1
|
Xie S, Yue C, Ye S, Li Z. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys 2024; 26:10408-10418. [PMID: 38502252 DOI: 10.1039/d3cp05957j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.
Collapse
Affiliation(s)
- Shangqiang Xie
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Congran Yue
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Sheng Ye
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| |
Collapse
|
2
|
Raj A, Thomas RK, Vidya L, Neelima S, Aparna VM, Sudarsanakumar C. A Minor Groove Binder with Significant Cytotoxicity on Human Lung Cancer Cells: The Potential of Hesperetin Functionalised Silver Nanoparticles. J Fluoresc 2023:10.1007/s10895-023-03409-7. [PMID: 37721707 DOI: 10.1007/s10895-023-03409-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023]
Abstract
Natural drug functionalised silver (Ag) nanoparticles (NPs) have gained significant interest in pharmacology related applications due to their therapeutic efficiency. We have synthesised silver nanoparticle using hesperetin as a reducing and capping agent. This work aims to discuss the relevance of the hesperetin functionalised silver nanoparticles (H-AgNPs) in the field of nano-medicine. The article primarily investigates the anticancer activity of H-AgNPs and then their interactions with calf thymus DNA (ctDNA) through spectroscopic and thermodynamic techniques. The green synthesised H-AgNPs are stable, spherical in shape and size of 10 ± 3 nm average diameter. The complex formation of H-AgNPs with ctDNA was established by UV-Visible absorption, fluorescent dye displacement assay, isothermal calorimetry and viscosity measurements. The binding constants obtained from these experiments were consistently in the order of 104 Mol-1. The melting temperature analysis and FTIR measurements confirmed that the structural alterations of ctDNA by the presence of H-AgNPs are minimal. All the thermodynamic variables and the endothermic binding nature were acquired from ITC experiments. All these experimental outcomes reveal the formation of H-AgNPs-ctDNA complex, and the results consistently verify the minor groove binding mode of H-AgNPs. The binding constant and limit of detection of 1.8 μM found from the interaction studies imply the DNA detection efficiency of H-AgNPs. The cytotoxicity of H-AgNPs against A549 and L929 cell lines were determined by in vitro MTT cell viability assay and lactate dehydrogenase (LDH) assay. The cell viability and LDH enzyme release are confirmed that the H-AgNPs has high anticancer activity. Moreover, the calculated LD50 value for H-AgNPs against lung cancer cells is 118.49 µl/ml, which is a low value comparing with the value for fibroblast cells (269.35 µl/ml). In short, the results of in vitro cytotoxicity assays revealed that the synthesised nanoparticles can be considered in applications related to cancer treatments. Also, we have found that, H-AgNPs is a minor groove binder, and having high DNA detection efficiency.
Collapse
Affiliation(s)
- Aparna Raj
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - Riju K Thomas
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
- Bharata Mata College, Thrikkakara, Ernakulam, Kerala, 682032, India
| | - L Vidya
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - S Neelima
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - V M Aparna
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - C Sudarsanakumar
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India.
| |
Collapse
|
3
|
Mousavi SE, Grützner F, Patil JG. Enhanced mitotic arrest and chromosome resolution for cytogenetic analysis in the eastern mosquitofish, Gambusia holbrooki. Acta Histochem 2023; 125:152029. [PMID: 37062122 DOI: 10.1016/j.acthis.2023.152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
Maximising the number of cells arrested at metaphase and their resolution is fundamentally important for molecular cytogenetic investigations, particularly in fish, which typically yield low mitotic index and have highly condensed chromosomes. To overcome these limitations, fish were injected with a mitotic stimulator (the yeast, Saccharomyces cerevisiae) to improve the mitotic index, and the intercalating agent ethidium bromide to produce elongated chromosomes. Specifically, adults were injected with activated yeast and then Colcemid (0.025 µg/µl solution, 10 µl per 1 g of body weight) at 24-96 h post yeast injections, followed by chromosome preparations from multiple tissues. Results showed that gill tissue had the highest number of dividing cells at 72 h post yeast exposure with no significant (p > 0.05) differences between the sexes. Nonetheless, sex-specific differences in the mitotic index were observed in spleen, kidney, and liver, which may be attributed to sex-specific differences in immune responses. For elongation of mitotic chromosomes, individuals (both sexes) were first injected with activated yeast and after 48 h with ethidium bromide (2 or 4 µg/ml) and Colcemid (0.05 µg/µl solution, 10 µl per 1 g of body weight). Following which, animals were sampled at three time points (1, 4 and 8 h) for chromosome preparations. The results show that the optimum elongation of metaphase chromosomes of males and females was achieved by using 2 µg/ml and 4 µg/ml, respectively, for 1 h. Interestingly, the average mitotic chromosome length (μm) of males and females post-ethidium bromide exposure was significantly different (p < 0.05) for both concentrations, except at 1 h exposure for 2 µg/ml EtBr. Such differences can be attributed to overall chromosomal condensation differences between sexes. Regardless, the increased mitotic index and chromosome resolution could benefit cytogenetic studies in other fish species.
Collapse
Affiliation(s)
- Seyed Ehsan Mousavi
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia; School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
| | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jawahar G Patil
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia
| |
Collapse
|
4
|
Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [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: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
Collapse
Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
5
|
Aggarwal S, Tanwar N, Singh A, Munde M. Formation of Protamine and Zn-Insulin Assembly: Exploring Biophysical Consequences. ACS OMEGA 2022; 7:41044-41057. [PMID: 36406544 PMCID: PMC9670714 DOI: 10.1021/acsomega.2c04419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The insulin-protamine interaction is at the core of the mode of action in many insulin formulations (Zn + insulin + protamine) and to treat diabetes, in which protamine is added to the stable form of hexameric insulin (Zn-insulin). However, due to the unavailability of quantitative data and a high-resolution structure, the binding mechanism of the insulin-protamine complex remains unknown. In this study, it was observed that Zn-insulin experiences destabilization as observed by the loss of secondary structure in circular dichroism (CD), and reduction in thermal stability in melting study, upon protamine binding. In isothermal titration calorimetry (ITC), it was found that the interactions were mostly enthalpically driven. This is in line with the positive ΔC m value (+880 cal mol-1), indicating the role of hydrophilic interactions in the complex formation, with the exposure of hydrophobic residues to the solvent, which was firmly supported by the 8-anilino-1-naphthalene sulfonate (ANS) binding study. The stoichiometry (N) value in ITC suggests the multiple insulin molecules binding to the protamine chain, which is consistent with the picture of the condensation of insulin in the presence of protamine. Atomic force microscopy (AFM) suggested the formation of a heterogeneous Zn-insulin-protamine complex. In fluorescence, Zn-insulin experiences strong Tyr quenching, suggesting that the location of the protamine-binding site is near Tyr, which is also supported by the molecular docking study. Since Tyr is critical in the stabilization of insulin self-assembly, its interaction with protamine may impair insulin's self-association ability and thermodynamic stability while at the same time promoting its flexible conformation desired for better biological activity.
Collapse
|
6
|
A Biophysical Study of DNA Condensation Mediated by Histones and Protamines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
7
|
Yadav V, Krishnan A, Baig MS, Majeed M, Nayak M, Vohora D. Decrypting the interaction pattern of Piperlongumine with calf thymus DNA and dodecamer d(CGCGAATTCGCG) 2 B-DNA: Biophysical and molecular docking analysis. Biophys Chem 2022; 285:106808. [PMID: 35358908 DOI: 10.1016/j.bpc.2022.106808] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/19/2022] [Accepted: 03/20/2022] [Indexed: 12/20/2022]
Abstract
The mechanisms of interaction of DNA with pharmacological molecules are critical to understanding their therapeutic actions on physiological systems. Piperlongumine is widely studied for its anticancer potential. Multi-spectrometry, calorimetry and in silico studies were employed to study the interaction of piperlongumine and calf thymus DNA. UV-Vis spectroscopy illustrated a hyperchromic pattern in spectra of the calf thymus DNA-piperlongumine complex, while fluorescent quenching was observed in emission spectral studies. Competitive displacement assay demonstrated higher displacement and binding constant for DNA-rhodamine B complex by piperlongumine than DNA-methylene blue complex. Differential scanning calorimetry presented non-significant changes in melting temperature and molecular docking presented the precise interaction site of piperlongumine with calf thymus DNA at minor groove. Further, piperlongumine treatment did not result in pBluescript KS plasmid DNA cleavage as revealed from the DNA topology assay. All these experiments confirmed the binding of piperlongumine with DNA through minor groove binding mode.
Collapse
Affiliation(s)
- Vaishali Yadav
- Neurobehavioral Pharmacology Laboratory, Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Anuja Krishnan
- Department of Molecular Medicine, School of Interdisciplinary Science and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Mirza Sarwar Baig
- Department of Molecular Medicine, School of Interdisciplinary Science and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Muhammed Majeed
- Sami-Sabinsa Group Limited, Bengaluru 560058, Karnataka, India
| | - Mahadeva Nayak
- Sami-Sabinsa Group Limited, Bengaluru 560058, Karnataka, India
| | - Divya Vohora
- Neurobehavioral Pharmacology Laboratory, Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Nayak S, Das P. Covalent Conjugation of Carbon Dots with Plasmid and DNA Condensation Thereafter: Realistic Insights into the Condensate Morphology, Energetics, and Photophysics. ACS OMEGA 2021; 6:21425-21435. [PMID: 34471745 PMCID: PMC8387987 DOI: 10.1021/acsomega.1c02247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
The use of carbon quantum dots (CDs) as trackable nanocarriers for plasmid and gene as hybrid DNA condensates has gained momentum, as evident from the significant recent research efforts. However, the in-depth morphology of the condensates, the energetics of the condensation process, and the photophysical aspects of the CD are not well understood and often disregarded. Herein, for the first time, we covalently attached linearized pUC19 with citric acid and cysteamine-derived CD through the reaction of the surface amine groups of CDs with the 5'-phospho-methyl imidazolide derivative of the plasmid to obtain a 1:1 CD-pUC19 covalent conjugate. The CD-pUC19 conjugates were further transformed into DNA condensates with spermine that displayed a toroidal morphology with a diameter of ∼200 nm involving ∼2-5 CD-pUC19 conjugates in a single condensate. While the interaction of pristine CD to spermine was exothermic, the binding of the CD-pUC19 conjugate with spermine was endothermic and primarily entropy-driven. The condensed plasmid displayed severe conformational stress and deviation from the B-form due to the compact packing of the DNA but better transfection ability than the pristine CD. The CDs in the condensates tend to come close to each other at the core that results in their shielding from excitation. However, this does not prevent them from emanating reactive oxygen species on visible light exposure that compromises the decondensation process and cell viability at higher exposure times, calling for utmost caution in establishing them as nonviral transfecting agents universally.
Collapse
Affiliation(s)
- Suman Nayak
- Department of Chemistry, Indian
Institute of Technology Patna, Bihta, Patna, 801106 Bihar, India
| | - Prolay Das
- Department of Chemistry, Indian
Institute of Technology Patna, Bihta, Patna, 801106 Bihar, India
| |
Collapse
|
10
|
Tiwari N, Mishra RK, Gupta S, Srivastava R, Aggarwal S, Bandyopadhyay P, Munde M. Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9385-9395. [PMID: 34313447 DOI: 10.1021/acs.langmuir.1c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The real motivation in the present work is to tune the synthesis variables that can result in a highly fluorescent and stable DNA copper nanocluster (CuNC) and also to understand the intricate mechanism behind this process. Here, carefully optimized concentrations of various reactants enabled the creation of a DNA-encapsulated CuNC for AT-DNA, displaying a size of <1.0 nm as confirmed by transmission electron microscopy and dynamic light scattering. The extremely small size of the AT-DNACuNC supports the discrete electronic transitions, also characterized by an exceptionally strong negative circular dichroism (CD) band around 350 nm, whose intensity is well correlated with the observed strong fluorescence emission intensity. This remarkably strong CD can open new applications in the detection and quantification of a specific DNACuNC. Further, time-dependent fluorescence analysis suggested stronger photostabilization of these DNACuNCs. The simulation study, based on Cu ion distribution, explained how AT-DNA is a better candidate for NC formation than GC-DNA. In conclusion, the better-tuned synthesis procedure has resulted in a highly compact, well-defined three-dimensional conformation that promotes a more favorable microenvironment to sequester a DNA-based CuNC with high brightness and outstanding photostability.
Collapse
Affiliation(s)
- Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
11
|
Kandari D, Joshi H, Tanwar N, Munde M, Bhatnagar R. Delineation of the Residues of Bacillus anthracis Zinc Uptake Regulator Protein Directly Involved in Its Interaction with Cognate DNA. Biol Trace Elem Res 2021; 199:3147-3158. [PMID: 33052530 DOI: 10.1007/s12011-020-02427-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
Zinc uptake regulator (Zur) is a negative transcriptional regulator of bacteria that belongs to the FUR superfamily of proteins and regulates zinc (Zn) homeostasis under extreme Zn conditions. The Zur protein of Bacillus anthracis (BaZur) was though characterized previously, but the residues of this transcriptional regulator, crucial for binding to the consensus Zur box in the cognate DNA, remain unexplored. In this study, we reveal the essential residues of the protein that govern the specific interaction with the cognate DNA, through mutational and binding studies. In silico predicted model of the BaZur protein with the promoter region of one of the regulon candidates was utilized to identify specific residues of the N-terminal domain (NTD), constituting the DNA-binding recognition helix. Our results suggest that two phenylalanine residues, a non-polar aliphatic leucine and a positively charged arginine residue of NTD, are predominantly involved in DNA binding of BaZur. Among these, the arginine residue (Arg58) is conserved among all the Zur proteins and the two Phe residues, namely Phe53 and Phe63, are conserved in the Zur proteins of Staphylococcus aureus and Listeria monocytogenes. Taken together, the current study represents an in-depth investigation into the key DNA-binding residues involved in the BaZur-DNA interaction.
Collapse
Affiliation(s)
- Divya Kandari
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Hemant Joshi
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neetu Tanwar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
- Banaras Hindu University, Banaras, Uttar Pradesh, 221005, India.
| |
Collapse
|
12
|
Saraswathi SK, Karunakaran V, Maiti KK, Joseph J. DNA Condensation Triggered by the Synergistic Self-Assembly of Tetraphenylethylene-Viologen Aggregates and CT-DNA. Front Chem 2021; 9:716771. [PMID: 34368086 PMCID: PMC8341308 DOI: 10.3389/fchem.2021.716771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/24/2021] [Indexed: 01/24/2023] Open
Abstract
Development of small organic chromophores as DNA condensing agents, which explore supramolecular interactions and absorbance or fluorescence-based tracking of condensation and gene delivery processes, is in the initial stages. Herein, we report the synthesis and electrostatic/groove binding interaction-directed synergistic self-assembly of the aggregates of two viologen-functionalized tetraphenylethylene (TPE-V) molecules with CT-DNA and subsequent concentration-dependent DNA condensation process. TPE-V molecules differ in their chemical structure according to the number of viologen units. Photophysical and morphological studies have revealed the interaction of the aggregates of TPE-V in Tris buffer with CT-DNA, which transforms the fibrous network structure of CT-DNA to partially condensed beads-on-a-string-like arrangement with TPE-V aggregates as beads via electrostatic and groove binding interactions. Upon further increasing the concentration of TPE-V, the "beads-on-a-string"-type assembly of TPE-V/CT-DNA complex changes to completely condensed compact structures with 40-50 nm in diameter through the effective charge neutralization process. Enhancement in the melting temperature of CT-DNA, quenching of the fluorescence emission of ethidium bromide/CT-DNA complex, and the formation of induced CD signal in the presence of TPE-V molecules support the observed morphological changes and thereby verify the DNA condensation abilities of TPE-V molecules. Decrease in the hydrodynamic size, increase in the zeta potential value with the addition of TPE-V molecules to CT-DNA, failure of TPE-V/cucurbit(8)uril complex to condense CT-DNA, and the enhanced DNA condensation ability of TPE-V2 with two viologen units compared to TPE-V1 with a single viologen unit confirm the importance of positively charged viologen units in the DNA condensation process. Initial cytotoxicity analysis on A549 cancer and WI-38 normal cells revealed that these DNA condensing agents are non-toxic in nature and hence could be utilized in further cellular delivery studies.
Collapse
Affiliation(s)
- Sajena Kanangat Saraswathi
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Varsha Karunakaran
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kaustabh Kumar Maiti
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
13
|
Franck CO, Fanslau L, Bistrovic Popov A, Tyagi P, Fruk L. Biopolymer-based Carriers for DNA Vaccine Design. Angew Chem Int Ed Engl 2021; 60:13225-13243. [PMID: 32893932 PMCID: PMC8247987 DOI: 10.1002/anie.202010282] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Indexed: 12/16/2022]
Abstract
Over the last 30 years, genetically engineered DNA has been tested as novel vaccination strategy against various diseases, including human immunodeficiency virus (HIV), hepatitis B, several parasites, and cancers. However, the clinical breakthrough of the technique is confined by the low transfection efficacy and immunogenicity of the employed vaccines. Therefore, carrier materials were designed to prevent the rapid degradation and systemic clearance of DNA in the body. In this context, biopolymers are a particularly promising DNA vaccine carrier platform due to their beneficial biochemical and physical characteristics, including biocompatibility, stability, and low toxicity. This article reviews the applications, fabrication, and modification of biopolymers as carrier medium for genetic vaccines.
Collapse
Affiliation(s)
- Christoph O. Franck
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhillipa Fawcett DriveCambridgeCB3 0ASUK
| | - Luise Fanslau
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhillipa Fawcett DriveCambridgeCB3 0ASUK
| | - Andrea Bistrovic Popov
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhillipa Fawcett DriveCambridgeCB3 0ASUK
| | - Puneet Tyagi
- Dosage Form Design and DevelopmentBioPharmaceuticals DevelopmentR&DAstra ZenecaGaithersburgMD20878USA
| | - Ljiljana Fruk
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhillipa Fawcett DriveCambridgeCB3 0ASUK
| |
Collapse
|
14
|
Perry CC, Ramos-Méndez J, Milligan JR. Boronated Condensed DNA as a Heterochromatic Radiation Target Model. Biomacromolecules 2021; 22:1675-1684. [PMID: 33750108 DOI: 10.1021/acs.biomac.1c00106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The compound 4-dihydroxyboryl-l-phenylalanine (BPA) has found use in clinical trials of boron neutron capture therapy (BNCT). Here, we have examined the interaction with DNA of an amide-blocked BPA derivative of hexa-l-arginine (Ac-BPA-Arg6-NH2). Physical and spectroscopic assays show that this peptide binds to and condenses DNA. The resulting condensates are highly resistant to the effects of nuclease incubation (68-fold) and gamma (38-fold) irradiation. Radioprotection was modeled by Monte Carlo track structure simulations of DNA single strand breaks (SSBs) with TOPAS-nBio. The differences between experimental and simulated SSB yields for uncondensed and condensed DNAs were ca. 2 and 18%, respectively. These observations indicate that the combination of a plasmid DNA target, the BPA-containing peptide, and track structure simulation provides a powerful approach to characterize DNA damage by the high-LET radiation associated with neutron capture on boron.
Collapse
Affiliation(s)
- Christopher C Perry
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, California 92350, United States
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, California 94115, United States
| | - Jamie R Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, California 92350, United States
| |
Collapse
|
15
|
Dukhopelnykov E, Bereznyak E, Gladkovskaya N, Skuratovska A, Krivonos D. Studies of eosin Y - DNA interaction using a competitive binding assay. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119114. [PMID: 33166781 DOI: 10.1016/j.saa.2020.119114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 06/11/2023]
Abstract
The interaction between xanthene dye eosin Y and double stranded DNA has been studied by spectrophotometry. The conventional titration study does not show the interaction in the eosin Y - DNA system. Therefore, the competitive binding assay was carried out. The DNA-targeted ligands proflavine and methylene blue were used as competitors. Multivariate curve resolution - alternative least squares method (MCR-ALS) was applied to analyze the spectrophotometric titration data. The experimental binding isotherms were fitted by Scatchard and McGee equations. The binding constant of eosin Y with DNA was found to be 1.7·104 M-1. It is shown that the competitive binding assay requires consideration of heteroassociation for the correct determination of ligand-DNA binding parameters.
Collapse
Affiliation(s)
- Evgeniy Dukhopelnykov
- Biological Physics Department, O.Ya. Usikov Institute for Radiophysics and Electronics of National Academy of Sciences of Ukraine, 12 Ak. Proskura Str., Kharkov 61085, Ukraine; Department of Biomedical and Medical Physics, V. N. Karazin Kharkiv National University, 4 Svoboda Sq., Kharkiv 61022, Ukraine.
| | - Ekaterina Bereznyak
- Biological Physics Department, O.Ya. Usikov Institute for Radiophysics and Electronics of National Academy of Sciences of Ukraine, 12 Ak. Proskura Str., Kharkov 61085, Ukraine
| | - Natalia Gladkovskaya
- Biological Physics Department, O.Ya. Usikov Institute for Radiophysics and Electronics of National Academy of Sciences of Ukraine, 12 Ak. Proskura Str., Kharkov 61085, Ukraine
| | - Anastasiia Skuratovska
- Biological Physics Department, O.Ya. Usikov Institute for Radiophysics and Electronics of National Academy of Sciences of Ukraine, 12 Ak. Proskura Str., Kharkov 61085, Ukraine
| | - Daria Krivonos
- Department of Biomedical and Medical Physics, V. N. Karazin Kharkiv National University, 4 Svoboda Sq., Kharkiv 61022, Ukraine
| |
Collapse
|
16
|
Franck CO, Fanslau L, Bistrovic Popov A, Tyagi P, Fruk L. Biopolymer‐based Carriers for DNA Vaccine Design. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Christoph O. Franck
- Department of Chemical Engineering and Biotechnology University of Cambridge Phillipa Fawcett Drive Cambridge CB3 0AS UK
| | - Luise Fanslau
- Department of Chemical Engineering and Biotechnology University of Cambridge Phillipa Fawcett Drive Cambridge CB3 0AS UK
| | - Andrea Bistrovic Popov
- Department of Chemical Engineering and Biotechnology University of Cambridge Phillipa Fawcett Drive Cambridge CB3 0AS UK
| | - Puneet Tyagi
- Dosage Form Design and Development BioPharmaceuticals Development R&D Astra Zeneca Gaithersburg MD 20878 USA
| | - Ljiljana Fruk
- Department of Chemical Engineering and Biotechnology University of Cambridge Phillipa Fawcett Drive Cambridge CB3 0AS UK
| |
Collapse
|
17
|
Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite. Biochem J 2020; 477:2153-2177. [PMID: 32484216 DOI: 10.1042/bcj20200145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022]
Abstract
Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
Collapse
|
18
|
Development of novel anti-malarial from structurally diverse library of molecules, targeting plant-like CDPK1, a multistage growth regulator of P. falciparum. Biochem J 2020; 477:1951-1970. [PMID: 32401306 DOI: 10.1042/bcj20200045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023]
Abstract
Upon Plasmodium falciparum merozoites exposure to low [K+] environment in blood plasma, there is escalation of cytosolic [Ca2+] which activates Ca2+-Dependent Protein Kinase 1 (CDPK1), a signaling hub of intra-erythrocytic proliferative stages of parasite. Given its high abundance and multidimensional attributes in parasite life-cycle, this is a lucrative target for designing antimalarials. Towards this, we have virtually screened MyriaScreenII diversity collection of 10,000 drug-like molecules, which resulted in 18 compounds complementing ATP-binding pocket of CDPK1. In vitro screening for toxicity in mammalian cells revealed that these compounds are non-toxic in nature. Furthermore, SPR analysis demonstrated differential binding affinity of these compounds towards recombinantly purified CDPK1 protein. Selection of lead compound 1 was performed by evaluating their inhibitory effects on phosphorylation and ATP binding activities of CDPK1. Furthermore, in vitro biophysical evaluations by ITC and FS revealed that binding of compound 1 is driven by formation of energetically favorable non-covalent interactions, with different binding constants in presence and absence of Ca2+, and TSA authenticated stability of compound 1 bound CDPK1 complex. Finally, compound 1 strongly inhibited intra-erythrocytic growth of P. falciparum in vitro. Conceivably, we propose a novel CDPK1-selective inhibitor, step towards developing pan-CDPK kinase inhibitors, prerequisite for cross-stage anti-malarial protection.
Collapse
|
19
|
Rahimmanesh I, Totonchi M, Khanahmad H. The challenging nature of primary T lymphocytes for transfection: Effect of protamine sulfate on the transfection efficiency of chemical transfection reagents. Res Pharm Sci 2020; 15:437-446. [PMID: 33628285 PMCID: PMC7879792 DOI: 10.4103/1735-5362.297846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Accepted: 09/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background and purpose: The optimization of an effective non-viral gene delivery method for genetic manipulation of primary human T cells has been a major challenge in immunotherapy researches. Due to the poor transfection efficiency of conventional methods in T cells, there has been an effort to increase the transfection rate in these cells. Protamine is an FDA-approved compound with a documented safety profile that enhances DNA condensation for gene delivery. Experimental approach: In this study, the effect of protamine sulfate on the transfection efficiency of standard transfection reagents, was evaluated to transfect primary human T cells. In this regard, pre-condensation of DNA was applied using protamine, and the value of the zeta potential of DNA/protamine/cargo complexes was determined. T cells were transfected with DNA/protamine/cargo complexes. The transfection efficiency rate was evaluated by flow cytometry. Also, the green fluorescent protein expression level and cytotoxicity of each complex were identified using real-time polymerase chain reaction and MTT assay, respectively. Findings/Results: Our results demonstrated that protamine efficiently increases the positive charge of DNA/cargo complex without any cytotoxic effect on the primary human T cells. We observed that the transfection efficiency in DNA/protamine/ Lipofectamine® 2000 and DNA/protamine/TurboFect™ was 87.2% and 78.9%, respectively, while transfection of T cells by Lipofectamine® 2000 and TurboFect™ would not result in sufficient transfection. Conclusion and implications: Protamine sulfate enhanced the transfection rate of T cells; and could be a promising non-viral gene delivery method to achieve a safe, rapid, cost-effective, and efficient system which will be further applied in gene therapy and T cells manipulation methods.
Collapse
Affiliation(s)
- Ilnaz Rahimmanesh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| |
Collapse
|
20
|
Kuba M, Kraus T, Pohl R, Hocek M. Nucleotide-Bearing Benzylidene-Tetrahydroxanthylium Near-IR Fluorophore for Sensing DNA Replication, Secondary Structures and Interactions. Chemistry 2020; 26:11950-11954. [PMID: 32633433 PMCID: PMC7361531 DOI: 10.1002/chem.202003192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Thymidine triphosphate bearing benzylidene-tetrahydroxanthylium near-IR fluorophore linked to the 5-methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348-times) presumably due to interactions in major groove and the fluorescence further increases in the single-stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light-up building block in real-time PCR for detection of SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Miroslav Kuba
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| |
Collapse
|
21
|
Łudzik K, Woloszczuk S, Zając W, Jazdzewska M, Rogachev A, Kuklin AI, Zawisza A, Jóźwiak M. Can the Isothermal Calorimetric Curve Shapes Suggest the Structural Changes in Micellar Aggregates? Int J Mol Sci 2020; 21:ijms21165828. [PMID: 32823747 PMCID: PMC7461569 DOI: 10.3390/ijms21165828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 11/30/2022] Open
Abstract
Inspired by the unusual shapes of the titration curve observed for many surfactants and mixed colloidal systems, we decided to extend the analysis to isothermal titration calorimetric curves (ITC) by paying special attention to potential structural changes in micellar aggregates. In this paper, we used isothermal titration calorimetry in conjunction with Scanning Transmission Electron Microscopy (STEM), Small-Angle Neutron Scattering (SANS) and X-ray Scattering (SAXS) methods support by Monte Carlo and semiempirical quantum chemistry simulations to confirm if the isothermal calorimetric curve shape can reflect micelle transition phenomena. For that purpose, we analysed, from the thermodynamic point of view, a group of cationic gemini surfactants, alkanediyl-α,ω-bis(dimethylalkylammonium) bromides. We proposed the shape of aggregates created by surfactant molecules in aqueous solutions and changes thereof within a wide temperature range. The results provide evidence for the reorganization processes and the relationship (dependence) between the morphology of the created aggregates and the conditions such as temperature, surfactant concentration and spacer chain length which affect the processes.
Collapse
Affiliation(s)
- Katarzyna Łudzik
- Department of Physical Chemistry, University of Lodz, 90-236 Lodz, Poland;
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; (M.J.); (A.R.); (A.I.K.)
- Correspondence:
| | | | - Wojciech Zając
- The Henryk Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Cracow, Poland;
| | - Monika Jazdzewska
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; (M.J.); (A.R.); (A.I.K.)
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland;
| | - Andrey Rogachev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; (M.J.); (A.R.); (A.I.K.)
- Moscow Institute of Physics and Technology, 9 Institutskiy per. 141701 Dolgoprudny, Russia
| | - Alexander Ivanowicz Kuklin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; (M.J.); (A.R.); (A.I.K.)
- Moscow Institute of Physics and Technology, 9 Institutskiy per. 141701 Dolgoprudny, Russia
| | - Anna Zawisza
- Department of Organic and Applied Chemistry, University of Lodz, 91-403 Lodz Poland;
| | - Małgorzata Jóźwiak
- Department of Physical Chemistry, University of Lodz, 90-236 Lodz, Poland;
| |
Collapse
|
22
|
Du K, Xia Q, Heng H, Feng F. Temozolomide-Doxorubicin Conjugate as a Double Intercalating Agent and Delivery by Apoferritin for Glioblastoma Chemotherapy. ACS APPLIED MATERIALS & INTERFACES 2020; 12:34599-34609. [PMID: 32648735 DOI: 10.1021/acsami.0c08531] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We designed a conjugated compound by coupling temozolomide (TMZ) with doxorubicin (DOX) via an acylhydrazone linkage as a potential prodrug used for glioblastoma multiforme (GBM) treatment. Viscosity and spectroscopic studies revealed that the drug conjugate could act as a nonclassical double intercalating agent. Although free TMZ is an inefficient DNA binder in comparison to DOX, the TMZ moiety interacted with DNA as an induced intercalator, arising from the synergistic effect of DOX moiety that mediated conformational changes of the DNA helix. Two binding modes were proposed to interpret the double intercalating effect of the drug conjugate on intra- and inter-DNA interactions that could cause DNA cross-linking and fibril aggregates. We also developed a delivery nanoplatform with a loading efficiency of 83% using copper-bound apoferritin as a nanocarrier. In sharp contrast to the short half-life of free TMZ, the nanocomposite was stable under physiological conditions without detectable drug decomposition after a 2 week storage, and drug release was activatable in the presence of glutathione at millimolar levels. The antitumor effect of the drug conjugate and nanocomposite against GBM cells was reported to demonstrate the potential therapeutic applications of double intercalating materials.
Collapse
Affiliation(s)
- Ke Du
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiuyu Xia
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hao Heng
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fude Feng
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
23
|
Auria-Luna F, Fernández-Moreira V, Marqués-López E, Gimeno MC, Herrera RP. Ultrasound-assisted multicomponent synthesis of 4H-pyrans in water and DNA binding studies. Sci Rep 2020; 10:11594. [PMID: 32665694 PMCID: PMC7360557 DOI: 10.1038/s41598-020-68076-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
A simple approach to synthesize new highly substituted 4H-pyran derivatives is described. Efficient Et3N acts as a readily accessible catalyst of this process performed in pure water and with only a 20 mol% of catalyst loading. The extremely simple operational methodology, short reaction times, clean procedure and excellent product yields render this new approach extremely appealing for the synthesis of 4H-pyrans, as potentially biological scaffolds. Additionally, DNA interaction analysis reveals that 4H-pyran derivatives behave preferably as minor groove binders over major groove or intercalators. Therefore, this is one of the scarce examples where pyrans have resulted to be interesting DNA binders with high binding constants (Kb ranges from 1.53 × 104 M-1 to 2.05 × 106 M-1).
Collapse
Affiliation(s)
- Fernando Auria-Luna
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Vanesa Fernández-Moreira
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Eugenia Marqués-López
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - M Concepción Gimeno
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Raquel P Herrera
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain.
| |
Collapse
|
24
|
Gupta S, Tiwari N, Verma J, Waseem M, Subbarao N, Munde M. Estimation of a stronger heparin binding locus in fibronectin domain III14using thermodynamics and molecular dynamics. RSC Adv 2020; 10:20288-20301. [PMID: 35520402 PMCID: PMC9054198 DOI: 10.1039/d0ra01773f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023] Open
Abstract
The HEP II (Heparin-binding site II) region of fibronectin (FN) containing domain III14 plays a crucial role in cell adhesion and migration through heparin-binding on the cell surface. There are two such fibronectin heparin interacting peptide (FHIP I and FHIP II) sequences present in HEP II. However, the molecular principles by which these sites orchestrate heparin-binding processes are poorly understood. Such knowledge would have great implications in the therapeutic targeting of FN. With this aim, we have explored the binding studies of FHIP I and FHIP II with heparin using various biophysical methods. A fluorescence melting study specifically revealed the preference of heparin for domain III in FN, indicating the key contribution of FHIP I and FHIP II in heparin binding. In isothermal titration calorimetry (ITC), the higher binding affinity observed for FHIP II (∼107 mol−1) compared to FHIP I (∼106 mol−1) is expected due to the presence of a superior cluster of Arg and Lys residues in FHIP II, which can facilitate specific H-bonding interactions with heparin. Based on heat capacity changes, the key role of H-bonding, electrostatic and hydrophobic interactions was demonstrated in binding. Finally, the molecular docking and MD simulation results reinforced that the interaction of heparin (dodecasaccharide) is stronger and stable with the FHIP II peptide. The results described here suggest that these peptides provide all the structural and thermodynamic elements necessary for heparin-binding of HEP II of FN. Subsequently, it can be concluded that FHIP II could be a better location for therapeutic intervention in cell adhesion activity by FN. Binding Thermodynamics of FHIP I and FHIP II with heparin.![]()
Collapse
Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Neha Tiwari
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Jyoti Verma
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Mohd Waseem
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Manoj Munde
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| |
Collapse
|
25
|
A Low-Cost Time-Correlated Single Photon Counting Portable DNA Analyzer. SENSORS 2019; 19:s19132838. [PMID: 31247893 PMCID: PMC6651547 DOI: 10.3390/s19132838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/29/2022]
Abstract
Photon-counting analysis of nucleic acids plays a key role in many diagnostics applications for its accurate and non-invasive nature. However, conventional photon-counting instrumentations are bulky and expensive due to the use of conventional optics and a lack of optimization of electronics. In this paper, we present a portable, low-cost time-correlated single photon-counting (TCSPC) analysis system for DNA detection. Both optical and electronic subsystems are carefully designed to provide effective emission filtering and size reduction, delivering good DNA detection and fluorescence lifetime extraction performance. DNA detection has been verified by fluorescence lifetime measurements of a V-carbazole conjugated fluorophore lifetime bioassay. The time-to-digital module of the proposed TCSPC system achieves a full width at half maximum (FWHM) timing resolution from 121 to 145 ps and a differential non-linearity (DNL) between −8.5% and +9.7% of the least significant bit (LSB) within the 500 ns full-scale range (FSR). With a detection limit of 6.25 nM and a dynamic range of 6.8 ns, the proposed TCSPC system demonstrates the enabling technology for rapid, point-of-care DNA diagnostics.
Collapse
|