-24214. [PMID: 35516214 PMCID: PMC9055135 DOI: 10.1039/d0ra02042g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
Artemisinin (ART) and its biogenetic precursors artemisinic acid (AA) and dihydroartemisinic acid (DHAA) are important traditional medicinal herb compounds with tumor growth inhibition properties. Herein, we have studied the cytotoxicity of ART, AA, and DHAA on different cancer cell lines (H1299, A431, and HCT 116) and investigated in detail their binding mechanisms with ctDNA by using spectroscopy, cyclic voltammetry, and computational methods. The UV absorbance, cyclic voltammetry, DNA helix melting, competition binding, and circular dichroism studies suggested that the complex formation of ART-ctDNA and AA-ctDNA occurs through groove binding. However, in the case of DHAA-ctDNA interaction, electrostatic interaction plays a major role. The thermodynamic parameters, viz., ΔG 0, ΔH 0, and ΔS 0 were calculated, which showed the involvement of hydrogen bonds and van der Waals interactions for drug-ctDNA interaction. FTIR and molecular docking results suggested that ART, AA, and DHAA were bound to the A-T rich region in the minor groove of ctDNA.
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Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia New Delhi-110025 India +91 11 26983409 +91 8860634100
| | - Khalid Imtiyaz
- Department of Biosciences, Jamia Millia Islamia New Delhi-110025 India
| | | | - Khaled Mohamed Khedher
- Department of Civil Engineering, College of Engineering, King Khalid University Abha 6421 Saudi Arabia
- Department of Civil Engineering, ISET, DGET Nabeul Tunisia
| | - Prashant Singh
- Department of Chemistry, ARSD College, University of Delhi New Delhi-110021 India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia New Delhi-110025 India +91 11 26983409 +91 8860634100
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17
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Chanphai P, Cloutier F, Reyes-Moreno C, Bérubé G, Tajmir-Riahi HA. Binding efficacy of aminobenzoic acid derivatives with DNA duplex: drug binding sites and DNA structure and dynamics. J Biomol Struct Dyn 2020; 39:2278-2283. [PMID: 32151202 DOI: 10.1080/07391102.2020.1740792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - F Cloutier
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - C Reyes-Moreno
- Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Department of Medical Biology, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - G Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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18
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Sych TS, Polyanichko AM, Ramazanov RR, Kononov AI. tRNA as a stabilizing matrix for fluorescent silver clusters: photophysical properties and IR study. NANOSCALE ADVANCES 2019; 1:3579-3583. [PMID: 36133554 PMCID: PMC9418588 DOI: 10.1039/c9na00112c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/22/2019] [Indexed: 06/16/2023]
Abstract
In this experimental study fluorescent silver clusters on a tRNA matrix were synthesized for the first time. Two types of fluorescent complexes emitting in the green (550 nm) and red (635 nm) regions of the visible spectrum were obtained. Using FTIR spectroscopy, we identified possible binding sites for the clusters, which appeared to be within the helical regions of tRNA. It was also shown that tRNA retained its double helical structure after the cluster formation, which is essential for its functionality.
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Affiliation(s)
- Tomash S Sych
- Saint Petersburg State University Saint-Petersburg 199034 Russia
| | | | | | - Alexei I Kononov
- Saint Petersburg State University Saint-Petersburg 199034 Russia
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19
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Chanphai P, Tajmir-Riahi H. Vitamin C binding efficacy with DNA and RNA. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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de Campos Vidal B, Mello MLS. Variable collagen-DNA complex formation in vitro as assessed by optical anisotropy and infrared microspectroscopy. Int J Biol Macromol 2019; 131:510-519. [DOI: 10.1016/j.ijbiomac.2019.03.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 02/01/2023]
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21
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Sarkar S, Shmatova OI, Nenajdenko VG, Bhadra K. Trifluoromethylated carboline compounds targeting DNA: Synthesis, binding and anti-proliferative effects on human cancer cell lines. Bioorg Chem 2019; 86:61-79. [DOI: 10.1016/j.bioorg.2019.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 01/26/2023]
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22
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Chanphai P, Tajmir-Riahi H. Structural dynamics of DNA binding to tea catechins. Int J Biol Macromol 2019; 125:238-243. [DOI: 10.1016/j.ijbiomac.2018.12.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
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23
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Chanphai P, Tajmir-Riahi HA. Effect of tea catechins on tRNA structure and dynamics. J Biomol Struct Dyn 2019; 38:302-306. [PMID: 30739592 DOI: 10.1080/07391102.2019.1570869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AbbreviationsCcatechinECGepicatechin gallateEGCGEpigallocatechin gallateAAdenineCcytosineGGuanineUuracilFTIRFourier transform infraredCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
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24
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Testo and testo-Pt(II) bind DNA at different locations. Chem Biol Interact 2018; 296:179-184. [PMID: 30253125 DOI: 10.1016/j.cbi.2018.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 01/27/2023]
Abstract
The development of new targeted anticancer agents able to efficiently and specifically destroy cancer cells with minimal toxic side effects is nowadays a subject of intensive research endeavors. We report the conjugation of testo and testo-Pt(II) (two semi-synthetic testosterone derivatives) with calf thymus DNA in aqueous solution at physiological pH. Multiple spectroscopic methods, thermodynamic analysis and modeling were used to determine the binding efficacy of these drugs to DNA duplex. Thermodynamic parameters showed drug-DNA conjugation occurs via ionic interactions with testo-Pt(II) forming more stable DNA adducts than testo with Ktesto-DNA = 1.80 (±0.5) x 105 M-1 and Ktesto-Pt(II)-DNA = 2.3 (±0.8) x 105 M-1. Molecular modeling shows that testo and testo-Pt(II) bind DNA at different locations.
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25
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Chanphai P, Ouellette V, Mandal S, Mandal SK, Bérubé G, Tajmir-Riahi HA. Location of multiple binding sites for testo and testo-Pt(II) with tRNA. J Biomol Struct Dyn 2018; 37:4133-4139. [PMID: 30417741 DOI: 10.1080/07391102.2018.1541142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the binding of testo and testo-Pt(II) complexes (testosterone derivatives) with tRNA in aqueous solution at physiological pH. Thermodynamic parameter ΔH0 -8 to -3 (kJ mol-1), ΔS0 35 to 18 (J mol-1K-1) and ΔG0 -14 to -13 (kJ mol-1) and other spectroscopic results showed drug-tRNA binding occurs via ionic contacts with testo-Pt(II) forming more stable tRNA complexes in comparison to testo: Ktesto-Pt(II)-tRNA= 3.2 (± 0.9) × 105 M-1 > Ktesto-tRNA= 2.1 (± 0.7) × 105 M-1. Molecular modeling showed multiple binding sites for testo and testo-Pt(II) on tRNA molecule. Some of the useful molecular descriptors are calculated. Major structural changes were observed for biopolymers upon drug complexation, while tRNA remains in the A-family structures.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - V Ouellette
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - S Mandal
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Department of Physiology and Pathophysiology, College of Medicine, Rady Faculty of Health Sciences, University of Manitoba , Winnipeg , MB , Canada
| | - S K Mandal
- St. John's, Newfoundland, Canada and College of the North Atlantic, Faculty of Medicine, Memorial University of Newfoundland , Newfoundland , Canada
| | - G Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
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26
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Han Y, Jian L, Yao Y, Wang X, Han L, Liu X. Insight into Rapid DNA-Specific Identification of Animal Origin Based on FTIR Analysis: A Case Study. Molecules 2018; 23:molecules23112842. [PMID: 30388819 PMCID: PMC6278494 DOI: 10.3390/molecules23112842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022] Open
Abstract
In this study, a methodology has been proposed to identify the origin of animal DNA, employing high throughput extension accessory Fourier transform infrared (HT-FTIR) spectroscopy coupled with chemometrics. Important discriminatory characteristics were identified in the FTIR spectral peaks of 51 standard DNA samples (25 from bovine and 26 from fish origins), including 1710, 1659, 1608, 1531, 1404, 1375, 1248, 1091, 1060, and 966 cm−1. In particular, the bands at 1708 and 1668 cm−1 were higher in fish DNA than in bovine DNA, while the reverse was true for the band at 1530 cm−1 was shown the opposite result. It was also found that the PO2− Vas/Vs ratio (1238/1094 cm−1) was significantly higher (p < 0.05) in bovine DNA than in fish DNA. These discriminatory characteristics were further revealed to be closely related to the base content and base sequences of different samples. Multivariate analyses, such as principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were conducted, and both the sensitivity and specificity values of PLS-DA model were one. This methodology has been further validated by 20 meat tissue samples (4 from bovine, 5 from ovine, 5 from porcine, and 6 from fish origins), and these were successfully differentiated. This case study demonstrated that FTIR spectroscopy coupled with PLS-DA discriminant model could provide a rapid, sensitive, and reliable approach for the identification of DNA of animal origin. This methodology could be widely applied in food, feed, forensic science, and archaeology studies.
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Affiliation(s)
- Yahong Han
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Lin Jian
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Yumei Yao
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Xinlei Wang
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Lujia Han
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Xian Liu
- College of Engineering, China Agricultural University, Beijing 100083, China.
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27
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Soares AC, Soares JC, Rodrigues VC, Follmann HDM, Arantes LMRB, Carvalho AC, Melendez ME, Fregnani JHTG, Reis RM, Carvalho AL, Oliveira ON. Microfluidic-Based Genosensor To Detect Human Papillomavirus (HPV16) for Head and Neck Cancer. ACS APPLIED MATERIALS & INTERFACES 2018; 10:36757-36763. [PMID: 30296059 DOI: 10.1021/acsami.8b14632] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
High-risk human papillomavirus (HPV) infection, mainly with HPV16 type, has been increasingly considered as an important etiologic factor in head and neck cancers. Detection of HPV16 is therefore crucial for these types of cancer, but clinical tests are not performed routinely in public health systems owing to the high cost and limitations of the existing tests. In this article, we report on a potentially low-cost genosensor capable of detecting low concentrations of HPV16 in buffer samples and distinguishing, with high accuracy, head and neck cancer cell lines according to their HPV16 status. The genosensor consisted of a microfluidic device that had an active layer of a HPV16 capture DNA probe (cpHPV16) deposited onto a layer-by-layer film of chitosan and chondroitin sulfate. Impedance spectroscopy was the principle of detection utilized, leading to a limit of detection of 10.5 pM for complementary ssDNA HPV16 oligos (ssHPV16). The genosensor was also able to distinguish among HPV16+ and HPV16- cell lines, using the multidimensional projection technique interactive document mapping. Hybridization between the ssHPV16 oligos and cpHPV16 probe was confirmed with polarization-modulated infrared reflection-absorption spectroscopy, where PO2 and amide I and amide II bands from adenine and thymine were monitored. The electrical response could be modeled as resulting from an adsorption process represented in a Freundlich model. Because the fabrication procedures of the microfluidic devices and genosensors and the data collection and analysis can be implemented at low cost, the results presented here amount to a demonstration of possible routine screening for HPV infections.
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Affiliation(s)
- Andrey Coatrini Soares
- São Carlos Institute of Physics , University of São Paulo , 13566-590 São Carlos , Brazil
| | | | | | | | | | - Ana Carolina Carvalho
- Molecular Oncology Research Center , Barretos Cancer Hospital , 14784-400 Barretos , Brazil
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center , Barretos Cancer Hospital , 14784-400 Barretos , Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center , Barretos Cancer Hospital , 14784-400 Barretos , Brazil
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences , University of Minho , 4710-057 Braga , Portugal
- ICVS/3B's-PT Government Associate Laboratory , 4710-057 Braga , Portugal
| | - André Lopes Carvalho
- Molecular Oncology Research Center , Barretos Cancer Hospital , 14784-400 Barretos , Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics , University of São Paulo , 13566-590 São Carlos , Brazil
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28
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DNA binding efficacy with functionalized folic acid-PAMAM nanoparticles. Chem Biol Interact 2018; 290:52-56. [DOI: 10.1016/j.cbi.2018.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/15/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023]
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29
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Baltazar C, Mun R, Tajmir-Riahi H, Bariyanga J. Spectroscopic studies on the interaction of mimosine with BSA and DNA. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Chanphai P, Tajmir-Riahi HA. tRNA conjugation with folic acid-chitosan conjugates. Int J Biol Macromol 2017; 105:810-815. [PMID: 28735004 DOI: 10.1016/j.ijbiomac.2017.07.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/15/2017] [Accepted: 07/17/2017] [Indexed: 01/06/2023]
Abstract
The conjugation of tRNA with folic acid-chitosan conjugates was studied, using multiple spectroscopic methods and transmission electron microscopy (TEM). Thermodynamic analysis ΔH -14 to -10 (KJMol-1) and ΔS 14 to -1 (JMol-1, K-1) showed tRNA-folic acid-chitosan bindings occur via H-bonding, hydrophobic and van der Waals contacts. The loading efficacy and the stability of tRNA conjugates were enhanced as folic acid-chitosan size increased. TEM analysis showed major tRNA morphological changes, upon folic acid-chitosan conjugation. No alteration of tRNA conformation was observed on conjugate formation. Folic acid-chitosan conjugates can deliver tRNA in vitro.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7, Canada.
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31
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Pedersen M, Wegner C, Phansak P, Sarath G, Gaussoin R, Schlegel V. Monitoring wheat mitochondrial compositional and respiratory changes using Fourier transform mid-infrared spectroscopy in response to agrochemical treatments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:727-732. [PMID: 27788471 DOI: 10.1016/j.saa.2016.10.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/25/2016] [Accepted: 10/16/2016] [Indexed: 06/06/2023]
Abstract
Fungicides and plant growth regulators can impact plant growth outside of their effects on fungal pathogens. Although many of these chemicals are inhibitors of mitochondrial oxygen uptake, information remains limited as to whether they are able to modify other mitochondrial constituents. Fourier transform mid-infrared spectroscopy (FT-mIR) offers a high sample throughput method to comparatively and qualitatively evaluate the effects of exogenously added compounds on mitochondrial components. Therefore the objective of this study was to determine the ability of FT-mIR to detect effects mitochondrial fractions isolated from wheat (Triticum aestivum L.) seedlings in response to several agrochemical treatments, with an emphasis on fungicides. The accessed need was to develop FT-mIR analytical and statistical routines as an effective approach to differentiate spectra obtained from chemically-treated or untreated mitochondria. An NADH-dependent oxygen uptake approach was initially used as a comparative method to determine whether the fungicides (azoxystrobin, boscalid, cyazofamid, fluazinam, isopyrazam, and pyraclostrobin) and the plant growth regulator, (trinexapac-ethyl) reduced respiration inhibition on isolated mitochondria. Pyraclostrobin was the most effective inhibitor, whereas amisulbrom did not impact oxygen uptake. However, hierarchical clustering of FT-mIR spectra of isolated mitochondria treated with these different compounds separated into clades consistent with each of their expected mode of action. Analysis of the FT-mIR amide protein region indicated that amisulbrom and pyraclostrobin interacted with the isolated wheat mitochondria. Both chemicals were statistically different from the control signifying that respiration was indeed influenced by these treatments. Moreover, the entire FT-mIR region showed differences in various biological bands thereby providing additional information on mitochondria responses to agrochemicals, if so warranted.
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Affiliation(s)
- Matthew Pedersen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Casey Wegner
- Zomedic Pharmacceuticals, 3928 Varsity Drive, Ann Arbor, MI 48103, USA.
| | - Piyaporn Phansak
- Division of Biology, Faculty of Science, Nakhon Phanom University, Muang, Nakhon Phanom 48000, Thailand.
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, 251 Filley Hall, East Campus, UNL, Lincoln, NE 68583-0937, USA.
| | - Roch Gaussoin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Vicki Schlegel
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Veronezi GMB, Felisbino MB, Gatti MSV, Mello MLS, Vidal BDC. DNA Methylation Changes in Valproic Acid-Treated HeLa Cells as Assessed by Image Analysis, Immunofluorescence and Vibrational Microspectroscopy. PLoS One 2017; 12:e0170740. [PMID: 28114349 PMCID: PMC5256918 DOI: 10.1371/journal.pone.0170740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
Valproic acid (VPA), a well-known histone deacetylase inhibitor, has been reported to affect the DNA methylation status in addition to inducing histone hyperacetylation in several cell types. In HeLa cells, VPA promotes histone acetylation and chromatin remodeling. However, DNA demethylation was not checked in this cell model for standing effects longer than those provided by histone acetylation, which is a rapid and transient phenomenon. Demonstration of VPA-induced DNA demethylation in HeLa cells would contribute to understanding the effect of VPA on an aggressive tumor cell line. In the present work, DNA demethylation in VPA-treated HeLa cells was assessed by image analysis of chromatin texture, the abundance of 5-methylcytosine (5mC) immunofluorescence signals and Fourier transform-infrared (FT-IR) microspectroscopy centered on spectral regions related to the vibration of–CH3 groups. Image analysis indicated that increased chromatin unpacking promoted by a 4-h-treatment with 1.0 mM VPA persisted for 24 h in the absence of the drug, suggesting the occurrence of DNA demethylation that was confirmed by decreased 5mC immunofluorescence signals. FT-IR spectra of DNA samples from 1 mM or 20 mM VPA-treated cells subjected to a peak fitting analysis of the spectral window for–CH3 stretching vibrations showed decreased vibrations and energy of these groups as a function of the decreased abundance of 5mC induced by increased VPA concentrations. Only the 20 mM-VPA treatment caused an increase in the ratio of -CH3 bending vibrations evaluated at 1375 cm-1 in relation to in-plane vibrations of overall cytosines evaluated at 1492 cm-1. CH3 stretching vibrations showed to be more sensitive than–CH3 bending vibrations, as detected with FT-IR microspectroscopy, for studies aiming to associate vibrational spectroscopy and changes in DNA 5mC abundance.
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Affiliation(s)
- Giovana M. B. Veronezi
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Marina Barreto Felisbino
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Sílvia V. Gatti
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Luiza S. Mello
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
- * E-mail:
| | - Benedicto de Campos Vidal
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
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Bonsaii M, Gholivand K, Khosravi M, Abdi K. Negative hyperconjugation effect on the reactivity of phosphoramide mustard derivatives as a DNA alkylating agent: theoretical and experimental insights. NEW J CHEM 2017. [DOI: 10.1039/c7nj01402c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we suggest new factors affecting the reactivity of compounds similar to cyclophosphamide; as their reactivity mainly relies on the frontier molecular orbitals, the factors causing changes in the frontier molecular orbitals, alter the reactivity of these compounds too.
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Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | | | - Morteza Khosravi
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
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Effect of testosterone and its aliphatic and aromatic dimers on DNA morphology. Int J Biol Macromol 2016; 95:850-855. [PMID: 27693340 DOI: 10.1016/j.ijbiomac.2016.09.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Conjugation of DNA with testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) was investigated in aqueous solution at pH 7.4. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-DNA binding and DNA morphology. Spectroscopic analysis showed that testosterone binds DNA via A7, A16, A17, T8, T15 and T18 nucleobases with overall binding constants Ktest-DNA=1.8 (±0.4)×104M-1, Ktest-dimeralip-DNA=5.7 (±0.7)×104M-1 and Ktest-dimer-arom-DNA=7.3 (±0.9)×104M-1. The binding affinity increases in this order: testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 40-50%. Transmission electron microscopy showed major changes in DNA morphology as testosterone-DNA interaction occurred with increase in the diameter of the DNA aggregate, indicating encapsulation of testosterone by DNA. Modeling showed the presence of several nucleobases attached to testosterone with the free binding energy of -4.93Kcal/mol.
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Review on the binding of anticancer drug doxorubicin with DNA and tRNA: Structural models and antitumor activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:274-9. [PMID: 26971631 DOI: 10.1016/j.jphotobiol.2016.02.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/13/2016] [Indexed: 01/08/2023]
Abstract
In this review, we have compared the results of multiple spectroscopic studies and molecular modeling of anticancer drug doxorubicin (DOX) bindings to DNA and tRNA. DOX was intercalated into DNA duplex, while tRNA binding is via major and minor grooves. DOX-DNA intercalation is close to A-7, C-5, *C-19 (H-bonding with DOX NH2 group), G-6, T-8 and T-18 with the free binding energy of -4.99kcal/mol. DOX-tRNA groove bindings are near A-29, A-31, A-38, C-25, C-27, C-28, *G-30 (H-bonding) and U-41 with the free binding energy of -4.44kcal/mol. Drug intercalation induced a partial B to A-DNA transition, while tRNA remained in A-family structure. The structural differences observed between DOX bindings to DNA and tRNA can be the main reasons for drug antitumor activity. The results of in vitro MTT assay on SKC01 colon carcinoma are consistent with the observed DNA structural changes. Future research should be focused on finding suitable nanocarriers for delivery of DOX in vivo in order to exploit the full capacity of this very important anticancer drug.
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Ray B, Agarwal S, Lohani N, Rajeswari MR, Mehrotra R. Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA. J Biomol Struct Dyn 2016; 34:2518-35. [DOI: 10.1080/07391102.2015.1118708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Neelam Lohani
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Moganty R. Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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Hufton J, Harding JH, Romero-González ME. The role of extracellular DNA in uranium precipitation and biomineralisation. Phys Chem Chem Phys 2016; 18:29101-29112. [DOI: 10.1039/c6cp03239g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The reaction mechanism for the formation of uranyl–eDNA precipitates was determined as a phosphate mediated process.
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Affiliation(s)
- Joseph Hufton
- Department of Geography
- The University of Sheffield
- Sheffield
- UK
| | - John H. Harding
- Department of Materials Science and Engineering
- Sir Robert Hadfield Building
- University of Sheffield
- Sheffield
- UK
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38
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Bonsaii M, Gholivand K, Abdi K, Valmoozi AAE, Khosravi M. A combined experimental and computational study on the interaction of nitrogen mustards with DNA. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00264a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, we suggest that the role of water in the reaction of nitrogen mustards with DNA is more than what was thought before. Nitrogen mustards become activated when they are hydrated by water.
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Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
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Kumar N, Kumar R, Nemaysh V, Lal N, Luthra PM. Bis((1,4-dimethyl-9H-carbazol-3-yl)methyl)amine-mediated anticancer effect triggered by sequence-specific cleavage of DNA leading to programmed cell death in the human U87 cell line. RSC Adv 2016. [DOI: 10.1039/c6ra12999d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bis((1,4-dimethyl-9H-carbazol-3-yl)methyl)amine (DMCM) has been designed as a novel anti-cancer agent which is believed to have a sequence-specific groove binding interaction with DNA, leading to anticancer effects.
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Affiliation(s)
- Nitin Kumar
- Neuropharmaceutical Chemistry Laboratory
- Dr B.R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi – 110007
- India
| | - Rakesh Kumar
- Neuropharmaceutical Chemistry Laboratory
- Dr B.R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi – 110007
- India
| | - Vishal Nemaysh
- Neuropharmaceutical Chemistry Laboratory
- Dr B.R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi – 110007
- India
| | - Neetika Lal
- Neuropharmaceutical Chemistry Laboratory
- Dr B.R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi – 110007
- India
| | - Pratibha Mehta Luthra
- Neuropharmaceutical Chemistry Laboratory
- Dr B.R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi – 110007
- India
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40
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Agudelo D, Kreplak L, Tajmir-Riahi HA. tRNA conjugation with chitosan nanoparticles: An AFM imaging study. Int J Biol Macromol 2015; 85:150-6. [PMID: 26723249 DOI: 10.1016/j.ijbiomac.2015.12.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 02/06/2023]
Abstract
The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H4R2, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada.
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41
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Agudelo D, Kreplak L, Tajmir-Riahi HA. Microscopic and spectroscopic analysis of chitosan-DNA conjugates. Carbohydr Polym 2015; 137:207-213. [PMID: 26686122 DOI: 10.1016/j.carbpol.2015.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 08/31/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022]
Abstract
Conjugations of DNA with chitosans 15 kD (ch-15), 100 kD (ch-100) and 200 kD (ch-200) were investigated in aqueous solution at pH 5.5-6.5. Multiple spectroscopic methods and atomic force microscopy (AFM) were used to locate the chitosan binding sites and the effect of polymer conjugation on DNA compaction and particle formation. Structural analysis showed that chitosan-DNA conjugation is mainly via electrostatic interactions through polymer cationic charged NH2 and negatively charged backbone phosphate groups. As polymer size increases major DNA compaction and particle formation occurs. At high chitosan concentration major DNA structural changes observed indicating a partial B to A-DNA conformational transition.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie, University, Lord Dalhousie Drive, Halifax, NS, Canada B3H 4R2
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7.
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42
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Structural modeling for DNA binding to antioxidants resveratrol, genistein and curcumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 151:69-75. [DOI: 10.1016/j.jphotobiol.2015.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/07/2023]
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Bao C, Conde J, Curtin J, Artzi N, Tian F, Cui D. Bioresponsive antisense DNA gold nanobeacons as a hybrid in vivo theranostics platform for the inhibition of cancer cells and metastasis. Sci Rep 2015; 5:12297. [PMID: 26189409 PMCID: PMC4507177 DOI: 10.1038/srep12297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/23/2015] [Indexed: 12/26/2022] Open
Abstract
Gold nanobeacons can be used as a powerful tool for cancer theranostics. Here, we proposed a nanomaterial platform based on gold nanobeacons to detect, target and inhibit the expression of a mutant Kras gene in an in vivo murine gastric cancer model. The conjugation of fluorescently-labeled antisense DNA hairpin oligonucleotides to the surface of gold nanoparticles enables using their localized surface plasmon resonance properties to directly track the delivery to the primary gastric tumor and to lung metastatic sites. The fluorescently labeled nanobeacons reports on the interaction with the target as the fluorescent Cy3 signal is quenched by the gold nanoparticle and only emit light following conjugation to the Kras target owing to reorganization and opening of the nanobeacons, thus increasing the distance between the dye and the quencher. The systemic administration of the anti-Kras nanobeacons resulted in approximately 60% tumor size reduction and a 90% reduction in tumor vascularization. More important, the inhibition of the Kras gene expression in gastric tumors prevents the occurrence of metastasis to lung (80% reduction), increasing mice survival in more than 85%. Our developed platform can be easily adjusted to hybridize with any specific target and provide facile diagnosis and treatment for neoplastic diseases.
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Affiliation(s)
- Chenchen Bao
- Institute of Nano Biomedicine and Engineering, Key Lab. of Thin Film and Microfabrication Technology of Ministry of Education, Department of instrument science and engineering, School of Electronic Information and Electrical Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, P.R.China
| | - João Conde
- 1] Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Harvard-MIT Division for Health Sciences and Technology, Cambridge, Massachusetts, USA [2] School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - James Curtin
- School of Food Science and Environmental Health, College of Sciences and Health, Dublin Institute of Technology, Cathal Brugha Street, Dublin, Ireland
| | - Natalie Artzi
- 1] Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Harvard-MIT Division for Health Sciences and Technology, Cambridge, Massachusetts, USA [2] Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Furong Tian
- Focas Research Institute, Dublin Institute of Technology, Camden Row, Dublin, Ireland
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Key Lab. of Thin Film and Microfabrication Technology of Ministry of Education, Department of instrument science and engineering, School of Electronic Information and Electrical Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, P.R.China
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44
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N'soukpoé-Kossi CN, Bourassa P, Mandeville JS, Bekale L, Bariyanga J, Tajmir-Riahi HA. Locating the binding sites of antioxidants resveratrol, genistein and curcumin with tRNA. Int J Biol Macromol 2015; 80:41-7. [PMID: 26093317 DOI: 10.1016/j.ijbiomac.2015.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/26/2022]
Abstract
We located the binding sites of antioxidants resveratrol, genistein and curcumin on tRNA in aqueous solution at physiological conditions using constant tRNA concentration and various polyphenol contents. FTIR, UV-visible, CD spectroscopic methods and molecular modeling were used to determine polyphenol binding sites, the binding constant and the effects of polyphenol complexation on tRNA conformation and particle formation. Structural analysis showed that polyphenols bind tRNA via G-C and A-U base pairs through hydrophilic, hydrophobic and H-bonding contacts with overall binding constants of K(res-tRNA)=8.95(±0.80)×10(3) M(-1), K(gen-tRNA)=3.07(±0.5)×10(3) M(-1) and K(cur-tRNA)=1.55(±0.3)×10(4) M(-1). Molecular modeling showed the participation of several nucleobases in polyphenol-tRNA adduct formation with free binding energy of -4.43 for resveratrol, -4.26 kcal/mol for genistein and -4.84 kcal/mol for curcumin, indicating that the interaction process is spontaneous at room temperature. While tRNA remains in A-family structure, major biopolymer aggregation and particle formation occurred at high polyphenol contents.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - P Bourassa
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J S Mandeville
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - L Bekale
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J Bariyanga
- Department of Chemistry, University of Hawaii-West O'ahu, 96-129 Ala Ike, Pearl City, HI 96782, USA
| | - H A Tajmir-Riahi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7.
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Abassi Joozdani F, Yari F, Abassi Joozdani P, Nafisi S. Interaction of sulforaphane with DNA and RNA. PLoS One 2015; 10:e0127541. [PMID: 26030290 PMCID: PMC4452540 DOI: 10.1371/journal.pone.0127541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/16/2015] [Indexed: 01/19/2023] Open
Abstract
Sulforaphane (SFN) is an isothiocyanate found in cruciferous vegetables with anti-inflammatory, anti-oxidant and anti-cancer activities. However, the antioxidant and anticancer mechanism of sulforaphane is not well understood. In the present research, we reported binding modes, binding constants and stability of SFN–DNA and -RNA complexes by Fourier transform infrared (FTIR) and UV–Visible spectroscopic methods. Spectroscopic evidence showed DNA intercalation with some degree of groove binding. SFN binds minor and major grooves of DNA and backbone phosphate (PO2), while RNA binding is through G, U, A bases with some degree of SFN–phosphate (PO2) interaction. Overall binding constants were estimated to be K(SFN–DNA)=3.01 (± 0.035)×104 M-1 and K(SFN–RNA)= 6.63 (±0.042)×103 M-1. At high SFN concentration (SFN/RNA = 1/1), DNA conformation changed from B to A occurred, while RNA remained in A-family structure.
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Affiliation(s)
| | - Faramarz Yari
- Department of Biology, IAU, Science and Research Branch, Tehran, Iran
| | | | - Shohreh Nafisi
- Department of Chemistry, IAU, Central Tehran Branch, Tehran, Iran
- Department of Dermatology, University of California, San Francisco, California, United States of America
- * E-mail:
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46
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de Lima SV, de Oliveira HP, Andrade CA, de Melo CP. A dielectric study of interpolymer complexes of polyaniline and DNA. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Bourassa P, Tajmir-Riahi H. Folic acid binds DNA and RNA at different locations. Int J Biol Macromol 2015; 74:337-42. [DOI: 10.1016/j.ijbiomac.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022]
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48
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Manojkumar K, Prabhu Charan KT, Sivaramakrishna A, Jha PC, Khedkar VM, Siva R, Jayaraman G, Vijayakrishna K. Biophysical characterization and molecular docking studies of imidazolium based polyelectrolytes-DNA complexes: role of hydrophobicity. Biomacromolecules 2015; 16:894-903. [PMID: 25671794 DOI: 10.1021/bm5018029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nonviral gene delivery vectors are acquiring greater attention in the field of gene therapy by replacing the biological viral vectors. DNA-cationic polymer complexes are one of the most promising systems to find application in gene therapy. Hence, a complete insight of their biophysical characterization and binding energy profile is important in understanding the mechanism involved in nonviral gene therapy. In this investigation, the interaction between calf thymus DNA (ctDNA) and imidazolium-based poly(ionic liquids) (PILs) also known as polyelectrolytes with three different alkyl side chains (ethyl, butyl, and hexyl) in physiological conditions using various spectroscopic experiments with constant DNA concentration and varying polyelectrolyte concentrations is reported. UV-visible absorption, fluorescence quenching studies, gel electrophoresis, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) have confirmed the binding of polyelectrolytes with DNA. UV-vis absorption measurements and fluorescence quenching revealed that the binding between DNA and the polyelectrolyte is dominated by electrostatic interactions. Additionally, CD and FTIR results indicated that the DNA retained its B-form with minor perturbation in the phosphate backbone without significant change in the conformation of its base pairs. Preference for alkyl side chains (K(PIL-Ethyl Br) < K(PIL-Butyl Br) < K(PIL-Hexyl Br)) toward efficient binding between the polyelectrolyte and DNA was inferred from the binding and quenching constants calculated from the absorption and emission spectra, respectively. Further, in silico molecular docking studies not only validated the observed binding trend but also provided insight into the binding mode of the polyelectrolyte-DNA complex.
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Affiliation(s)
- Kasina Manojkumar
- Organic Chemistry Division, School of Advanced Sciences, ∥Plant Biotechnology Division, School of Biosciences and Technology, and ⊥Bioinformatics Division, School of Biosciences and Technology, VIT University , Vellore-632014, Tamil Nadu, India
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Das T, Kutty SK, Tavallaie R, Ibugo AI, Panchompoo J, Sehar S, Aldous L, Yeung AWS, Thomas SR, Kumar N, Gooding JJ, Manefield M. Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation. Sci Rep 2015; 5:8398. [PMID: 25669133 PMCID: PMC4323658 DOI: 10.1038/srep08398] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/12/2015] [Indexed: 01/22/2023] Open
Abstract
Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation.
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Affiliation(s)
- Theerthankar Das
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Samuel K Kutty
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Roya Tavallaie
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Amaye I Ibugo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Janjira Panchompoo
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Shama Sehar
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Leigh Aldous
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Amanda W S Yeung
- Centre for Vascular Research and School of Medical Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Shane R Thomas
- Centre for Vascular Research and School of Medical Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Naresh Kumar
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, University of New South Wales (UNSW), Sydney 2052, Australia
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney 2052, Australia
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Agarwal S, Chadha D, Mehrotra R. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine–DNA adduct formation. J Biomol Struct Dyn 2014; 33:1653-68. [DOI: 10.1080/07391102.2014.968874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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