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Nial PS, Subudhi U. Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA. Int J Biol Macromol 2024; 266:131238. [PMID: 38554916 DOI: 10.1016/j.ijbiomac.2024.131238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Zeta potential is commonly referred as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acids. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, for the first time we discover the zeta potential difference between B-DNA and lanthanum chloride-induced Z-DNA. A series of linear repeat i.e. (CG)n and (GC)n DNA as well as branched DNA (bDNA) structures was used for the B-to-Z DNA transition. Herein, the positive zeta potential of Z-DNA has been demonstrated as a powerful tool to discriminate between B-form and Z-form of DNA. The generality of the approach has been validated both in linear and bDNA nanostructures. Thus, we suggest zeta potential can be used as an ideal signature for the left-handed Z-DNA.
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Affiliation(s)
- Partha S Nial
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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Travagliante G, Gaeta M, Gangemi CMA, Alaimo S, Ferro A, Purrello R, D'Urso A. Interactions between achiral porphyrins and a mature miRNA. NANOSCALE 2024; 16:5137-5148. [PMID: 38305723 DOI: 10.1039/d3nr05504c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Recent discoveries have revealed that mature miRNAs could form highly ordered structures similar to aptamers, suggesting diverse functions beyond mRNA recognition and degradation. This study focuses on understanding the secondary structures of human miR-26b-5p (UUCAAGUAAUUCAGGAUAGGU) using circular dichroism (CD) and chiroptical probes; in particular, four achiral porphyrins were utilized to both act as chiroptical probes and influence miRNA thermodynamic stability. Various spectroscopic techniques, including UV-Vis, fluorescence, resonance light scattering (RLS), electronic circular dichroism (ECD), and CD melting, were employed to study their interactions. UV-Vis titration revealed that meso-tetrakis(4-N-methylpyridyl) porphyrin (H2T4) and meso-tetrakis(4-carboxyphenylspermine) porphyrin (H2TCPPSpm4) formed complexes with distinct binding stoichiometries up to 6 : 1 and 3 : 1 ratios, respectively, and these results were supported by RLS and fluorescence, while the zinc(II) derivative porphyrin ZnT4 exhibited a weaker interaction. ZnTCPPSpm4 formed aggregates in PBS with higher organization in the presence of miRNA. CD titrations displayed an induced CD signal in the Soret region for every porphyrin investigated, indicating that they can be used as chiroptical probes for miR-26b-5p. Lastly, CD melting experiments revealed that at a 1 : 1 ratio, porphyrins did not significantly affect miRNA stability, except for H2TCPPSpm4. However, at a 3 : 1 ratio, all porphyrins, except ZnTCPPSpm4, exhibited a strong destabilizing effect on miRNA secondary structures. These findings shed light on the structural versatility of miR-26b-5p and highlight the potential of porphyrins as chiroptical probes and modulators of miRNA stability.
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Affiliation(s)
- Gabriele Travagliante
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Massimiliano Gaeta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Chiara M A Gangemi
- Dipartimento di Scienze chimiche, biologiche, farmaceutiche e ambientali, Università degli Studi di Messina, V.le Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore Alaimo
- Dipartimento di Medicina Clinica e Sperimentale, c/o Dipartimento di Matematica e Informatica, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Alfredo Ferro
- Dipartimento di Medicina Clinica e Sperimentale, c/o Dipartimento di Matematica e Informatica, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
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D'Urso A. Chiroptical Properties of Z-DNA Using Ionic Porphyrins and Metalloporphyrins. Methods Mol Biol 2023; 2651:131-141. [PMID: 36892764 DOI: 10.1007/978-1-0716-3084-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The non-covalent interaction of achiral porphyrins with nucleic acids has been extensively studied, and various macrocycles have been indeed utilized as reporters of different sequences of DNA bases. Nevertheless, few studies have been published on the capability of these macrocycles to discriminate among the various nucleic acid conformations. Circular dichroism spectroscopy allowed to characterize the binding of several cationic and anionic mesoporphyrins and metallo derivatives with Z-DNA, in order to exploit the functionality of these systems as probes, storing system, and logic gate.
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Affiliation(s)
- Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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Gaeta M, Farini S, Gangemi CMA, Purrello R, D'Urso A. Interactions of mono spermine porphyrin derivative with DNAs. Chirality 2020; 32:1243-1249. [PMID: 32794305 DOI: 10.1002/chir.23272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/04/2020] [Accepted: 07/20/2020] [Indexed: 11/12/2022]
Abstract
In this work, we have characterized the interactions of monospermine porphyrin derivative with calf thymus DNA (ct-DNA) and poly (dG-dC)2 in both B and Z conformation. By several spectroscopic techniques (UV-vis, electronic circular dichroism and resonance light scattering), the binding modes of monospermine porphyrin derivative with different DNA sequences have been elucidated. In the presence of ct-DNA, the porphyrin binds along the external double helix as well as in the presence of B conformation of poly (dG-dC)2 . Whilst when the Z form of the poly (dG-dC)2 is induced, a slight intercalation of the porphyrin between the basis has been detected.
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Affiliation(s)
- Massimiliano Gaeta
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Salvatore Farini
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Chiara M A Gangemi
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Roberto Purrello
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
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Gangemi CM, Randazzo R, Gaeta M, Fortuna CG, Fragalà ME, Purrello R, D’Urso A. Synthesis and characterization of 5-(4-carboxyphenylspermine)-10,15,20-triphenylporphyrin. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619501839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We synthetized and characterized a mono spermine porphyrin derivative by NMR, UV-vis and fluorescence spectroscopy. The photophysical properties and the protonation equilibria of 5-(4-carboxyphenylspermine)-10,15,20-triphenylporphyrin have been investigated, showing that porphyrin does not aggregate in acidic solutions, differently from what occurs as soon as the core of the porphyrin is deprotonated. These aggregation processes have been detected by the rising of new fluorescence band and a significant splitting of the Soret band.
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Affiliation(s)
| | - Rosalba Randazzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | - Massimiliano Gaeta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | - Cosimo G. Fortuna
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | - Maria E. Fragalà
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
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Chen WT. A one-dimensional manganese(III)-porphyrin coordination polymer: crystal structure and photophysical properties. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:375-380. [PMID: 32367816 DOI: 10.1107/s2053229620004350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/30/2020] [Indexed: 11/10/2022]
Abstract
A novel manganese(III)-porphyrin complex, namely, catena-poly[[chloridomanganese(III)]-μ2-5,10,15,20-tetrakis(pyridin-3-yl)-21H,23H-porphinato(2-)-κ5N21,N22,N23,N24:N5], [MnCl(C40H24N8)]n, 1, was prepared by the hydrothermal reaction of manganese chloride with 5,10,15,20-tetrakis(pyridin-3-yl)-21H,23H-porphine. The crystal structure was determined by single-crystal X-ray diffraction. The porphyrin macrocycle exhibits a saddle-like distortion geometry. The MnIII atom has a six-coordination geometry. Each porphyrin unit links to two neighbouring units to yield a one-dimensional coordination polymer. These chains are further interlinked by hydrogen bonds to form a two-dimensional network. The complex shows red photoluminescence emission bands in ethanol solution, which can be attributed to ligand-to-ligand charge transfer (LLCT) accompanied by partial metal-to-ligand charge transfer (MLCT), as revealed by TDDFT calculations.
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Affiliation(s)
- Wen Tong Chen
- Institute of Applied Chemistry, School of Chemistry and Chemical Engineering, Jiangxi Province Key Laboratory of Coordination Chemistry, Jinggangshan University, Ji'an, Jiangxi 343009, People's Republic of China
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Zavarykina TM, Atkarskaya MV, Zhizhina GP. The Structural and Functional Properties of Z-DNA. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919050270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Interactions Between Spermine-Derivatized Tentacle Porphyrins and The Human Telomeric DNA G-Quadruplex. Int J Mol Sci 2018; 19:ijms19113686. [PMID: 30469358 PMCID: PMC6274827 DOI: 10.3390/ijms19113686] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 01/31/2023] Open
Abstract
G-rich DNA sequences have the potential to fold into non-canonical G-Quadruplex (GQ) structures implicated in aging and human diseases, notably cancers. Because stabilization of GQs at telomeres and oncogene promoters may prevent cancer, there is an interest in developing small molecules that selectively target GQs. Herein, we investigate the interactions of meso-tetrakis-(4-carboxysperminephenyl)porphyrin (TCPPSpm4) and its Zn(II) derivative (ZnTCPPSpm4) with human telomeric DNA (Tel22) via UV-Vis, circular dichroism (CD), and fluorescence spectroscopies, resonance light scattering (RLS), and fluorescence resonance energy transfer (FRET) assays. UV-Vis titrations reveal binding constants of 4.7 × 106 and 1.4 × 107 M−1 and binding stoichiometry of 2–4:1 and 10–12:1 for TCPPSpm4 and ZnTCPPSpm4, respectively. High stoichiometry is supported by the Job plot data, CD titrations, and RLS data. FRET melting indicates that TCPPSpm4 stabilizes Tel22 by 36 ± 2 °C at 7.5 eq., and that ZnTCPPSpm4 stabilizes Tel22 by 33 ± 2 °C at ~20 eq.; at least 8 eq. of ZnTCPPSpm4 are required to achieve significant stabilization of Tel22, in agreement with its high binding stoichiometry. FRET competition studies show that both porphyrins are mildly selective for human telomeric GQ vs duplex DNA. Spectroscopic studies, combined, point to end-stacking and porphyrin self-association as major binding modes. This work advances our understanding of ligand interactions with GQ DNA.
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