1
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Parvin SI, Mandal MK, Gopi P, Singh S, Khan MR, Pandya P, Islam MM, Gazi HAR. A comparative study on DNA and protein binding properties of thymol and thymoquinone. J Biomol Struct Dyn 2023; 41:10944-10956. [PMID: 36841618 DOI: 10.1080/07391102.2023.2180665] [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: 08/13/2022] [Accepted: 12/10/2022] [Indexed: 02/27/2023]
Abstract
Two phytochemicals, thymol and thymoquinone obtained from thymes (Thymus vulgaris L., Lamiaceae etc.) and Nagila Sativa seed, respectively. Both the phytochemicals show several biochemical activities like anticancer, antimicrobial etc. In this paper, we studied the affinities of thymol and thymoquinone towards calf thymus DNA (CT-DNA) and protein (bovine serum albumin). Spectroscopic and molecular modelling studies revealed that both compounds have a high affinity toward both the receptors; DNA and protein. Both phytochemicals binds to the minor grooves of DNA and suitable pockets of protein. Several free energy function and hydrogen bonding play significant role during the binding phenomenon.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | | | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida, India
| | - Md Maidul Islam
- Department of Chemistry, Aliah University, New Town, Kolkata, India
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2
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Mati SS, Chowdhury S, Sarkar S, Bera N, Sarkar N. Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study. Int J Biol Macromol 2023:124933. [PMID: 37230444 DOI: 10.1016/j.ijbiomac.2023.124933] [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: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023]
Abstract
Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding preference with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (Kabs = 6.3 × 105 M-1, 5.6 × 104 M-1, 4.3 × 104 M-1 and Kemiss = 6.1 × 105 M-1, 5.7 × 104 M-1 and 3.5 × 104 M-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5/-GCGAATTCGC-3/ and 3/-CGCTTAAGCG-5/). Cell viability assays (86.13 % in 6.58 μM and 84.01 % in 9.88 μM concentrations) and confocal microscopy revealed low cytotoxicity (IC50 25.86 μM) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encompassing nucleic acid therapeutics.
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Affiliation(s)
- Soumya Sundar Mati
- Department of Chemistry, Government General Degree College, Keshiary, Paschim Medinipur,WB 721135, India.
| | - Sourav Chowdhury
- Structural Biology and Bio-informatics division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Soumen Sarkar
- Department of Chemistry, Balurghat College, Dakshin Dinajpur, WB 733101, India
| | - Nanigopal Bera
- Department of Chemistry, Indian Institute of Technology, Kharagpur, Paschim Medinipur, WB 721302, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, Paschim Medinipur, WB 721302, India.
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3
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Mohammad M, Saha I, Pal K, Karmakar P, Pandya P, Gazi HAR, Islam MM. A comparison on the biochemical activities of Fluorescein disodium, Rose Bengal and Rhodamine 101 in the light of DNA binding, antimicrobial and cytotoxic study. J Biomol Struct Dyn 2022; 40:9848-9859. [PMID: 34121614 DOI: 10.1080/07391102.2021.1936180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biochemical activities of Fluorescein, Rose Bengal and Rhodamine 101 were studied by DNA binding, antibacterial and cytotoxic studies. DNA binding studies were done using spectroscopic, thermodynamic and molecular modeling techniques. Antibacterial activities were investigated against a gram-negative bacteria Escherichia coli and a gram-positive bacteria Staphylococcus aureus. Cytotoxic activities were studied against Wi-38 cell line. We observed these dyes bound to minor groove of DNA and structural diversity of dyes affect the phenomenon. No significant antibacterial and cytotoxic activities of these dyes were found in our observations.
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Affiliation(s)
- Mukti Mohammad
- Department of Chemistry, Aliah University, Kolkata, India
| | - Ishita Saha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Kunal Pal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, India
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4
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Gopi P, Singh S, Islam MM, Yadav A, Gupta N, Pandya P. Thermodynamic and structural profiles of multi-target binding of vinblastine in solution. J Mol Recognit 2022; 35:e2989. [PMID: 36054496 DOI: 10.1002/jmr.2989] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/05/2023]
Abstract
Structural information about drug-receptor interactions is paramount in drug discovery and subsequent optimization processes. Drugs can bind to multiple potential targets as they contain common chemical entities in their structures. Understanding the details of such interactions offer possibilities for repurposing and developing potent inhibitors of disease pathways. Vinblastine (VLB) is a potent anticancer molecule showing multiple receptor interactions with different affinities and degrees of structural perturbations. We have investigated the multi-target binding profile of VLB with DNA and human serum albumin (HSA) in a dynamic physiological environment using spectroscopic, molecular dynamics simulations, and quantum mechanical calculations to evaluate the structural features, mode, ligand and receptor flexibility, and energetics of complexation. These results confirm that VLB prefers to bind in the major groove of DNA with some inclination toward Thymidine residue and the TR-5 binding site in HSA with its catharanthine half making important contacts with both the receptors. Spectroscopic investigation at multiple temperatures has also proved that VLB binding is entropy driven indicating the major groove and TR-5 binding site of interaction. Finally, the overall binding is facilitated by van der Waals contacts and a few conventional H-bonds. VLB portrays reasonable conformational diversity on binding with multiple receptors.
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Affiliation(s)
- Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
| | | | - Akankasha Yadav
- Department of Chemistry, University of Rajasthan, Jaipur, India
| | - Neelima Gupta
- Department of Chemistry, University of Rajasthan, Jaipur, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
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5
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Raza A, Mahmood R, Habib S, Talha M, Khan S, Hashmi MA, Mohammad T, Ali A. Fructosylation of human insulin causes AGEs formation, structural perturbations and morphological changes: an in silico and multispectroscopic study. J Biomol Struct Dyn 2022:1-13. [DOI: 10.1080/07391102.2022.2098820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Ali Raza
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Riaz Mahmood
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Talha
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shifa Khan
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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6
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Nandy A, Shekhar S, Paul BK, Mukherjee S. Exploring the Nucleobase-Specific Hydrophobic Interaction of Cryptolepine Hydrate with RNA and Its Subsequent Sequestration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11176-11187. [PMID: 34499515 DOI: 10.1021/acs.langmuir.1c02123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The study of the interactions of drug molecules with genetic materials plays a key role underlying the development of new drugs for many life-threatening diseases in pharmaceutical industries. Understanding their fundamental base-specific and/or groove-binding interaction is crucial to target the genetic material with an external drug, which can pave the way to curing diseases related to the genetic material. Here, we studied the interaction of cryptolepine hydrate (CRYP) with RNA under physiological conditions knowing the antimalarial and anticancer activities of the drug. Our experiments explicitly demonstrate that CRYP interacts with the guanine- and adenine-rich region within the RNA duplex. The pivotal role of the hydrophobic interaction governing the interaction is substantiated by temperature-dependent isothermal titration calorimetry experiments and spectroscopic studies. Circular dichroism study underpins a principally intercalative mode of binding of CRYP with RNA. This interaction is found to be drastically affected in the presence of magnesium salt, which has a strong propensity to coordinate with RNA nucleobases, which can in turn modulate the interaction of the drug with RNA. The temperature-dependent calorimetric results substantiate the occurrence of entropy-enthalpy compensation, which enabled us to rule out the possibility of groove binding of the drug with RNA. Furthermore, our results also show the application of host-guest chemistry in sequestering the RNA-bound drug, which is crucial to the development of safer therapeutic applications.
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Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Shashi Shekhar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Bijan K Paul
- Department of Chemistry, Mahadevananda Mahavidyalaya, Barrackpore, Kolkata 700120, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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7
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Yoshinaga M, Rocha WR. Theoretical Investigation of the 4,5-Dibromorodamine Methyl Ester (TH9402) Photosensitizer Used in Photodynamic Therapy: Photophysics, Reactions in the Excited State, and Interactions with DNA. J Phys Chem B 2021; 125:8932-8943. [PMID: 34324360 DOI: 10.1021/acs.jpcb.1c05463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Photosensitizer (PS) molecules play a critical role in photodynamic therapy of cancer and the understanding of the molecular mechanism involved in the photophysics of these compounds, and their reactions in the excited state are, therefore, of great interest for the development of this technique. In this article, the photophysics of the cationic PS 4,5-dibromorodamine methyl ester (TH9402), its electron- and energy-transfer reactions in the excited triplet state, with molecular oxygen, nitric oxide, guanosine-5'-monophosphate (GMP), and guanine, and the interaction with DNA were evaluated. Time-dependent density functional theory calculations at the TPSSh/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water solution reveals that the PS has a bright S1 state 2.33 eV above the ground state that produces a fluorescent rate constant of 5.40 × 107 s-1, calculated using Fermi's golden rule within a path integral formalism. Once excited to the bright state, the main intersystem crossing (ISC) channel involves the coupling with the T2 state just below S1 (S1 → T2 → T1) with an overall ISC rate constant of 10.1 × 107 s-1, in good agreement with the experimental data. Excited-state reaction thermodynamics, computed at the M06-2X/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water, showed that from all the excited-state electron-transfer reactions studied, only the transfer from GMP to the PS is thermodynamically favorable, independent of the protonation state of guanosine, which indicates a possible DNA photo-oxidation mechanism for the PS. Triplet-triplet energy-transfer reactions from TH9402 to molecular oxygen, producing reactive singlet oxygen, and to the deprotonated guanosine, producing 3GMP2-, are also thermodynamically favorable, with ΔG = -2.0 and -24.0 kcal//mol, respectively. However, the energy transfer to the monoprotonated guanosine is not favorable, (ΔG = 36.1), suggesting that in the DNA double-strand environment, this energy-transfer process may not be observed. The results show that the PS can act through electron transfer and triplet-triplet energy-transfer reactions involved in mechanism types I and II in photodynamic therapy. Interactions of TH9402 with the d(AGACGTCT)2 octanucleotide revealed that the PS can intercalate between the d(GpC)-d(CpG) base pairs in three different orientations and, upon intercalation, the π → π* transition of the PS shows a bathochromic shift up to 90 nm and up to 60% decrease in intensity. Interactions through groove binding showed a smaller bathochromic shift of 52.2 nm and a 56% decrease in intensity of the main transition band.
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Affiliation(s)
- Mariana Yoshinaga
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Pampulha, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Willian R Rocha
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Pampulha, 31270-901 Belo Horizonte, Minas Gerais, Brazil
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8
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El-Bindary AA, Anwar ZM, El-Shafaie T. Effect of some amino acids on the binding of quercetin and rutin flavonoids with DNA. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Mohammad M, Al Rasid Gazi H, Pandav K, Pandya P, Islam MM. Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies. ACS OMEGA 2021; 6:2613-2625. [PMID: 33553879 PMCID: PMC7859944 DOI: 10.1021/acsomega.0c04775] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/04/2021] [Indexed: 05/31/2023]
Abstract
Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.
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Affiliation(s)
- Mukti Mohammad
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
| | - Harun Al Rasid Gazi
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
| | - Kumud Pandav
- Department
of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee 247667, India
| | - Prateek Pandya
- Amity
Institute of Forensic Sciences, Amity University, Noida 201313, Uttar Pradesh, India
| | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, West Bengal 700 160, India
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10
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Akhtaruzzaman, Mohammad M, Khan S, Dutta B, Maity S, Naaz S, Alam SM, Ghosh P, Islam MM, Mir MH. One-pot crystallization of two 1,4-cyclohexanedicarboxylate-based tetranuclear Cu(ii) compounds and their DNA binding affinities. CrystEngComm 2021. [DOI: 10.1039/d0ce01734e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new tetranuclear Cu(ii) compounds have been synthesized using flexible linker 1,4-cyclohexanedicarboxylic acid in an one-pot crystallization which exhibit dissimilar affinities to DNA binding.
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Affiliation(s)
- Akhtaruzzaman
- Department of Chemistry
- Aliah University
- Kolkata 700 156
- India
| | - Mukti Mohammad
- Department of Chemistry
- Aliah University
- Kolkata 700 156
- India
| | - Samim Khan
- Department of Chemistry
- Aliah University
- Kolkata 700 156
- India
| | - Basudeb Dutta
- Department of Chemistry
- Aliah University
- Kolkata 700 156
- India
| | - Suvendu Maity
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Sanobar Naaz
- Department of Chemistry
- Aliah University
- Kolkata 700 156
- India
| | | | - Prasanta Ghosh
- Department of Chemistry
- R. K. M. Residential College
- Kolkata 700 103
- India
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11
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Akhtaruzzaman, Khan S, Alothman AA, Dutta B, Mohammad Wabaidur S, Mafiz Alam S, Maidul Islam M, Hedayetullah Mir M. Synthesis, crystal structure and DNA binding of a new Ni(II) coordination compound based on 4-(1-naphthylvinyl)pyridine ligand. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
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Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
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13
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Khan S, Alothman ZA, Mohammad M, Islam MS, Slawin A, Wabaidur SM, Islam MM, Mir MH. Synthesis and characterization of a hydrogen bonded metal-organic cocrystal: Exploration of its DNA binding study. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Ghosh S, Khan MA, Bhattacharyya A, Alam MA, Zangrando E, Guchhait N. Cu(ii)-induced twisting of the biphenyl core: exploring the effect of structure and coordination environment of biphenyl-based chiral copper(ii) complexes on interaction with calf-thymus DNA. NEW J CHEM 2020. [DOI: 10.1039/c9nj06184c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biphenyl core-based clip-like receptors get twisted after complexation with Cu2+. The extent of interaction of the optically active complexes with ct-DNA varies depending on the structure and coordination environment.
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Affiliation(s)
- Soumen Ghosh
- Department of Chemistry
- University of Calcutta
- Kolkata 700 009
- India
| | - Mehebub Ali Khan
- Department of Chemistry
- Aliah University
- IIA/27
- Action Area II
- Newtown
| | | | | | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste
- 34127 Trieste
- Italy
| | - Nikhil Guchhait
- Department of Chemistry
- University of Calcutta
- Kolkata 700 009
- India
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15
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Mandal T, Pathak S, Dey A, Islam MM, Seth SK, Masum AA, Ortega-Castro J, Ray PP, Frontera A, Mukhopadhyay S. Structures, Photoresponse Properties, and Biological Activity of Dicyano-Substituted 4-Aryl-2-pyridone Derivatives. ACS OMEGA 2019; 4:7200-7212. [PMID: 31459825 PMCID: PMC6649035 DOI: 10.1021/acsomega.9b00289] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/08/2019] [Indexed: 05/20/2023]
Abstract
Described in this work is the synthesis of a novel dicyano-substituted N-2-aminoethyl-4-(3-pyridinyl)-2-pyridone organic compound (1) that is characterized by several spectroscopic methods. Compound (1) was utilized for the preparation of its perchlorate (2), chloride (3), and bromide (4) salts. Single-crystal X-ray structures of these three salts were determined, and noncovalent weak interactions involving the aromatic rings, anions, and water molecules in (2-4) were investigated in detail. Solid-state UV-vis spectrum of the reported compounds (1-4) was utilized to calculate their optical band gaps, which clearly indicated that they belong to the semiconductor family. Under illumination condition, the magnitudes of electrical properties of (1) and its salts (2-4) improve remarkably although the improvement differs from salt to salt and the result was analyzed theoretically. Salt (2) was tested for its DNA binding ability.
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Affiliation(s)
- Tripti Mandal
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
| | - Sudipta Pathak
- Department
of Chemistry, Haldia Government College, Debhog, Purba
Medinipur, West Bengal 721657, India
| | - Arka Dey
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
- Department
of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sec. III, Salt Lake, Kolkata 700106, India
| | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Action Area IIA/27, Kolkata 700156, India
| | - Saikat Kumar Seth
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
| | - Abdulla Al Masum
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
| | - Joaquín Ortega-Castro
- Departament
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa
km 7.5, 07122 Palma
de Mallorca, Baleares, Spain
| | - Partha Pratim Ray
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
| | - Antonio Frontera
- Departament
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa
km 7.5, 07122 Palma
de Mallorca, Baleares, Spain
| | - Subrata Mukhopadhyay
- Department
of Chemistry, Department of Physics, and Department of Life Science &
Bio-technology, Jadavpur University, Kolkata 700032, India
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16
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Mandal T, Dey A, Pathak S, Islam MM, Konar S, Ortega-Castro J, Seth SK, Ray PP, Frontera A, Mukhopadhyay S. Structures, photoresponse properties and DNA binding abilities of 4-(4-pyridinyl)-2-pyridone salts. RSC Adv 2019; 9:9663-9677. [PMID: 35520716 PMCID: PMC9062393 DOI: 10.1039/c9ra00666d] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
Three salts [perchlorate (2), chloride (3) and tetrafluoroborate (4)] were synthesized from a 1-(2-aminoethyl)-6-hydroxy-2-oxo-1,2-dihydro-[4,4′-bipyridine]-3,5-dicarbonitrile compound (1) and characterized by spectroscopic and single crystal X-ray diffraction methods. Various noncovalent interactions (e.g., anion⋯π+, π⋯π, lp⋯π) are explored in the solid state crystal structure of the salts. Optical band gaps of all the four compounds were determined from their solid-state UV-vis spectrum. Electrical properties like electrical conductivity, photosensitivity, etc. were calculated and the results revealed that they have potential to act as optoelectronic devices. The values of the electrical parameters increase several times when they are exposed to visible light rather than in dark conditions. The light sensing properties of the salts (2–4) are enhanced compared to that of the mother organic compound 1 but the magnitude of this enhancement is not same for the three salts. This observation has been rationalized by theoretical considerations. Moreover, the DNA binding ability of one of the representative salts (compound 2) was examined to check the biological importance of the synthesized salts. The optical band gap energies in several 2-pyridone derivatives have been measured using solid state UV to explore their semiconductor behavior. The electric current measurements for the four compounds exhibit enhanced photoconduction properties under irradiation of light.![]()
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Affiliation(s)
- Tripti Mandal
- Department of Chemistry
- Jadavpur University
- Kolkata 700032
- India
| | - Arka Dey
- Department of Condensed Matter Physics and Material Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700106
- India
- Department of Physics
| | | | | | - Saugata Konar
- Department of Chemistry
- Bhawanipur Education Society College
- Kolkata 700020
- India
| | | | | | | | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palmade Mallorca
- Spain
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17
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Gupta N, Pandya P, Verma S. Computational Predictions for Multi-Target Drug Design. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Diversity-oriented sustainable synthesis of antimicrobial spiropyrrolidine/thiapyrrolizidine oxindole derivatives: New ligands for a metallo-β-lactamase from Klebsiella pneumonia. Bioorg Med Chem Lett 2017; 27:2873-2880. [DOI: 10.1016/j.bmcl.2017.04.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/13/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022]
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19
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Ghosh S, Al Masum A, Ganguly A, Islam MM, Alam MA, Guchhait N. A selective chemosensor for fluoride ion and its interaction with Calf Thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 178:24-31. [PMID: 28160723 DOI: 10.1016/j.saa.2017.01.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/21/2017] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
The amido-Schiff base 1 (N1, N3-bis (2-nitrobenzylidene)benzene-1,3-dicabohydrazide) containing a CONH group and CHN linkage has been synthesized by the condensation between isophthalic acid dihydrazide and o-nitrobenzaldehyde. This molecule can act as a fluoride ion sensor with high selectivity and sensitivity. Presence of nitro group in the phenyl ring may be responsible for the detection of fluoride ion visually with a dramatic color change from colorless to deep red in aqueous dimethyl sulphoxide solution. This Schiff base can be used as test kit for sensing of fluoride ion in the solid state. Compound 1 can detect fluoride also in commercially available toothpaste. As the compound has adequate solubility in DMSO-water mixture (7:93, v/v) and having some hydrogen bond donor and acceptor centers, we have investigated its nature of binding with Calf Thymus-DNA (CT-DNA) using theoretical molecular modelling and other experimental methods like UV-vis spectroscopy, circular dichroic and thermal melting studies. Thermodynamic parameters have been obtained using the well known Van't Hoff's equation. From both theoretical and experimental findings it has been observed that it can interact effectively with CT-DNA with binding energy -7.55kcal/mol to -7.50kcal/mol.
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Affiliation(s)
- Soumen Ghosh
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India
| | - Abdulla Al Masum
- Department of Chemistry, Aliah University, IIA/27, New Town, Kolkata 700 156, West Bengal, India
| | - Aniruddha Ganguly
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India
| | - Md Maidul Islam
- Department of Chemistry, Aliah University, IIA/27, New Town, Kolkata 700 156, West Bengal, India
| | - Md Akhtarul Alam
- Department of Chemistry, Aliah University, IIA/27, New Town, Kolkata 700 156, West Bengal, India.
| | - Nikhil Guchhait
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India.
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20
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Haris P, Mary V, Aparna P, Dileep KV, Sudarsanakumar C. A comprehensive approach to ascertain the binding mode of curcumin with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 175:155-163. [PMID: 28033562 DOI: 10.1016/j.saa.2016.11.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Curcumin is a natural phytochemical from the rhizoma of Curcuma longa, the popular Indian spice that exhibits a wide range of pharmacological properties like antioxidant, anticancer, anti-inflammatory, antitumor, and antiviral activities. In the published literatures we can see different studies and arguments on the interaction of curcumin with DNA. The intercalative binding, groove binding and no binding of curcumin with DNA were reported. In this context, we conducted a detailed study to understand the mechanism of recognition of dimethylsulfoxide-solubilized curcumin by DNA. The interaction of curcumin with calf thymus DNA (ctDNA) was confirmed by agarose gel electrophoresis. The nature of binding and energetics of interaction were studied by Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC), UV-visible, fluorescence and melting temperature (Tm) analysis. The experimental data were compared with molecular modeling studies. Our investigation confirmed that dimethylsulfoxide-solubilized curcumin binds in the minor groove of the ctDNA without causing significant structural alteration to the DNA.
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Affiliation(s)
- P Haris
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560, India
| | - Varughese Mary
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560, India
| | - P Aparna
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560, India
| | - K V Dileep
- Department of Biotechnology and Microbiology, Kannur University, Thalassery Campus, Palayad, Kerala 670661, India
| | - C Sudarsanakumar
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560, India; Center for High Performance Computing, Mahatma Gandhi University, Kottayam, Kerala 686560, India.
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21
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Das S, Islam MM, Jana GC, Patra A, Jha PK, Hossain M. Molecular binding of toxic phenothiazinium derivatives, azures to bovine serum albumin: A comparative spectroscopic, calorimetric, and in silico study. J Mol Recognit 2017; 30. [PMID: 28101950 DOI: 10.1002/jmr.2609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Somnath Das
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Md. Maidul Islam
- Department of Chemistry; Aliah University; Kolkata West Bengal India
| | - Gopal Chandra Jana
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Anirudha Patra
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Pradeep K. Jha
- SMST; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Maidul Hossain
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
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22
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Biochemical activity of a fluorescent dye rhodamine 6G: Molecular modeling, electrochemical, spectroscopic and thermodynamic studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 164:369-379. [DOI: 10.1016/j.jphotobiol.2016.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
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23
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Srinivasan V, Manne AK, Patnaik SG, Ramamurthy SS. Cellphone Monitoring of Multi-Qubit Emission Enhancements from Pd-Carbon Plasmonic Nanocavities in Tunable Coupling Regimes with Attomolar Sensitivity. ACS APPLIED MATERIALS & INTERFACES 2016; 8:23281-8. [PMID: 27529116 DOI: 10.1021/acsami.6b07445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate for the first time the tuning of qubit emission based on cavity engineering on plasmonic silver thin films. This tunable transition from weak to strong coupling regime in plasmon-coupled fluorescence platform was achieved with the use of palladium nanocomposites. In addition to our recently established correlation between Purcell factor and surface plasmon-coupled emission enhancements, we now show that the qubit-cavity environment experiences the Purcell effect, Casimir force, internal fano resonance, and Rabi splitting. Finite-difference time-domain simulations and time correlated single photon counting studies helped probe the molecular structure of the radiating dipole, rhodamine-6G, in palladium-based nanocavities. The sensitivity of the qubit-cavity mode helped attain a DNA detection limit of 1 aM (attomolar) and multianalyte sensing at picomolar concentration with the use of a smartphone camera and CIE color space. We believe that this low-cost technology will lay the groundwork for mobile phone-based next-gen plasmonic sensing devices.
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Affiliation(s)
- Venkatesh Srinivasan
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning , Prasanthi Nilayam, Puttaparthi, Anantapur, Andhra Pradesh, India 515134
| | - Anupam Kumar Manne
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning , Prasanthi Nilayam, Puttaparthi, Anantapur, Andhra Pradesh, India 515134
| | - Sai Gourang Patnaik
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning , Prasanthi Nilayam, Puttaparthi, Anantapur, Andhra Pradesh, India 515134
| | - Sai Sathish Ramamurthy
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning , Prasanthi Nilayam, Puttaparthi, Anantapur, Andhra Pradesh, India 515134
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24
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Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Interaction of an anti-cancer photosensitizer with a genomic DNA: From base pair specificity and thermodynamic landscape to tuning the rate of detergent-sequestered dissociation. J Colloid Interface Sci 2016; 470:211-220. [PMID: 26945117 DOI: 10.1016/j.jcis.2016.02.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
Abstract
A detailed characterization of the binding interaction of a potent cancer cell photosensitizer, norharmane (NHM) with a genomic DNA (herring sperm; hsDNA) is undertaken with particular emphasis on deciphering the strength, mode, dynamics, energetics and kinetics of binding. A major focus of the study underlies a successful exploration of the concept of detergent-sequestered dissociation of drug from the drug-DNA complex. Biophysical techniques such as absorption, steady-state and time-resolved fluorescence spectroscopy, circular dichroism, DNA helix melting, stopped-flow fluorescence kinetics and calorimetry have been used. A primarily intercalative mode of binding of NHM with DNA is shown. However, the overall interaction is governed by more than one type of binding forces. We demonstrate that the essential prerequisite of a slower dissociation rate of drug from DNA helix is achieved by tenable choice surfactants. Our results also highlight an effective tunability of the rate of dissociation of the DNA-intercalated drug via detergent-sequestration. A detailed isothermal titration calorimetric study unveils the key role of hydrophobic force underlying NHM-hsDNA association. This is further substantiated by the enthalpy-entropy compensation behavior. The major entropic contribution in detergent-induced dissociation of NHM from NHM-hsDNA complex is also demonstrated. Our results present not only a comprehensive structural and thermodynamic profile, base pair specificity, association kinetics for binding of NHM with DNA but also explore the thermodynamic and kinetic aspects of dissociation of bound drug. Characterization and tuning of the essential prerequisites for a drug to be efficient in anti-cancer functionality bear direct and widespread significance in contemporary global research.
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26
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S. V, Badiya PK, Ramamurthy SS. Purcell factor based understanding of enhancements in surface plasmon-coupled emission with DNA architectures. Phys Chem Chem Phys 2016; 18:681-4. [DOI: 10.1039/c5cp05410a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tuning the Purcell factor with DNA architectures to realize >130-fold fluorescence enhancements in surface plasmon-coupled emission.
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Affiliation(s)
- Venkatesh S.
- Plasmonics Laboratory
- Department of Chemistry
- Sri Sathya Sai Institute of Higher Learning
- Prasanthi Nilayam Campus
- Anantapur
| | - Pradeep Kumar Badiya
- Plasmonics Laboratory
- Department of Chemistry
- Sri Sathya Sai Institute of Higher Learning
- Prasanthi Nilayam Campus
- Anantapur
| | - Sai Sathish Ramamurthy
- Plasmonics Laboratory
- Department of Chemistry
- Sri Sathya Sai Institute of Higher Learning
- Prasanthi Nilayam Campus
- Anantapur
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27
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Topkaya SN, Serindere G, Ozder M. Determination of DNA Hypermethylation Using Anti-cancer Drug-Temozolomide. ELECTROANAL 2015. [DOI: 10.1002/elan.201501027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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Pabbathi A, Samanta A. Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid. J Phys Chem B 2015; 119:11099-105. [PMID: 26061788 DOI: 10.1021/acs.jpcb.5b02939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural integrity of a nucleic acid under various conditions determines its utility in biocatalysis and biotechnology. Exploration of the ionic liquids (ILs) for extraction of DNA and other nucleic acid based applications requires an understanding of the nature of interaction between the IL and DNA. Considering these aspects, we have studied the interaction between calf-thymus DNA and a less toxic morpholinium IL, [Mor1,2][Br], employing fluorescence correlation spectroscopy (FCS), conventional steady state and time-resolved fluorescence, circular dichroism (CD) and molecular docking techniques. While the CD spectra indicate the stability of DNA and retention of its B-form in the presence of the morpholinium IL, the docking study reveals that [Mor1,2](+) binds to the minor groove of DNA with a binding energy of -4.57 kcal mol(-1). The groove binding of the cationic component of the IL is corroborated by the steady state fluorescence data, which indicated displacement of a known minor groove binder, DAPI, from its DNA-bound state on addition of [Mor1,2][Br]. The FCS measurements show that the hydrodynamic radius of DNA remains more or less constant in the presence of [Mor1,2][Br], thus suggesting that the structure of DNA is retained in the presence of the IL. DNA melting experiments show that the thermal stability of DNA is enhanced in the presence of morpholinium IL.
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Affiliation(s)
- Ashok Pabbathi
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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29
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Rehman SU, Sarwar T, Husain MA, Ishqi HM, Tabish M. Studying non-covalent drug-DNA interactions. Arch Biochem Biophys 2015; 576:49-60. [PMID: 25951786 DOI: 10.1016/j.abb.2015.03.024] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/09/2015] [Accepted: 03/28/2015] [Indexed: 12/14/2022]
Abstract
Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.
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Affiliation(s)
- Sayeed Ur Rehman
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Tarique Sarwar
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammed Amir Husain
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Hassan Mubarak Ishqi
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India.
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30
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Tu B, Liu ZJ, Chen ZF, Ouyang Y, Hu YJ. Understanding the structure–activity relationship between quercetin and naringenin: in vitro. RSC Adv 2015. [DOI: 10.1039/c5ra22551e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The interactions of quercetin and naringenin with DNA have been studied at molecular level, which may throw light on their structure–activity relationships, helpful for the design of analogs flavonoids and their application in drug industries.
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Affiliation(s)
- Bao Tu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Zhi-Juan Liu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Zhi-Feng Chen
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Yu Ouyang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Yan-Jun Hu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
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