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Halder S, Paul M, Dyagala S, Aggrawal R, Aswal VK, Biswas S, Saha SK. Role of Gemini Surfactants with Variable Spacers and SiO 2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/ In Vivo Gene Delivery. ACS APPLIED BIO MATERIALS 2023. [PMID: 37277159 DOI: 10.1021/acsabm.3c00256] [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: 06/07/2023]
Abstract
Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO2 nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO2 NPs. While 50% ct-DNA compaction in the presence of SiO2 NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO2 NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO2 NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO2 NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO2 has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO2 NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.
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Affiliation(s)
- Sayantan Halder
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Milan Paul
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Shalini Dyagala
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Rishika Aggrawal
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, Maharashtra 400085, India
| | - Swati Biswas
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Subit K Saha
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
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Perevozchikova PS, Chernikova EY, Shepel NE, Fedorova OA, Fedorov YV. DNA-based assemblies with bischromophoric styryl dye-chromene conjugates and cucurbit[7]uril. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121971. [PMID: 36288627 DOI: 10.1016/j.saa.2022.121971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Novel conjugates consist of 4-styrylpyridinium dye and 2,2-diphenyl-2H-chromene moiety were obtained, and their affinity to double stranded DNA and cucurbit[7]uril was investigated. With a combination of absorption, fluorescence and circular dichroism spectroscopies as well as MALDI-TOF mass spectrometry, we demonstrate that these compounds can interact with macromolecules to form of the supramolecular assemblies due to two suitable binding sites. The ternary complex is formed as a result of the intercalation of a positively charged styryl part between DNA base pairs, while cucurbit[7]uril is located on the alkyl chain between two moieties of conjugate. All these findings provide valuable information into controlling the interaction between organic molecules, DNA and cucurbit[7]uril.
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Affiliation(s)
- Polina S Perevozchikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow, Russia; Department of Fine Organic Synthesis and Chemistry of Dyes, D. I. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia.
| | - Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow, Russia
| | - Nikolai E Shepel
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow, Russia
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow, Russia; Department of Fine Organic Synthesis and Chemistry of Dyes, D. I. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia.
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow, Russia
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3
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Bisoi A, Sarkar S, Chandra Singh P. Contrasting Effect of Salts on the Binding of Antimalarial Drug Hydroxychloroquine with Different Sequences of Duplex DNA. J Phys Chem B 2022; 126:5605-5612. [PMID: 35867068 DOI: 10.1021/acs.jpcb.2c02755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxychloroquine (HCQ) is an important antimalarial drug which functions plausibly by targeting the DNA of parasites. Salts play a crucial role in the functionality of various biological processes. Hence, the effect of salts (NaCl and MgCl2) on the binding of HCQ with AT- and CG-DNAs as well as the binding-induced stability of both sequences of DNAs have been investigated using the spectroscopic and molecular dynamics (MD) simulation methods. It has been found that the effect of salts on the binding of HCQ is highly sensitive to the nature of ions as well as DNA sequences. The effect of ions is opposite for the binding of AT- and CG-DNAs as the presence of Mg2+ ions enhances the binding of HCQ with AT-DNA, whereas the binding of HCQ with CG-DNA gets decreased on the addition of both ions. Similarly, the presence of Mg2+ enhances the stabilization of HCQ-bound AT-DNA, whereas the effect is opposite for the CG-DNA in the presence of both the ions. The MD simulation study suggests that the hydration states of both ions are different and they interact differently in the minor and major grooves of both the sequences of DNA which may be one of the reasons for the different binding of HCQ with these two sequences of DNA in the presence of salts. The information about the effect of salts on the binding of HCQ with DNAs in a sequence-specific manner may be useful in understanding the mechanism of the action and toxicity effect of HCQ against malaria.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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Cizkova K, Koubova K, Tauber Z. Replacement of DAPI with propidium iodide could extend the utilisation of archival tissue samples for immunofluorescent techniques. Histopathology 2022; 81:409-411. [PMID: 35506312 DOI: 10.1111/his.14676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- K Cizkova
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University, 779 00, Olomouc, Czech Republic
| | - K Koubova
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University, 779 00, Olomouc, Czech Republic
| | - Z Tauber
- Department of Histology and Embryology, Faculty of Medicine and Dentistry, Palacky University, 779 00, Olomouc, Czech Republic
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5
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Pandey S, Tripathi P, Parashar P, Maurya V, Malik MZ, Singh R, Yadav P, Tandon V. Synthesis and Biological Evaluation of Novel 1 H-Benzo[ d]imidazole Derivatives as Potential Anticancer Agents Targeting Human Topoisomerase I. ACS OMEGA 2022; 7:2861-2880. [PMID: 35097282 PMCID: PMC8793051 DOI: 10.1021/acsomega.1c05743] [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: 10/14/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Small molecules that modulate biological functions are targets of modern-day drug discovery efforts. A new series of novel 1H-benzo[d]imidazoles (BBZs) were designed and synthesized with different functional groups at the phenyl ring and variable lengths of the alkyl chain at the piperazine end as anticancer agents. We identified human topoisomerase I (Hu Topo I) as a probable target of these molecules through a computational study and DNA relaxation assay, a functional assay of the Hu Topo I enzyme. UV absorption, fluorescence, and circular dichroism spectroscopy were used to study interactions between BBZ and DNA. Out of 16 compounds, 11a, 12a, and 12b showed strong binding affinity and thermal stabilization of AT sequence-specific DNA. BBZs were screened against a panel of 60 human cancer cell lines at National Cancer Institute, USA. Most potent molecules 11a, 12a, and 12b showed 50% growth inhibition (GI50) in a concentration range from 0.16 to 3.6 μM cancer cells. Moreover, 12b showed 50% inhibition of the relaxation of DNA by Hu Topo I at 16 μM. Furthermore, flow cytometry revealed that 11a, 12a, and 12b cause prominent G2M arrest of cancer cells. In view of the above, we propose that 12b deserves to be further evaluated for its therapeutic use as an anticancer agent.
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Affiliation(s)
- Stuti Pandey
- Department
of Chemistry, University of Delhi, Delhi 110007, India
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Pragya Tripathi
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Palak Parashar
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Vikas Maurya
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Md. Zubbair Malik
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Raja Singh
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Pooja Yadav
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Vibha Tandon
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
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6
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Rashid FZM, Mahlandt E, van der Vaart M, Boer DEC, Varela Alvarez M, Henneman B, Brocken DJW, Voskamp P, Blok A, Shimizu T, Meijer A, Luijsterburg M, Goedhart J, Crémazy FGE, Dame R. HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic Acids Res 2021; 50:e10. [PMID: 34734265 PMCID: PMC8789088 DOI: 10.1093/nar/gkab993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023] Open
Abstract
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Eike Mahlandt
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Michiel van der Vaart
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Monica Varela Alvarez
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Bram Henneman
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Daan J W Brocken
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Anneloes J Blok
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Thomas S Shimizu
- Systems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands
| | - Annemarie H Meijer
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Joachim Goedhart
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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7
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DNA Intercalators Inhibit Eukaryotic Ribosomal RNA Synthesis by Impairing the Initiation of Transcription. Genes (Basel) 2021; 12:genes12091412. [PMID: 34573394 PMCID: PMC8466728 DOI: 10.3390/genes12091412] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/11/2023] Open
Abstract
In eukaryotes, ribosome biogenesis is driven by the synthesis of the ribosomal RNA (rRNA) by RNA polymerase I (Pol-I) and is tightly linked to cell growth and proliferation. The 3D-structure of the rDNA promoter plays an important, yet not fully understood role in regulating rRNA synthesis. We hypothesized that DNA intercalators/groove binders could affect this structure and disrupt rRNA transcription. To test this hypothesis, we investigated the effect of a number of compounds on Pol-I transcription in vitro and in cells. We find that intercalators/groove binders are potent inhibitors of Pol-I specific transcription both in vitro and in cells, regardless of their specificity and the strength of its interaction with DNA. Importantly, the synthetic ability of Pol-I is unaffected, suggesting that these compounds are not targeting post-initiating events. Notably, the tested compounds have limited effect on transcription by Pol-II and III, demonstrating the hypersensitivity of Pol-I transcription. We propose that stability of pre-initiation complex and initiation are affected as result of altered 3D architecture of the rDNA promoter, which is well in line with the recently reported importance of biophysical rDNA promoter properties on initiation complex formation in the yeast system.
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8
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Sarkar S, Roy S, Singh PC. Groove Switching of Hydroxychloroquine Modulates the Efficacy of Binding and Induced Stability to DNA. J Phys Chem B 2021; 125:6889-6896. [PMID: 34137627 DOI: 10.1021/acs.jpcb.1c03869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxychloroquine (HCQ) is an important drug for the treatment of rheumatoid arthritis and malaria. HCQ targets specifically to nucleic acids for its action. However, the mechanism of HCQ binding and the effect of its binding on the stability of DNA are elusive. In this study, the binding mechanism of HCQ and the effect of binding on stability of different sequences of DNA have been investigated using spectroscopic and molecular dynamics (MD) simulation techniques. HCQ binds with all of the sequences of DNA and stabilizes them. However, binding efficacy of HCQ with DNA depends on its sequences as the binding constant is highest for pure guanine-cytosine (G-C) rich DNA and decreases with the increase of adenine-thymine (A-T) bases. HCQ prefers to interact with AT DNA through the minor groove whereas the major groove along with intercalation are the favorable binding mode in the case of GC DNA. The binding of HCQ in the major groove of GC DNA enhances the stacking between the bases compared to the case of AT DNA which leads to higher stability for GC DNA. It appears that the groove switching of HCQ is correlated with binding affinity as well as stability of different sequences of DNA.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sarita Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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9
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Ganguly S, Murugan NA, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
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Affiliation(s)
- Sudakshina Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
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10
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Sarkar S, Chandra Singh P. Spectroscopic and Simulation Studies of the Sequence-Dependent DNA Destabilization by a Fungicide. ACS OMEGA 2021; 6:14371-14378. [PMID: 34124459 PMCID: PMC8190899 DOI: 10.1021/acsomega.1c01228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/17/2021] [Indexed: 05/08/2023]
Abstract
The understanding of the structural change of DNA induced by fungicides is essential as the non-targeted action of fungicides causes genotoxicity, leading to several serious diseases such as cancer, behavioral change, and nausea. In this study, the binding of an important fungicide, namely, n-dodecylguanidine acetate (dodine), with B-DNA having different sequences of nucleobases and its effect on the structure of B-DNA has been investigated using spectroscopic and simulation methods. In general, the addition of dodine destabilizes DNA; however, the binding of dodine causing the destabilization of DNA is highly sequence dependent. In the case of adenine(A)-thymine(T)-based DNA, dodine intrudes into the minor groove of DNA and interacts with the A-T bases mainly through its hydrocarbon tail, which destabilizes the stacking interaction of the flanking bases. In contrast, the polar group of dodine interacts with guanine(G)-cytosine(C)-rich DNA, and the interaction is dynamic as it shuttles between the minor groove and terminal regions. The binding of dodine with G-C-rich DNA affects the stacking interaction of the terminal base regions specifically. This study reveals the base-specific binding mode of dodine, which causes destabilization of the duplex DNA.
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11
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Parameswaran P, Arora Y, Patidar R, Ranjan N. Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding. Biophys Chem 2021; 274:106589. [PMID: 33901777 DOI: 10.1016/j.bpc.2021.106589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
The bacterial A-site RNA is one of the key targets towards the development of new antibacterials including new treatment options for tuberculosis. Using DAPI as a prototype, we have explored the potential of bisamidines as a potential chemical motif for bacterial A-site recognition. We have demonstrated that the binding of DAPI shows a concentration-dependent thermal stabilization of the bacterial A-site RNA (ΔTm = 9.9 °C). The binding, however, does not show pH-dependent changes upon lowering of pH. Both UV-vis and CD experiments show that the DAPI binding involves base stacking with the RNA bases in a manner that is analogous to intercalation. Scatchard analysis of the UV-vis titration data revealed a micromolar affinity of the DAPI to the bacterial rRNA A-Site (Ka = 1.14 × 106 M-1) which was corroborated by the FID-based relative binding affinity comparison with aminoglycosides. The molecular docking studies showed binding poses consistent with polar and stacking interactions with the RNA. These studies highlight the role of amidines in bacterial A-site recognition and the need for the development of their structural analogs towards the making of aminoglycoside mimics.
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Affiliation(s)
- Preethi Parameswaran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Yashaswina Arora
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Rajesh Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India.
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12
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Cárdenas G, Nogueira JJ. Stacking Effects on Anthraquinone/DNA Charge-Transfer Electronically Excited States. Molecules 2020; 25:E5927. [PMID: 33333751 PMCID: PMC7765225 DOI: 10.3390/molecules25245927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022] Open
Abstract
The design of more efficient photosensitizers is a matter of great importance in the field of cancer treatment by means of photodynamic therapy. One of the main processes involved in the activation of apoptosis in cancer cells is the oxidative stress on DNA once a photosensitizer is excited by light. As a consequence, it is very relevant to investigate in detail the binding modes of the chromophore with DNA, and the nature of the electronically excited states that participate in the induction of DNA damage, for example, charge-transfer states. In this work, we investigate the electronic structure of the anthraquinone photosensitizer intercalated into a double-stranded poly(dG-dC) decamer model of DNA. First, the different geometric configurations are analyzed by means of classical molecular dynamics simulations. Then, the excited states for the most relevant poses of anthraquinone inside the binding pocket are computed by an electrostatic-embedding quantum mechanics/molecular mechanics approach, where anthraquinone and one of the nearby guanine residues are described quantum mechanically to take into account intermolecular charge-transfer states. The excited states are characterized as monomer, exciton, excimer, and charge-transfer states based on the analysis of the transition density matrix, and each of these contributions to the total density of states and absorption spectrum is discussed in terms of the stacking interactions. These results are relevant as they represent the footing for future studies on the reactivity of anthraquinone derivatives with DNA and give insights on possible geometrical configurations that potentially favor the oxidative stress of DNA.
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Affiliation(s)
- Gustavo Cárdenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
| | - Juan J. Nogueira
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain;
- IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
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13
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Sarkar S, Singh PC. Sequence specific hydrogen bond of DNA with denaturants affects its stability: Spectroscopic and simulation studies. Biochim Biophys Acta Gen Subj 2020; 1865:129735. [PMID: 32946929 DOI: 10.1016/j.bbagen.2020.129735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Several different small molecules have been used to target the DNA helix in order to treat the diseases caused by its mutation. Guanidinium(Gdm+) and urea based drugs have been used for the diseases related to central nervous system, also as the anti-inflammatory and chemotherapeutic agent. However, the role of Gdm+ and urea in the stabilization/destabilization of DNA is not well understood. METHODS Spectroscopic techniques along with molecular dynamics (MD) simulation have been performed on different sequences of DNA in the presence of guanidinium chloride (GdmCl) and urea to decode the binding of denaturants with DNA and the role of hydrogen bond with the different regions of DNA in its stability/destability. RESULTS AND CONCLUSION Our study reveals that, Gdm+ of GdmCl and urea both intrudes into the groove region of DNA along with the interaction with its phosphate backbone. However, interaction of Gdm+ and urea with the nucleobases in the groove region is different. Gdm+ forms the intra-strand hydrogen bond with the central region of the both sequences of DNA whereas inter-strand hydrogen bond along with water assisted hydrogen bond takes place in the case of urea. The intra-strand hydrogen bond formation capability of Gdm+ with the nucleobases in the minor groove of DNA decreases its groove width which probably causes the stabilization of B-DNA in GdmCl. In contrast, the propensity of the formation of inter-strand hydrogen bond of urea with the nucleobases in the groove region of DNA without affecting the groove width destabilizes B-DNA as compared to GdmCl. This study depicts that the opposite effect of GdmCl and urea on the stability is a general property of B-DNA. However, the extent of stabilization/destabilization of DNA in Gdm+ and urea depend on its sequence probably due to the difference in the intra/inter-strand hydrogen bonding with different bases present in both the sequences of DNA. GENERAL SIGNIFICANCE The information obtained from this study will be useful for the designing of Gdm+ based drug molecule which can target the DNA more specifically and selectively.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India.
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14
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Nanostructured Polyelectrolyte Complexes Based on Water-Soluble Thiacalix[4]Arene and Pillar[5]Arene: Self-Assembly in Micelleplexes and Polyplexes at Packaging DNA. NANOMATERIALS 2020; 10:nano10040777. [PMID: 32316551 PMCID: PMC7221682 DOI: 10.3390/nano10040777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/27/2023]
Abstract
Controlling the self-assembly of polyfunctional compounds in interpolyelectrolyte aggregates is an extremely challenging task. The use of macrocyclic compounds offers new opportunities in design of a new generation of mixed nanoparticles. This approach allows creating aggregates with multivalent molecular recognition, improved binding efficiency and selectivity. In this paper, we reported a straightforward approach to the synthesis of interpolyelectrolytes by co-assembling of the thiacalix[4]arene with four negatively charged functional groups on the one side of macrocycle, and pillar[5]arene with 10 ammonium groups located on both sides. Nanostructured polyelectrolyte complexes show effective packaging of high-molecular DNA from calf thymus. The interaction of co-interpolyelectrolytes with the DNA is completely different from the interaction of the pillar[5]arene with the DNA. Two different complexes with DNA, i.e., micelleplex- and polyplex-type, were formed. The DNA in both cases preserved its secondary structure in native B form without distorting helicity. The presented approach provides important advantage for the design of effective biomolecular gene delivery systems.
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15
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Dierig L, Schmidt M, Wiegand P. Looking for the pinpoint: Optimizing identification, recovery and DNA extraction of micro traces in forensic casework. Forensic Sci Int Genet 2020; 44:102191. [DOI: 10.1016/j.fsigen.2019.102191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022]
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16
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Liu MX, Ma LL, Liu XY, Liu JY, Lu ZL, Liu R, He L. Combination of [12]aneN 3 and Triphenylamine-Benzylideneimidazolone as Nonviral Gene Vectors with Two-Photon and AIE Properties. ACS APPLIED MATERIALS & INTERFACES 2019; 11:42975-42987. [PMID: 31657894 DOI: 10.1021/acsami.9b15169] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Three nonviral gene vectors, TPA-BI-A/B/C, have been designed and synthesized by the combination of one or two hydrophilic [12]aneN3 moieties and two-photon fluorescent triphenylamine-benzylideneimidazolone (TPA-BI) units through different ester linkage. Spectroscopic characterization demonstrated that TPA-BI-A/B/C had strong aggregation-induced emissions (AIE), large Stokes shifts (230, 284, and 263 nm), and large two-photon absorption cross sections (δ2PA) (67, 592, and 80 GM). Gel electrophoresis indicated that the three compounds completely condensed DNA at 15 μM in the presence of DOPE, and showed the lipase- and pH-triggered reversible release of DNA and the fluorescent recognition of the different lengths of ssDNA and dsDNA. The optimal TPA-BI-C/DOPE-mediated luciferase and GFP activity was 146% and 290% higher than those of Lipo2000. The transfection process of DNA could be traced clearly through one- and two-photon fluorescence spectra, and displayed in a 3D-video. TPA-BI-C/DOPE successfully transfected the GFP gene into zebrafish, which was superior to Lipo2000 (192%). In conclusion, TPA-BI-C/DOPE is the first nonviral gene vector with the abilities of pH/lipase enzyme responsiveness, one/two-photon fluorescent tracking of intracellular delivery of DNA, and successful transfection in vivo and in vitro, even better than Lipo2000.
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Affiliation(s)
- Ming-Xuan Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Le-Le Ma
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Xu-Ying Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Jin-Yu Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Zhong-Lin Lu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Rui Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education; College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Lan He
- National Institute for Food and Drug Control , Institute of Chemical Drug Control , TianTanXiLi 2 , Beijing 100050 , China
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17
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Sardana D, Yadav K, Shweta H, Clovis NS, Alam P, Sen S. Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA. J Phys Chem B 2019; 123:10202-10216. [PMID: 31589442 DOI: 10.1021/acs.jpcb.9b09275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na+ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na+, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na+ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.
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Affiliation(s)
- Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
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18
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Jia T, Chen ZH, Guo P, Yu J. An insight into DNA binding properties of newly designed cationic δ,δ'‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:260-271. [PMID: 30557843 DOI: 10.1016/j.saa.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/19/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Two cationic δ,δ'‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH3 (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'‑diazacarbazoles and DNA were weakened, but δ,δ'‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.
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Affiliation(s)
- Tao Jia
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Zhi-Hang Chen
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peng Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, PR China.
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19
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Zehra S, Shavez Khan M, Ahmad I, Arjmand F. New tailored substituted benzothiazole Schiff base Cu(II)/Zn(II) antitumor drug entities: effect of substituents on DNA binding profile, antimicrobial and cytotoxic activity. J Biomol Struct Dyn 2018; 37:1863-1879. [DOI: 10.1080/07391102.2018.1467794] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Siffeen Zehra
- Department of Chemistry, Aligarh Muslim University , Aligarh
202002, Uttar Pradesh, India
| | - Mohammad Shavez Khan
- Department of Agricultural Microbiology, Aligarh Muslim University , Aligarh
202002, Uttar Pradesh, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University , Aligarh
202002, Uttar Pradesh, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University , Aligarh
202002, Uttar Pradesh, India
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20
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Ali MS, Farah MA, Al-Lohedan HA, Al-Anazi KM. Comprehensive exploration of the anticancer activities of procaine and its binding with calf thymus DNA: a multi spectroscopic and molecular modelling study. RSC Adv 2018; 8:9083-9093. [PMID: 35541873 PMCID: PMC9078652 DOI: 10.1039/c7ra13647a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/21/2018] [Indexed: 11/21/2022] Open
Abstract
Procaine is an anesthetic drug commonly administrated topically or intravenously for use in local anesthesia. Promisingly, some anticancer activities of procaine have also been reported. Therefore, the mechanism of interaction between anesthetic drug procaine with ct-DNA was determined collectively by means of various spectroscopic and molecular docking methods. Minor groove 1 : 1 binding of procaine to the ct-DNA was evidenced from absorption spectroscopy, fluorescence quenching, DNA melting, competitive binding measurements with EB and DAPI dyes, viscosity and CD spectroscopy together with molecular docking simulations and DFT calculations. Molecular docking on five different B-DNA structures (taken from the Protein Data Bank) shows that procaine binds in the AT rich region of all five B-DNA structures. Thermodynamic parameters, evaluated using van't Hoff's isotherm, shown that the interaction was feasible and the binding forces involved were hydrophobic as well as hydrogen bonding which were, further, confirmed by molecular docking. The frontier molecular orbitals (HOMO and LUMO) of procaine and DNA bases have been calculated by DFT method and the chemical potential (μ), chemical hardness (η) and fraction number of electrons (ΔN) from procaine to DNA bases were evaluated, which have shown that procaine acts as an electron donor to the DNA bases. Simultaneously, anticancer activities of procaine alone and in combination with doxorubicin were observed on the MCF-7 breast cancer cell line. The results showed that the combined treatment with both procaine and doxorubicin enhanced the cytotoxic and apoptotic inducing potential of doxorubicin.
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Affiliation(s)
- Mohd Sajid Ali
- Department of Chemistry, College of Science, King Saud University P.O. Box-2455 Riyadh-11451 Saudi Arabia +966-14679972 +966-598878428
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University P.O. Box-2455 Riyadh-11451 Saudi Arabia
| | - Hamad A Al-Lohedan
- Department of Chemistry, College of Science, King Saud University P.O. Box-2455 Riyadh-11451 Saudi Arabia +966-14679972 +966-598878428
| | - Khalid Mashay Al-Anazi
- Department of Zoology, College of Science, King Saud University P.O. Box-2455 Riyadh-11451 Saudi Arabia
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21
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Holmgaard List N, Knoops J, Rubio-Magnieto J, Idé J, Beljonne D, Norman P, Surin M, Linares M. Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder. J Am Chem Soc 2017; 139:14947-14953. [DOI: 10.1021/jacs.7b05994] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nanna Holmgaard List
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
| | - Jérémie Knoops
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Jenifer Rubio-Magnieto
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Julien Idé
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - David Beljonne
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Patrick Norman
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
| | - Mathieu Surin
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Mathieu Linares
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
- Swedish
e-Science Research Centre, KTH Royal Institute of Technology, 104 50 Stockholm, Sweden
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22
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Shweta H, Singh MK, Yadav K, Verma SD, Pal N, Sen S. Effect of T·T Mismatch on DNA Dynamics Probed by Minor Groove Binders: Comparison of Dynamic Stokes Shifts of Hoechst and DAPI. J Phys Chem B 2017; 121:10735-10748. [PMID: 28922599 DOI: 10.1021/acs.jpcb.7b06937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recognition of DNA base mismatches and their subsequent repair by enzymes is vital for genomic stability. However, it is difficult to comprehend such a process in which enzymes sense and repair different types of mismatches with different ability. It has been suggested that the differential structural changes of mismatched bases act as cues to the repair enzymes, although the effect of such DNA structural changes on surrounding water and ion dynamics is inevitable due to strong electrostatic coupling among them. Thus, collective dynamics of DNA, water, and ions near the mismatch site is believed to be important for mismatch recognition and repair mechanism. Here we show that introduction of a T·T mismatch in the minor groove of DNA induces dispersed (collective) power-law solvation dynamics (of exponent ∼0.24), measured by monitoring the time-resolved fluorescence Stokes shifts (TRFSS) of two popular minor groove binders (Hoechst 33258 and DAPI) over five decades of time from 100 fs to 10 ns. The same ligands however sense different dynamics (power-law of exponent ∼0.15 or power-law multiplied with biexponential relaxation) in the minor groove of normal-DNA. The similar fluorescence anisotropy decays of ligands measured in normal- and T·T-DNA suggest that Stokes shift dynamics and their changes in T·T-DNA purely originate from the solvation process, and not from any internal rotational motion of probe-ligands. The dispersed power-law solvation dynamics seen in T·T-DNA indicate that the ligands do not sense any particular (exponential) relaxation specific to T·T wobbling and/or other conformational changes. This could be the reason why T·T mismatch is recognized by enzymes with lower efficiency compared to purine-pyrimidine and purine-purine mismatches.
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Affiliation(s)
- Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Sachin Dev Verma
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Nibedita Pal
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
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23
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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24
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Wei J, Wang S, Pei D, Qu L, Li Y, Chen J, Di D, Gao K. Antibacterial Activity of Hydroxytyrosol Acetate from Olive Leaves (Olea Europaea L.). Nat Prod Res 2017; 32:1967-1970. [DOI: 10.1080/14786419.2017.1356830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jianteng Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P.R. China
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences(CAS), Lanzhou, P.R. China
- Center of Resource Chemical & New Material, Qingdao, P.R. China
| | - Shuxian Wang
- Center of Fishery Disease and Drug, Marine Biology Institute of Shandong Province, Qingdao, P.R. China
| | - Dong Pei
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences(CAS), Lanzhou, P.R. China
- Center of Resource Chemical & New Material, Qingdao, P.R. China
| | - Liangjing Qu
- Center of Fishery Disease and Drug, Marine Biology Institute of Shandong Province, Qingdao, P.R. China
| | - Ya Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P.R. China
| | - Jianjun Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P.R. China
| | - Duolong Di
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences(CAS), Lanzhou, P.R. China
- Center of Resource Chemical & New Material, Qingdao, P.R. China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P.R. China
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25
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Paul S, Ahmed T, Samanta A. Influence of Divalent Counterions on the Dynamics in DNA as Probed by Using a Minor-Groove Binder. Chemphyschem 2017; 18:2058-2064. [DOI: 10.1002/cphc.201700251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Sneha Paul
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
| | - Tasnim Ahmed
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
| | - Anunay Samanta
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
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26
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Grimmelsmann L, Marefat Khah A, Spies C, Hättig C, Nuernberger P. Ultrafast Dynamics of a Triazene: Excited-State Pathways and the Impact of Binding to the Minor Groove of DNA and Further Biomolecular Systems. J Phys Chem Lett 2017; 8:1986-1992. [PMID: 28426228 DOI: 10.1021/acs.jpclett.7b00472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many synthetic DNA minor groove binders exhibit a strong increase in fluorescence when bound to DNA. The pharmaceutical-relevant berenil (diminazene aceturate) is an exception with an extremely low fluorescence quantum yield (on the order of 10-4). We investigate the ultrafast excited-state dynamics of this triazene by femtosecond time-resolved fluorescence experiments in water, ethylene glycol, and buffer and bound to the enzyme β-trypsin, the minor groove of AT-rich DNA, and G-quadruplex DNA. Ab initio calculations provide additional mechanistic insight. The complementing studies unveil that the excited-state motion initiated by ππ* excitation occurs in two phases: a subpicosecond phase associated with the lengthening of the central N═N double bond, followed by a bicycle-pedal-type motion of the triazene bridge, which is almost volume-conserving and can proceed efficiently within only a few picoseconds even under spatially confined conditions. Our results elucidate the excited-state relaxation mechanism of aromatic triazenes and explain the modest sensitivity of the fluorescence quantum yield of berenil even when it is bound to various biomolecules.
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Affiliation(s)
- Lena Grimmelsmann
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Alireza Marefat Khah
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christian Spies
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christof Hättig
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Patrick Nuernberger
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
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27
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Reis LA, Rocha MS. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes. Biopolymers 2017; 107. [DOI: 10.1002/bip.23015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/10/2023]
Affiliation(s)
- L. A. Reis
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
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28
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Dömötör O, de Almeida RFM, Côrte-Real L, Matos CP, Marques F, Matos A, Real C, Kiss T, Enyedy ÉA, Helena Garcia M, Tomaz AI. Studies on the mechanism of action of antitumor bis(aminophenolate) ruthenium(III) complexes. J Inorg Biochem 2016; 168:27-37. [PMID: 28006663 DOI: 10.1016/j.jinorgbio.2016.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 01/13/2023]
Abstract
Two recently published Ru(III) complexes bearing (N2O2) tetradentate bis(aminophenolate) ligands, formulated as [Ru(III)(salan)(PPh3)Cl] (salan is the tetradentate ligand 6,6'-(1S,2S)-cyclohexane-1,2-diylbis(azanediyl)bis(methylene)bis(3-methoxyphenol) in complex 1, or 2,2'-(1S,2S)-cyclohexane-1,2-diylbis(azanediyl)bis(methylene)bis(4-methoxyphenol) in complex 2; PPh3 is triphenylphosphane) and found very active against ovarian and breast adenocarcinoma human cells were studied to outline their antitumor mode of action. The human cisplatin-sensitive ovarian adenocarcinoma line A2780 was used herein as the cell model. At a 24h challenge (similarly as found before for 72h) both complexes are active, their cytotoxicity being comparable to that of cisplatin in the same conditions. As a possible target in the cell for their action, the interaction of 1 and 2 with DNA was assessed through displacement of well-established DNA fluorescent probes (ethidium bromide, EB, and 4',6-diamidino-2-phenylindole, DAPI) through steady-state and time-resolved fluorescence spectroscopy. The whole emission spectra were analyzed globally for the binary DNA-probe and ternary DNA-probe-Ru(III) complex systems. Both Ru(III) complexes can displace EB and bind to DNA with similar and moderate strong affinity with conditional stability constants of logK'=(5.05±0.01) for 1 and logK'=(4.79±0.01) for 2. The analysis of time-domain fluorescence intensity decays confirmed both qualitatively and quantitatively the model used to describe the binding and competition processes. Cell studies indicated that apoptosis is the major mechanism of cell death for both complexes, with 2 (the more active complex) promoting that process more efficiently than 1. Transmission electron micrographs revealed clear alterations on intracellular organization consistent with the induction of programmed cell death processes.
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Affiliation(s)
- Orsolya Dömötör
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary; MTA-SZTE Bioinorganic Chemistry Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Rodrigo F M de Almeida
- Centro de Química e Bioquímica (CQB), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal
| | - Leonor Côrte-Real
- Centro de Química Estrutural (CQE), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal
| | - Cristina P Matos
- Centro de Química Estrutural (CQE), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal; Centro de Química Estrutural (CQE), Instituto Superior Técnico, ULisboa, Av. Rovisco Pais, 1, Lisbon, Portugal
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares (C2TN), Instituto Superior Técnico, ULisboa, Estrada Nacional 10, Bobadela, Loures, Portugal
| | - António Matos
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Quinta da Granja, Monte da Caparica, Portugal
| | - Carla Real
- Centro de Química e Bioquímica (CQB), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal
| | - Tamás Kiss
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary; MTA-SZTE Bioinorganic Chemistry Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Éva Anna Enyedy
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - M Helena Garcia
- Centro de Química Estrutural (CQE), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal
| | - Ana Isabel Tomaz
- Centro de Química Estrutural (CQE), Faculdade de Ciências, ULisboa, Campo Grande, Lisbon, Portugal.
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29
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Kasyanenko N, Bakulev V, Perevyazko I, Nekrasova T, Nazarova O, Slita A, Zolotova Y, Panarin E. Model system for multifunctional delivery nanoplatforms based on DNA-Polymer complexes containing silver nanoparticles and fluorescent dye. J Biotechnol 2016; 236:78-87. [DOI: 10.1016/j.jbiotec.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/07/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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30
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Singh MK, Shweta H, Sen S. Dispersed dynamics of solvation in G-quadruplex DNA: comparison of dynamic Stokes shifts of probes in parallel and antiparallel quadruplex structures. Methods Appl Fluoresc 2016; 4:034009. [PMID: 28355155 DOI: 10.1088/2050-6120/4/3/034009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G-quadruplex DNA (GqDNA) structures play an important role in many specific cellular functions and are promising anti-tumor targets for small molecules (ligands). Here, we measured the dynamic Stokes shift of a ligand (Hoechst) bound to parallel c-Myc (mPu22) GqDNA over five decades of time from 100 fs to 10 ns, and compared it with the previously reported dynamics of DAPI bound to antiparallel human telomeric (hTelo22) GqDNA (Pal et al 2015 J. Phys. Chem. Lett. 6 1754). Stokes shift data from fluorescence up-conversion and time-correlated single photon counting experiments was combined to cover the broad dynamic range. The results show that the solvation dynamics of Hoechst in parallel mPu22 GqDNA follow a power law relaxation, added to fast 2 ps exponential relaxation, from 100 fs to 10 ns, with only a subtle difference of power law exponents in the two ligand-GqDNA systems (0.06 in Hoechst-mPu22 compared to 0.16 in DAPI-hTelo22). We measured steady-state fluorescence spectra and time-resolved anisotropy decays which confirm the tight binding of Hoechst to parallel mPu22 with a binding constant of ~1 × 105 M-1. The molecular docking of Hoechst in parallel GqDNA followed by a 50 ns molecular dynamics (MD) simulation on a Hoechst-GqDNA complex reveals that Hoechst binds to one of the outer G-tetrads by end-stacking near G13 and G4, which is different from the binding site of DAPI inside a groove of antiparallel hTelo22 GqDNA. Reconciling previous experimental and simulation results, we assign the 2 ps component to the hydration dynamics of only weakly perturbed water near mPu22 and the power law relaxation to the coupled motion of water and DNA (i.e. DNA backbone, unpaired bases and loops connecting G-tetrads) which come near the Hoechst inside parallel GqDNA.
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Affiliation(s)
- Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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31
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Dziuba D, Pospíšil P, Matyašovský J, Brynda J, Nachtigallová D, Rulíšek L, Pohl R, Hof M, Hocek M. Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions. Chem Sci 2016; 7:5775-5785. [PMID: 30034716 PMCID: PMC6021979 DOI: 10.1039/c6sc02548j] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/20/2016] [Indexed: 12/16/2022] Open
Abstract
A nucleoside bearing a solvatochromic push-pull fluorene fluorophore (dCFL ) was designed and synthesized by the Sonogashira coupling of alkyne-linked fluorene 8 with 5-iodo-2'-deoxycytidine. The fluorene building block 8 and labeled nucleoside dCFL exerted bright fluorescence with significant solvatochromic effect providing emission maxima ranging from 421 to 544 nm and high quantum yields even in highly polar solvents, including water. The solvatochromism of 8 was studied by DFT and ADC(2) calculations to show that, depending on the polarity of the solvent, emission either from the planar or the twisted conformation of the excited state can occur. The nucleoside was converted to its triphosphate variant dCFLTP which was found to be a good substrate for DNA polymerases suitable for the enzymatic synthesis of oligonucleotide or DNA probes by primer extension or PCR. The fluorene-linked DNA can be used as fluorescent probes for DNA-protein (p53) or DNA-lipid interactions, exerting significant color changes visible even to the naked eye. They also appear to be suitable for time-dependent fluorescence shift studies on DNA, yielding information on DNA hydration and dynamics.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Petr Pospíšil
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Martin Hof
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
- Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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32
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Polley N, Sarkar PK, Chakrabarti S, Lemmens P, Pal SK. DNA Biomaterial Based Fiber Optic Sensor: Characterization and Application for Monitoringin situMercury Pollution. ChemistrySelect 2016. [DOI: 10.1002/slct.201600391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nabarun Polley
- Department of Chemical, Biological and Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD, Sector III, Salt Lake Kolkata 700 106 India
| | - Probir Kumar Sarkar
- Department of Chemical, Biological and Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD, Sector III, Salt Lake Kolkata 700 106 India
| | - Subhananda Chakrabarti
- Dept. of Electrical Engineering; Indian Institute of Technology Bombay, Powai; Mumbai 400 076, Maharashtra India
| | - Peter Lemmens
- Institute for Condensed Matter Physics; TU Braunschweig; Mendelssohnsstr 3 38106 Braunschweig Germany
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD, Sector III, Salt Lake Kolkata 700 106 India
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33
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Ding AX, Tang Q, Gao YG, Shi YD, Uzair A, Lu ZL. [12]aneN3 Modified Tetraphenylethene Molecules as High-Performance Sensing, Condensing, and Delivering Agents toward DNAs. ACS APPLIED MATERIALS & INTERFACES 2016; 8:14367-14378. [PMID: 27215542 DOI: 10.1021/acsami.6b01949] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Four [12]aneN3 modified tetraphenylethene (TPE) compounds with different numbers of polyamine units and structure configurations, namely 1, 2, 3, and 4, were designed and synthesized. All compounds showed strong aggregation-induced emission (AIE) features. Compounds 2 and 4 showed significant emission enhancement after the addition of ssDNAs and dsDNAs of different lengths as well as calf thymus DNA (ctDNA). Compounds 1 and 3 showed very poor fluorescent responses toward DNAs. Gel electrophoresis demonstrated the abilities of 1-4 to condense DNA effectively. Complete retardation of plasmid DNA can be achieved at a concentration of 25 μM (1), 8 μM (for 2 and 3) and 4 μM (4). Experiments including fluorescent contrastive titrations, scanning electron microscopy, dynamic laser scattering, EB displacement, and gel electrophoresis demonstrated that the four compounds were able to integrate with DNA through electrostatic interactions and supramolecular stacking. A vicinal configuration around TPE (2) and more triazole-[12]aneN3 recognition sites (4) evidently enhanced the sensing capability toward oligonucleotides, and the TPE unit played an important role in the plasmid DNA condensation process because of its strong binding. With the advantages of low cytotoxicity, effective DNA sensing, and DNA condensing properties, compound 4 was successfully applied as a nonviral DNA vector and fluorescent tracer for label-free gene delivery, which is the first example of a nonviral gene vector with AIE activity.
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Affiliation(s)
- Ai-Xiang Ding
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Quan Tang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Yong-Guang Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - You-Di Shi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Alam Uzair
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Zhong-Lin Lu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education; College of Chemistry, Beijing Normal University , Beijing 100875, China
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34
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Duboué-Dijon E, Fogarty AC, Hynes JT, Laage D. Dynamical Disorder in the DNA Hydration Shell. J Am Chem Soc 2016; 138:7610-20. [DOI: 10.1021/jacs.6b02715] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elise Duboué-Dijon
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Aoife C. Fogarty
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - James T. Hynes
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Damien Laage
- École Normale
Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS,
Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités,
UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
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35
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Haines AM, Linacre A. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling. Forensic Sci Int 2016; 262:190-5. [DOI: 10.1016/j.forsciint.2016.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/16/2016] [Accepted: 03/12/2016] [Indexed: 12/24/2022]
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36
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Shinde MN, Bhasikuttan AC, Mohanty J. Recognition-mediated contrasting fluorescence behaviour of 4′,6-diamidino-2-phenylindole (DAPI): probing the pKa of p-sulfonatocalix[4/6]arenes. Supramol Chem 2016. [DOI: 10.1080/10610278.2015.1126591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Meenakshi N. Shinde
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, , India
- Student under BARC-SPPU PhD Program, Department of Chemistry, Savitribai Phule Pune University, Pune, India
| | - Achikanath C. Bhasikuttan
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, , India
- Chemical Sciences, Homi Bhabha National Institute, , India
| | - Jyotirmayee Mohanty
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, , India
- Chemical Sciences, Homi Bhabha National Institute, , India
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37
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Patra A, Hazra S, Samanta N, Suresh Kumar G, Mitra RK. Micelle induced dissociation of DNA–ligand complexes: The effect of ligand binding specificity. Int J Biol Macromol 2016; 82:418-24. [DOI: 10.1016/j.ijbiomac.2015.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 11/16/2022]
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38
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Choudhury S, Ghosh B, Singh P, Ghosh R, Roy S, Pal SK. Ultrafast differential flexibility of Cro-protein binding domains of two operator DNAs with different sequences. Phys Chem Chem Phys 2016; 18:17983-90. [DOI: 10.1039/c6cp02522f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crucial ultrafast domain fluctuation of the operator DNA OR3 over OR2 upon complexation with the repressor Cro-protein dimer has been investigated.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 098
- India
| | - Basusree Ghosh
- Division of Structural Biology and Bioinformatics
- Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Priya Singh
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 098
- India
| | - Raka Ghosh
- Division of Structural Biology and Bioinformatics
- Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Siddhartha Roy
- Division of Structural Biology and Bioinformatics
- Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Samir Kumar Pal
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 098
- India
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39
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Haines AM, Tobe SS, Kobus H, Linacre A. Successful direct STR amplification of hair follicles after nuclear staining. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Duration of in situ fluorescent signals within hairs follicles. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Haines AM, Tobe SS, Kobus HJ, Linacre A. Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing. Electrophoresis 2015. [DOI: 10.1002/elps.201500170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alicia M. Haines
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Shanan S. Tobe
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Hilton J. Kobus
- School of Chemical and Physical Sciences; Flinders University; Adelaide South Australia
| | - Adrian Linacre
- School of Biological Sciences; Flinders University; Adelaide South Australia
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42
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Shinde MN, Bhasikuttan AC, Mohanty J. The Contrasting Recognition Behavior of β-Cyclodextrin and Its Sulfobutylether Derivative towards 4′,6-Diamidino-2-phenylindole. Chemphyschem 2015; 16:3425-32. [DOI: 10.1002/cphc.201500638] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Meenakshi N. Shinde
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Student under BARC-SPPU PhD Program; Department of Chemistry; Savitribai Phule Pune University; Pune 411007 India
| | - Achikanath C. Bhasikuttan
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai 400 094 India
| | - Jyotirmayee Mohanty
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Homi Bhabha National Institute, Anushaktinagar; Mumbai 400 094 India
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43
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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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44
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A label-free fluorescence turn-on sensor for rapid detection of cysteine. Talanta 2015; 138:144-148. [DOI: 10.1016/j.talanta.2015.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/18/2022]
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45
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Verma SD, Pal N, Singh MK, Sen S. Sequence-Dependent Solvation Dynamics of Minor-Groove Bound Ligand Inside Duplex-DNA. J Phys Chem B 2015; 119:11019-29. [DOI: 10.1021/acs.jpcb.5b01977] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sachin Dev Verma
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nibedita Pal
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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46
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Pal N, Shweta H, Singh MK, Verma SD, Sen S. Power-Law Solvation Dynamics in G-Quadruplex DNA: Role of Hydration Dynamics on Ligand Solvation inside DNA. J Phys Chem Lett 2015; 6:1754-1760. [PMID: 26263345 DOI: 10.1021/acs.jpclett.5b00653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
G-quadruplex DNA (GqDNA) structures act as promising anticancer targets for small-molecules (ligands). Solvation dynamics of a ligand (DAPI: 4',6-diamidino-2-phenylindole) inside antiparallel-GqDNA is studied through direct comparison of time-resolved experiments to molecular dynamics (MD) simulation. Dynamic Stokes shifts of DAPI in GqDNA prepared in H2O buffer and D2O are compared to find the effect of water on ligand solvation. Experimental dynamics (in H2O) is then directly compared with the dynamics computed from 65 ns simulation on the same DAPI-GqDNA complex. Ligand solvation follows power-law relaxation (summed with fast exponential relaxation) from ~100 fs to 10 ns. Simulation results show relaxation below ~5 ps is dominated by water motion, while both water and DNA contribute comparably to dictate long-time power-law dynamics. Ion contribution is, however, found to be negligible. Simulation results also suggest that anomalous solvation dynamics may have origin in subdiffusive motion of perturbed water near GqDNA.
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Affiliation(s)
- Nibedita Pal
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sachin Dev Verma
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Sengupta C, Basu S. A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains. RSC Adv 2015. [DOI: 10.1039/c5ra13035b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.
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Affiliation(s)
- Chaitrali Sengupta
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
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Ferl S, Wunderlich G, Smits R, Hoepping A, Naumann A, Kotzerke J. Synthesis of a new HYNIC-DAPI derivative for labelling with 99mTechnetium and its in vitro evaluation in an FRTL5 cell line. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00574k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A new multifunctional compound that includes the fluorescent dye 4′,6-diamidine-2-phenylindole (DAPI) and the chelator 6-hydrazinonicotinic acid (HYNIC) was developed and radiolabelled with 99mTc for in vitro evaluation in an FRTL5 cell line.
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Affiliation(s)
- Sandra Ferl
- Technische Universität Dresden
- Faculty of Medicine Carl Gustav Carus
- Department of Nuclear Medicine
- 01307 Dresden
- Germany
| | - Gerd Wunderlich
- Technische Universität Dresden
- Faculty of Medicine Carl Gustav Carus
- Department of Nuclear Medicine
- 01307 Dresden
- Germany
| | - René Smits
- ABX advanced biochemical compounds GmbH
- 01454 Radeberg
- Germany
| | | | - Anne Naumann
- Technische Universität Dresden
- Faculty of Medicine Carl Gustav Carus
- Department of Nuclear Medicine
- 01307 Dresden
- Germany
| | - Jörg Kotzerke
- Technische Universität Dresden
- Faculty of Medicine Carl Gustav Carus
- Department of Nuclear Medicine
- 01307 Dresden
- Germany
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Bis(2,3-dibromo-4,5-dihydroxybenzyl) ether, a marine algae derived bromophenol, inhibits the growth of Botrytis cinerea and interacts with DNA molecules. Mar Drugs 2014; 12:3838-51. [PMID: 24979270 PMCID: PMC4113801 DOI: 10.3390/md12073838] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 12/31/2022] Open
Abstract
Bis(2,3-dibromo-4,5-dihydroxybenzyl) ether (BDDE) is a bromophenol isolated from marine algae. Previous reports have shown that BDDE possesses cytotoxic and antibacterial activity. In the present study, we demonstrate that BDDE displays broad-spectrum antifungal activities, especially on Botrytis cinerea. BDDE inhibits the growth of B. cinerea cultured on a solid medium of potato dextrose agar (PDA) as well as on the potato dextrose broth (PDB) medium. Moreover, BDDE decreases the incidence of fruit decay and severity of strawberries infected with B. cinerea. Further studies have revealed that BDDE decreases the germination rate and inhibits the mycelial growth of B. cinerea. The inhibition mechanisms are related to the disruption of the cell membrane integrity in B. cinerea spores and newly formed germ tubes. This study also suggests that BDDE possibly interacts with DNA via intercalation and minor groove binding. The studies provide evidence that BDDE has potential application in the control of gray mold after fruit harvest and the compound could serve as a candidate or lead template for rational drug design and for the development of antifungal agents.
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Nogueira JJ, González L. Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences. Biochemistry 2014; 53:2391-412. [DOI: 10.1021/bi500068z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Juan J. Nogueira
- Institute
of Theoretical
Chemistry, University of Vienna, Währinger Strasse 17 A-1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical
Chemistry, University of Vienna, Währinger Strasse 17 A-1090 Vienna, Austria
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