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Pavlović Saftić D, Krošl Knežević I, de Lera Garrido F, Tolosa J, Majhen D, Piantanida I, García Martínez JC. Trimeric and Tetrameric Cationic Styryl Dyes as Novel Fluorescence and CD Probes for ds-DNA and ds-RNA. Int J Mol Sci 2024; 25:5724. [PMID: 38891911 PMCID: PMC11171523 DOI: 10.3390/ijms25115724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The wide use of mono- or bis-styryl fluorophores in biomedical applications prompted the presented design and study of a series of trimeric and tetrameric homo-analogues, styryl moieties arranged around a central aromatic core. The interactions with the most common biorelevant targets, ds-DNA and ds-RNA, were studied by a set of spectrophotometric methods (UV-VIS, fluorescence, circular dichroism, thermal denaturation). All studied dyes showed strong light absorption in the 350-420 nm range and strongly Stokes-shifted (+100-160 nm) emission with quantum yields (Φf) up to 0.57, whereby the mentioned properties were finely tuned by the type of the terminal cationic substituent and number of styryl components (tetramers being red-shifted in respect to trimers). All studied dyes strongly interacted with ds-DNA and ds-RNA with 1-10 nM-1 affinity, with dye emission being strongly quenched. The tetrameric analogues did not show any particular selectivity between ds-DNA or ds-RNA due to large size and consequent partial, non-selective insertion into DNA/RNA grooves. However, smaller trimeric styryl series showed size-dependent selective stabilization of ds-DNA vs. ds-RNA against thermal denaturation and highly selective or even specific recognition of several particular ds-DNA or ds-RNA structures by induced circular dichroism (ICD) bands. The chiral (ICD) selectivity was controlled by the size of a terminal cationic substituent. All dyes entered efficiently live human cells with negligible cytotoxic activity. Further prospects in the transfer of ICD-based selectivity into fluorescence-chiral methods (FDCD and CPL) is proposed, along with the development of new analogues with red-shifted absorbance properties.
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Affiliation(s)
- Dijana Pavlović Saftić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (D.P.S.); (I.K.K.)
| | - Ivona Krošl Knežević
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (D.P.S.); (I.K.K.)
| | - Fernando de Lera Garrido
- Department of Inorganic and Organic Chemistry and Biochemistry, Faculty of Pharmacy, Universidad de Castilla-La Mancha, C/José María Sánchez Ibáñez s/n, 02008 Albacete, Spain; (F.d.L.G.); (J.T.)
- Regional Center for Biomedical Research (CRIB), Universidad de Castilla-La Mancha, C/Almansa 13, 02008 Albacete, Spain
| | - Juan Tolosa
- Department of Inorganic and Organic Chemistry and Biochemistry, Faculty of Pharmacy, Universidad de Castilla-La Mancha, C/José María Sánchez Ibáñez s/n, 02008 Albacete, Spain; (F.d.L.G.); (J.T.)
- Regional Center for Biomedical Research (CRIB), Universidad de Castilla-La Mancha, C/Almansa 13, 02008 Albacete, Spain
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (D.P.S.); (I.K.K.)
| | - Joaquín Calixto García Martínez
- Department of Inorganic and Organic Chemistry and Biochemistry, Faculty of Pharmacy, Universidad de Castilla-La Mancha, C/José María Sánchez Ibáñez s/n, 02008 Albacete, Spain; (F.d.L.G.); (J.T.)
- Regional Center for Biomedical Research (CRIB), Universidad de Castilla-La Mancha, C/Almansa 13, 02008 Albacete, Spain
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Alcalde-Ordóñez A, Barreiro-Piñeiro N, McGorman B, Gómez-González J, Bouzada D, Rivadulla F, Vázquez ME, Kellett A, Martínez-Costas J, López MV. A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells. Chem Sci 2023; 14:14082-14091. [PMID: 38098723 PMCID: PMC10718067 DOI: 10.1039/d3sc03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.
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Affiliation(s)
- Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Natalia Barreiro-Piñeiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Bríonna McGorman
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Francisco Rivadulla
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Física, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Andrew Kellett
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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Lelouche SNK, Albentosa-González L, Clemente-Casares P, Biglione C, Rodríguez-Diéguez A, Tolosa Barrilero J, García-Martínez JC, Horcajada P. Antibacterial Cu or Zn-MOFs Based on the 1,3,5-Tris-(styryl)benzene Tricarboxylate. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2294. [PMID: 37630879 PMCID: PMC10458854 DOI: 10.3390/nano13162294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Metal-organic frameworks (MOFs) are highly versatile materials. Here, two novel MOFs, branded as IEF-23 and IEF-24 and based on an antibacterial tricarboxylate linker and zinc or copper cations, and holding antibacterial properties, are presented. The materials were synthesized by the solvothermal route and fully characterized. The antibacterial activity of IEF-23 and IEF-24 was investigated against Staphylococcus epidermidis and Escherichia coli via the agar diffusion method. These bacteria are some of the most broadly propagated pathogens and are more prone to the development of antibacterial resistance. As such, they represent an archetype to evaluate the efficiency of novel antibacterial treatments. MOFs were active against both strains, exhibiting higher activity against Staphylococcus epidermidis. Thus, the potential of the developed MOFs as antibacterial agents was proved.
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Affiliation(s)
- Sorraya Najma Kinza Lelouche
- Advanced Porous Materials Unit, IMDEA Energy Institute, Av. Ramón de la Sagra 3, Mostoles, 28935 Madrid, Spain; (S.N.K.L.); (C.B.)
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, c/ Tulipan, s/n, Mostoles, 28933 Madrid, Spain
| | - Laura Albentosa-González
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, C/Almansa 14, 02008 Albacete, Spain; (L.A.-G.); (P.C.-C.); (J.T.B.)
- Facultad de Farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain
| | - Pilar Clemente-Casares
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, C/Almansa 14, 02008 Albacete, Spain; (L.A.-G.); (P.C.-C.); (J.T.B.)
- Facultad de Farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain
| | - Catalina Biglione
- Advanced Porous Materials Unit, IMDEA Energy Institute, Av. Ramón de la Sagra 3, Mostoles, 28935 Madrid, Spain; (S.N.K.L.); (C.B.)
| | - Antonio Rodríguez-Diéguez
- Departamento de Química Inorgánica, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain;
| | - Juan Tolosa Barrilero
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, C/Almansa 14, 02008 Albacete, Spain; (L.A.-G.); (P.C.-C.); (J.T.B.)
- Facultad de Farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain
| | - Joaquín Calixto García-Martínez
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, C/Almansa 14, 02008 Albacete, Spain; (L.A.-G.); (P.C.-C.); (J.T.B.)
- Facultad de Farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain
| | - Patricia Horcajada
- Advanced Porous Materials Unit, IMDEA Energy Institute, Av. Ramón de la Sagra 3, Mostoles, 28935 Madrid, Spain; (S.N.K.L.); (C.B.)
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Craig JS, Melidis L, Williams HD, Dettmer SJ, Heidecker AA, Altmann PJ, Guan S, Campbell C, Browning DF, Sigel RKO, Johannsen S, Egan RT, Aikman B, Casini A, Pöthig A, Hannon MJ. Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks. J Am Chem Soc 2023. [PMID: 37318835 DOI: 10.1021/jacs.3c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination, and repair) and are dynamic structures that adopt either open or closed conformations, the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core, an ideal structure to interact with open DNA junction cavities. Combining experimental studies and MD simulations, we show that an Au pillarplex can bind DNA 4-way (Holliday) junctions in their open form, a binding mode not accessed by synthetic agents before. Pillarplexes can bind 3-way junctions too, but their large size leads them to open up and expand that junction, disrupting the base pairing, which manifests in an increased hydrodynamic size and lower junction thermal stability. At high loading, they rearrange both 4-way and 3-way junctions into Y-shaped forks to increase the available junction-like binding sites. Isostructural Ag pillarplexes show similar DNA junction binding behavior but lower solution stability. This pillarplex binding contrasts with (but complements) that of metallo-supramolecular cylinders, which prefer 3-way junctions and can rearrange 4-way junctions into 3-way junction structures. The pillarplexes' ability to bind open 4-way junctions creates exciting possibilities to modulate and switch such structures in biology, as well as in synthetic nucleic acid nanostructures. In human cells, the pillarplexes do reach the nucleus, with antiproliferative activity at levels similar to those of cisplatin. The findings provide a new roadmap for targeting higher-order junction structures using a metallo-supramolecular approach, as well as expanding the toolbox available to design bioactive junction binders into organometallic chemistry.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Roland K O Sigel
- Department of Chemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
| | - Silke Johannsen
- Department of Chemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
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