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Kuba M, Khoroshyy P, Lepšík M, Kužmová E, Kodr D, Kraus T, Hocek M. Real-time Imaging of Nascent DNA in Live Cells by Monitoring the Fluorescence Lifetime of DNA-Incorporated Thiazole Orange-Modified Nucleotides. Angew Chem Int Ed Engl 2023; 62:e202307548. [PMID: 37498132 DOI: 10.1002/anie.202307548] [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: 05/29/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 07/28/2023]
Abstract
A modified 2'-deoxycytidine triphosphate derivative (dCTO TP) bearing a thiazole orange moiety tethered via an oligoethylene glycol linker was designed and synthesized. The nucleotide was incorporated into DNA by DNA polymerases in vitro as well as in live cells. Upon incorporation of dCTO TP into DNA, the thiazole orange moiety exhibited a fluorescence lifetime that differed significantly from the non-incorporated (i.e. free and non-covalently intercalated) forms of dCTO TP. When dCTO TP was delivered into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it allowed us to distinguish and monitor cells that were actively synthesizing DNA in real time, from the very first moments after the treatment. We anticipate that this probe could be used to study chromatin organization and dynamics.
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Affiliation(s)
- Miroslav Kuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Petro Khoroshyy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
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2
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Binacchi F, Elia C, Cirri D, Van de Griend C, Zhou XQ, Messori L, Bonnet S, Pratesi A, Biver T. A biophysical study of the interactions of palladium(II), platinum(II) and gold(III) complexes of aminopyridyl-2,2'-bipyridine ligands with RNAs and other nucleic acid structures. Dalton Trans 2023; 52:598-608. [PMID: 36562298 DOI: 10.1039/d2dt03483b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal compounds form an attractive class of ligands for a variety of nucleic acids. Five metal complexes bearing aminopyridyl-2,2'-bipyridine tetradentate ligands and possessing a quasi-planar geometry were challenged toward different types of nucleic acid molecules including RNA polynucleotides in the duplex or triplex form, an RNA Holliday four-way junction, natural double helix DNA and a DNA G-quadruplex. The binding process was monitored comparatively using different spectroscopic and melting methods. The binding preferences that emerge from our analysis are discussed in relation to the structural features of the metal complexes.
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Affiliation(s)
- Francesca Binacchi
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Cassandra Elia
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Damiano Cirri
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Corjan Van de Griend
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Xue-Quan Zhou
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Alessandro Pratesi
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Tarita Biver
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
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Fabijanić I, Kurutos A, Tomašić Paić A, Tadić V, Kamounah FS, Horvat L, Brozovic A, Crnolatac I, Radić Stojković M. Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential. Biomolecules 2023; 13:biom13010128. [PMID: 36671513 PMCID: PMC9856044 DOI: 10.3390/biom13010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect.
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Affiliation(s)
- Ivana Fabijanić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 9, 1113 Sofia, Bulgaria
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Vanja Tadić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Fadhil S. Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Lucija Horvat
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-14571220; Fax: +385-14680195
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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Sánchez-González Á, Grenut P, Gil A. Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. J Comput Chem 2022; 43:804-821. [PMID: 35297513 PMCID: PMC9313584 DOI: 10.1002/jcc.26836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
Abstract
The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH2. The trends in the energy decomposition analysis for the interaction energy, ΔEint, showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp. Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.
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Affiliation(s)
- Ángel Sánchez-González
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Pierre Grenut
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Adrià Gil
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal.,ARAID Foundation, Zaragoza, Spain.,Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza, c/ Pedro Cerbuna 12, Zaragoza, Spain
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Zhao Z, Cao S, Li H, Li D, He Y, Wang X, Chen J, Zhang S, Xu J, Knutson JR. Ultrafast excited-state dynamics of thiazole orange. Chem Phys 2022; 553. [DOI: 10.1016/j.chemphys.2021.111392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Macii F, Cupellini L, Stifano M, Santolaya J, Pérez-Arnaiz C, Pucci A, Barone G, García B, Busto N, Biver T. Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119914. [PMID: 34015745 DOI: 10.1016/j.saa.2021.119914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
We present here a combined spectroscopic and theoretical analysis of the binding of N,N'-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggregates disruption and monomers intercalation. Oppositely, for RNAs, no intercalation but groove binding with the formation of supramolecular aggregates is observed. Among all the tested biosubstrates, the affinity of PZPERY towards DNA G-quadruplexes (G4) is the greatest one with a preference for human telomeric G4s. Focusing on hybrid G4 forms, either sitting-atop ("tetrad-parallel") or lateral ("groove-parallel") binding modes were considered in the discussion of the experimental results and molecular dynamics (MD) simulations. Both turned out to be possible concurrently, in agreement also with the experimental binding stoichiometries higher than 2:1.
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Affiliation(s)
- Francesca Macii
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Mariassunta Stifano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Javier Santolaya
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Cristina Pérez-Arnaiz
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Andrea Pucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Begoña García
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Busto
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
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Kandinska M, Cheshmedzhieva D, Kostadinov A, Rusinov K, Rangelov M, Todorova N, Ilieva S, Ivanov D, Videva V, Lozanov V, Baluschev S, Landfester K, Vasilev A. Tricationic asymmetric monomeric monomethine cyanine dyes with chlorine and trifluoromethyl functionality – Fluorogenic nucleic acids probes. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Sánchez-González Á, Bandeira NAG, Ortiz de Luzuriaga I, Martins FF, Elleuchi S, Jarraya K, Lanuza J, Lopez X, Calhorda MJ, Gil A. New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes. Molecules 2021; 26:4737. [PMID: 34443326 PMCID: PMC8397986 DOI: 10.3390/molecules26164737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.
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Affiliation(s)
- Ángel Sánchez-González
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Nuno A. G. Bandeira
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
| | - Frederico F. Martins
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Jose Lanuza
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Maria José Calhorda
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Adrià Gil
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
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Fu F, Liao K, Liu Z, Hong D, Yang H, Tian Y, Wei W, Liu C, Li S, Ma J, Li W. Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO. J Phys Chem B 2021; 125:518-527. [PMID: 33426891 DOI: 10.1021/acs.jpcb.0c09611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Ziteng Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Daocheng Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuxi Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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Sánchez-González Á, Gil A. Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions. RSC Adv 2021; 11:1553-1563. [PMID: 35424132 PMCID: PMC8693566 DOI: 10.1039/d0ra07646e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.
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Affiliation(s)
- Ángel Sánchez-González
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Portugal
| | - Adrià Gil
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Portugal
- CIC nanoGUNE BRTA Tolosa Hiribidea 76 E-20018 Donostia - San Sebastian Euskadi Spain
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12
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Macii F, Salvadori G, Bonini R, Giannarelli S, Mennucci B, Biver T. Binding of model polycyclic aromatic hydrocarbons and carbamate-pesticides to DNA, BSA, micelles and liposomes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 223:117313. [PMID: 31277031 DOI: 10.1016/j.saa.2019.117313] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
The binding to biosubstrates and micellar systems of pollutants as the polycyclic aromatic hydrocarbon (PAH) derivatives 1-aminopyrene (1-PyNH2) and 1-hydroxymethylpyrene (1-PyMeOH) and the carbamate-pesticides 1-naphthyl-N-methylcarbamate (carbaryl, CA) and methyl benzimidazol-2-ylcarbamate (carbendazim, CBZ) was analysed through an integrated strategy combining spectroscopy and quantum chemistry. As biosubstrates, natural DNA and bovine serum albumin (BSA) were taken into account for a thermodynamic analysis of the binding features through spectrophotometric and spectrofluorometric techniques. In all cases, a strong DNA interaction is present and intercalation is supposed as the major binding mode. For the PAH derivatives, DNA binding is found to be favoured under high salt conditions and BSA static quenching and binding with 1:1 stoichiometry occurs. The molecular structure and optical properties of 1-PyNH2, CA and CBZ together with their intercalated adducts in DNA were studied also by means of quantum chemical approach. The (TD)DFT calculations on intercalated dye/DNA adducts quantitatively reproduce the experimentally observed spectroscopic changes, thus confirming the intercalation hypothesis. The theoretical approach also provides information on the adducts' geometries and on the amount of charge transfer with DNA. Moreover, ultrafiltration tests in the presence of anionic (SDS), cationic (DTAC) and neutral (Triton X) micellar aggregates and liposomes provided insights into lipophilicity and cellular membrane affinity. PAH derivatives show high retention coefficient in all cases, whereas in the case of carbamate-pesticides micellar retention might be significantly reduced and is very limited in the case of liposomes.
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Affiliation(s)
- Francesca Macii
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Rachele Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Stefania Giannarelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tarita Biver
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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13
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Botti V, Cesaretti A, Ban Ž, Crnolatac I, Consiglio G, Elisei F, Piantanida I. Fine structural tuning of styryl-based dyes for fluorescence and CD-based sensing of various ds-DNA/RNA sequences. Org Biomol Chem 2019; 17:8243-8258. [PMID: 31464340 DOI: 10.1039/c9ob01186b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A set of styryl- and bis-styryl dyes, varying in length, aromatic surface, net positive charge and steric positioning or bulkiness of substituents, was tested for interactions with various ds-DNA or ds-RNA. Most of the compounds showed strong affinity toward ds-DNA/RNA, directly correlated to the synergistic contribution of the aromatic-conjugated surface and net positive charge. The volume or positioning of terminal aromatic substituents directly controlled the binding mode of the core structure, shifting between DNA/RNA groove binding or DNA/RNA intercalation. Consequently, upon binding to DNA/RNA the fluorimetric and induced CD (ICD) response varied for different compounds, for instance one derivative showed specific fluorescence increase with AT-DNA, while another derivative showed specific ICD response with AU-RNA. Preliminary screening on human tumour cell lines revealed an efficient cellular uptake for all dyes. Only mono-styryl-quinoline derivatives showed a strong antiproliferative activity combined with efficient fluorescent localisation, thus showing promising theragnostic potential, while other compounds were negligibly cytotoxic but still efficient fluorescent markers of cytoplasmic organelles.
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Affiliation(s)
- Valentina Botti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Giuseppe Consiglio
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN) University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
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14
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Gil A, Sanchez-Gonzalez A, Branchadell V. Unraveling the Modulation of the Activity in Drugs Based on Methylated Phenanthroline When Intercalating between DNA Base Pairs. J Chem Inf Model 2019; 59:3989-3995. [DOI: 10.1021/acs.jcim.9b00500] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrià Gil
- CIC Nanogune, Tolosa Hiribidea 76, Donostia - San Sebastian, Gipuzkoa, Basque Country 20029, Spain
- Centro de Química e Bioquímica and BioISI − Biosystems and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Angel Sanchez-Gonzalez
- Centro de Química e Bioquímica and BioISI − Biosystems and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, Campus UAB, Bellaterra, Catalonia 08193, Spain
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15
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Aydinoglu S, Pasti A, Biver T, Mennucci B. Auramine O interaction with DNA: a combined spectroscopic and TD-DFT analysis. Phys Chem Chem Phys 2019; 21:20606-20612. [DOI: 10.1039/c9cp03071a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AuO fluorescent molecular rotor intercalation into DNA: calculations and experiments uncover binding details as absorbance/fluorescence features, energies involved and geometries.
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Affiliation(s)
- Sabriye Aydinoglu
- Department of Analytical Chemistry
- Faculty of Pharmacy – Cukurova University
- 01250 Sarıçam/Adana
- Turkey
| | - Andrea Pasti
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- 56124 Pisa
- Italy
| | - Tarita Biver
- Department of Analytical Chemistry
- Faculty of Pharmacy – Cukurova University
- 01250 Sarıçam/Adana
- Turkey
- Department of Pharmacy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- 56124 Pisa
- Italy
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16
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Shiraogawa T, Candel G, Fukuda R, Ciofini I, Adamo C, Okamoto A, Ehara M. Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study. J Comput Chem 2018; 40:127-134. [PMID: 30144120 DOI: 10.1002/jcc.25553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023]
Abstract
Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near-infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC-CI and TD-DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD-DFT methods, have been examined regarding the photo-absorption and emission spectra. The SAC-CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD-DFT calculations is difficult for these chromophores. Some stable structures of H-aggregate system were computationally located and two of the configurations were examined for the photo-absorption. The present results support for the assumption based on experimental measurement in which strong fluorescence is due to the monomer unit in nearly planar structure and its suppression of probes is to the H-aggregates of two exciton units. Stokes shifts of these three chromophores were qualitatively reproduced by the theoretical calculations, while the energy splitting due to H-aggregate in the hybridized probe was slightly overestimated. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Takafumi Shiraogawa
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
| | - G Candel
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France
| | - Ryoichi Fukuda
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, 615-8245, Japan.,Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8520, Japan
| | - Ilaria Ciofini
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France
| | - Carlo Adamo
- Institut de Recherche de Chimie Paris, PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie, Paris, F-75005, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005, Paris, France
| | - Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masahiro Ehara
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, 615-8245, Japan.,Institute for Molecular Science and Research Center for Computational Science, Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
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17
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Loco D, Jurinovich S, Cupellini L, Menger MFSJ, Mennucci B. The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach. Photochem Photobiol Sci 2018; 17:552-560. [DOI: 10.1039/c8pp00033f] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a polarizable QM/MM strategy to simulate the absorption line shape of chromophores embedded in complex matrices, including both homogeneous and inhomogeneous broadening.
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Affiliation(s)
- Daniele Loco
- Department of Chemistry
- University of Pisa
- Pisa
- Italy
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18
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Górecki M, Zinna F, Biver T, Di Bari L. Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes. J Pharm Biomed Anal 2017; 144:6-11. [DOI: 10.1016/j.jpba.2017.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/13/2017] [Accepted: 02/04/2017] [Indexed: 11/28/2022]
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19
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Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
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20
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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21
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Crnolatac I, Rogan I, Majić B, Tomić S, Deligeorgiev T, Horvat G, Makuc D, Plavec J, Pescitelli G, Piantanida I. Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response. Anal Chim Acta 2016; 940:128-35. [PMID: 27662767 DOI: 10.1016/j.aca.2016.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 01/24/2023]
Abstract
Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400-500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU.
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Affiliation(s)
- Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia
| | - Iva Rogan
- Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia
| | - Boris Majić
- Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia
| | | | - Gordan Horvat
- Department of Physical Chemistry, Faculty of Science/Chemistry, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana, Slovenia
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, Via Moruzzi 13, Pisa, Italy
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia.
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22
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Pei X, Huang H, Chen Y, Li C, Liu F, Li N. Modulating fluorescence anisotropy of dye-labeled DNA without involving mass amplification. Talanta 2016; 154:567-73. [DOI: 10.1016/j.talanta.2016.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 11/25/2022]
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23
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Zakharova GV, Konstantinov RR, Odinokov AV, Chibisov AK, Alfimov MV, Kasheverov IE, Utkin YN, Zhmak MN, Tsetlin VI. Effect of a peptide modeling the nicotinic receptor binding site on the spectral and luminescent properties of dye complexes with cucurbit[8]uril. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916020090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Gil A, Branchadell V, Calhorda MJ. A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs. RSC Adv 2016. [DOI: 10.1039/c6ra15495f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.
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Affiliation(s)
- A. Gil
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - V. Branchadell
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - M. J. Calhorda
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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25
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Biancardi A, Biver T, Burgalassi A, Mattonai M, Secco F, Venturini M. Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves. Phys Chem Chem Phys 2015; 16:20061-72. [PMID: 25130260 DOI: 10.1039/c4cp02838d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.
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Affiliation(s)
- A Biancardi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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26
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Liu K, Wen Y, Shi T, Li Y, Li F, Zhao YL, Huang C, Yi T. DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene. Chem Commun (Camb) 2015; 50:9141-4. [PMID: 24989898 DOI: 10.1039/c4cc02783c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Thiazole orange-modified diarylethene (1) shows weak fluorescence but no photochromism in aqueous solution. When binding with DNA, the fluorescence of 1 is enhanced drastically and the photochromic reactivity is unlocked. This kind of DNA-responsive photoswitchable system can be used for imaging nucleic acids within cells.
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Affiliation(s)
- Keyin Liu
- Department of Chemistry, and Concerted Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China.
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27
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Rastede EE, Tanha M, Yaron D, Watkins SC, Waggoner AS, Armitage BA. Spectral fine tuning of cyanine dyes: electron donor-acceptor substituted analogues of thiazole orange. Photochem Photobiol Sci 2015; 14:1703-12. [PMID: 26171668 PMCID: PMC4557812 DOI: 10.1039/c5pp00117j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022]
Abstract
The introduction of electron donor and acceptor groups at strategic locations on a fluorogenic cyanine dye allows fine-tuning of the absorption and emission spectra while preserving the ability of the dye to bind to biomolecular hosts such as double-stranded DNA and a single-chain antibody fragment originally selected for binding to the parent unsubstituted dye, thiazole orange (TO). The observed spectral shifts are consistent with calculated HOMO-LUMO energy gaps and reflect electron density localization on the quinoline half of TO in the LUMO. A dye bearing donating methoxy and withdrawing trifluoromethyl groups on the benzothiazole and quinoline rings, respectively, shifts the absorption spectrum to sufficiently longer wavelengths to allow excitation at green wavelengths as opposed to the parent dye, which is optimally excited in the blue.
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Affiliation(s)
- Elizabeth E Rastede
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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28
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Gil A, Melle-Franco M, Branchadell V, Calhorda MJ. How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine–Thymine and Guanine–Cytosine Tetramers. J Chem Theory Comput 2015; 11:2714-28. [DOI: 10.1021/ct5006104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrià Gil
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Vicenç Branchadell
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Calhorda
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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29
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Laurent AD, Adamo C, Jacquemin D. Dye chemistry with time-dependent density functional theory. Phys Chem Chem Phys 2015; 16:14334-56. [PMID: 24548975 DOI: 10.1039/c3cp55336a] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.
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Affiliation(s)
- Adèle D Laurent
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
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30
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Mao Y, Liu K, Lv G, Wen Y, Zhu X, Lan H, Yi T. CB[8] gated photochromism of a diarylethene derivative containing thiazole orange groups. Chem Commun (Camb) 2015; 51:6667-70. [DOI: 10.1039/c5cc01390a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochromism in a diarylethene derivative (1O) can be gated by a host–guest interaction where the thiazole orange groups are bound into the hydrophobic cavity of CB[8] in water.
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Affiliation(s)
- Yueyuan Mao
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Keyin Liu
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Guanglei Lv
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Ying Wen
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Xingjun Zhu
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Haichuang Lan
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
| | - Tao Yi
- Department of Chemistry and Concerted Innovation Center of Chemistry for Energy Materials
- Fudan University
- Shanghai 200433
- China
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31
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Ghimire S, Fanwick PE, McMillin DR. DNA-Binding Studies of a Tetraalkyl-Substituted Porphyrin and the Mutually Adaptive Distortion Principle. Inorg Chem 2014; 53:11108-18. [PMID: 25271570 DOI: 10.1021/ic501683t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Phillip E. Fanwick
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - David R. McMillin
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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32
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Bohländer PR, Wagenknecht HA. Synthesis and evaluation of cyanine-styryl dyes with enhanced photostability for fluorescent DNA staining. Org Biomol Chem 2014; 11:7458-62. [PMID: 24088963 DOI: 10.1039/c3ob41717d] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photostability of cyanine-styryl dyes of the indole-quinolinium type can be significantly improved by structural variations while the excellent optical properties including the bright fluorescence in the presence of DNA can be maintained or even improved, too.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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33
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Gaier AJ, Ghimire S, Fix SE, McMillin DR. Internal Versus External Binding of Cationic Porphyrins to Single-Stranded DNA. Inorg Chem 2014; 53:5467-73. [PMID: 24828700 DOI: 10.1021/ic403105q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Abby J. Gaier
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Sarah E. Fix
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - David R. McMillin
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
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34
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Biancardi A, Burgalassi A, Terenzi A, Spinello A, Barone G, Biver T, Mennucci B. A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex. Chemistry 2014; 20:7439-47. [DOI: 10.1002/chem.201304876] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 01/22/2023]
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35
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Biancardi A, Biver T, Secco F, Mennucci B. An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools. Phys Chem Chem Phys 2013; 15:4596-603. [PMID: 23423468 DOI: 10.1039/c3cp44058c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.
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Affiliation(s)
- Alessandro Biancardi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento, 35-56126 Pisa, Italy.
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36
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Gao GQ, Xu AW. A new fluorescent probe for monitoring amyloid fibrillation with high sensitivity and reliability. RSC Adv 2013. [DOI: 10.1039/c3ra43259a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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37
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Mooi SM, Heyne B. Size does matter: how to control organization of organic dyes in aqueous environment using specific ion effects. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16524-16530. [PMID: 23145855 DOI: 10.1021/la3034885] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Understanding the role played by external factors on the organization of molecules has the potential to contribute greatly to fundamental research and applications in fields as diverse as nanotechnology, medicine, material chemistry, etc. Countless studies involve the organization of small organic molecules in environments rich in ionic species, yet their participation in molecular organization is often overlooked. Herein, we critically assess the organization in aqueous solution of the cationic cyanine dye, thiazole orange, in the presence of different monovalent sodium salts. Our findings clearly indicate that not all ions are identical with regards to the organization of thiazole orange molecules and specific ions effects are at play. The conventional Debye and Hückel model is not sufficient to explain our results, and the participation of ionic species in molecular organization is explained in terms of the recent theory of water matching affinity. Herein, by choosing the right counterion with the appropriate size, we have shown that it is possible to either induce a simple shift in the monomer-dimer equilibrium of thiazole orange or to turn on the formation of larger organized structures.
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Affiliation(s)
- Sara M Mooi
- Chemistry Department, University of Calgary , 2500 University Drive NW, Calgary, T2N 1N4 AB, Canada
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38
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Abstract
The interactions of a triangle-shaped [2.2.2]heptamethinecyanine dye 1, namely 1,5,7-tris-[3-methylbenzothiazol-2-yl]-[2.2.2]heptamethindiium, with quadruplex DNA were studied with photometric and fluorimetric titrations, thermal DNA denaturation, CD and (1)H-NMR spectroscopy. The ligand binds to the quadruplex DNA with moderate affinity (K = 8 × 10(5) M(-1)), mainly by terminal π stacking. Remarkably, the ligand 1 exhibits a selectivity for quadruplex DNA relative to duplex DNA. Whereas the cyanine dye is very weakly fluorescent in aqueous solution, the emission intensity increases by a factor of >100 upon association with quadruplex DNA. Thus, it is shown that trinuclear cyanine derivatives may be employed as selective probes for the fluorimetric detection of quadruplex DNA.
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Affiliation(s)
- Heiko Ihmels
- University of Siegen, Organic Chemistry II, Adolf-Reichwein-Str. 2, D-57068, Siegen, Germany.
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39
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Biancardi A, Cammi R, Cappelli C, Mennucci B, Tomasi J. Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1157-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Mohanty J, Thakur N, Choudhury SD, Barooah N, Pal H, Bhasikuttan AC. Recognition-mediated light-up of thiazole orange with cucurbit[8]uril: exchange and release by chemical stimuli. J Phys Chem B 2011; 116:130-5. [PMID: 22136417 DOI: 10.1021/jp210432t] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article reports a convenient supramolecular strategy to construct fluorescent photoswitchable molecular assemblies between a macrocyclic host, cucurbit[8]uril (CB8), and a fluorogenic dye, thiazole orange (TO). The interaction mechanism and the stable stoichiometric host-guest arrangements have been claimed on the basis of the optical absorption, steady-state and time-resolved fluorescence lifetime and anisotropy measurements, and also the geometry optimization studies. The CB8 recognized TO in its 2:2 stoichiometry exhibited spectacular fluorescence enhancement of the order of 1700 fold, which is the largest directly determined value so far reported for a dye in an organic macrocyclic system. This prospective 2CB8:2TO assembly responded to selected chemical stimuli such as metal ions, adamantylamine, and tryptophan, providing different dissociation mechanisms and demonstrating a controlled exchange and release action desired with such noncovalently linked assemblies. Positively, considering the aqueous solubility and biocompatibility of the host-guest constituents, this methodology can evolve into a general approach to deliver and operate intracellularly functional molecular components under chemical/thermal/optical trigger control, especially for therapeutic applications.
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Affiliation(s)
- Jyotirmayee Mohanty
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai, India.
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41
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Choudhury SD, Bhasikuttan AC, Pal H, Mohanty J. Surfactant-induced aggregation patterns of thiazole orange: a photophysical study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12312-12321. [PMID: 21902267 DOI: 10.1021/la202414h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The aggregation behavior of the DNA marker dye thiazole orange (TO), has been investigated in two types of surfactant assemblies, namely, premicelles/micelles of sodium dodecyl sulfate (SDS) and pre reverse micelles/reverse micelles of sodium bis(2-ethylhexyl) sulfosuccinate (AOT). In the case of an SDS/water system, absorption spectral changes of TO signify the formation of H-aggregates and H-dimers of the dye at premicellar concentrations, which subsequently convert to the monomeric form beyond the critical micellar concentration (cmc). Interestingly, the observed changes in the absorption and emission characteristics due to the surfactant-induced formation of H-aggregates/dimers of TO are found to be useful to estimate the surfactant concentration parameters for premicellar aggregation of SDS. In the case of an AOT/n-heptane system, similarly, H-aggregates/dimers are observed at low AOT concentrations, below the cmc. However, in this case, the H-dimers persist even beyond the cmc. This is attributed to the strong tendency of TO for self-aggregation and its favorable electrostatic interactions with the AOT head groups. With increasing water content in the AOT reverse micelles, the hydration of the dye leads to the conversion of H-dimers to the monomeric form. The steady-state fluorescence results are nicely corroborated with those from time-resolved fluorescence studies and demonstrate the interesting behavior of the surfactant-induced aggregation of TO dye.
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