| 1. |
- Rubio-Magnieto, Jenifer, et al.
(author)
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Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G-Quadruplexes
- 2018
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In: Chemistry - A European Journal. - : WILEY-V C H VERLAG GMBH. - 0947-6539 .- 1521-3765. ; 24:58, s. 15577-15588
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Journal article (peer-reviewed)abstract
- Metal complexes constitute an important class of DNA binders. In particular, a few ruthenium polyazaaromatic complexes are attractive as light switches because of their strong luminescence enhancement upon DNA binding. In this paper, a comprehensive study on the binding modes of several mononuclear and binuclear ruthenium complexes to human telomeric sequences, made of repeats of the d(TTAGGG) fragment is reported. These DNA sequences form G-quadruplexes (G4s) at the ends of chromosomes and constitute a relevant biomolecular target in cancer research. By combining spectroscopy experiments and molecular modelling simulations, several key properties are deciphered: the binding modes, the stabilization of G4 upon binding, and the selectivity of these complexes towards G4 versus double-stranded DNA. These results are rationalized by assessing the possible deformation of G4 and the binding free energies of several binding modes via modelling approaches. Altogether, this comparative study provides fundamental insights into the molecular recognition properties and selectivity of Ru complexes towards this important class of DNA G4s.
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| 2. |
- Holmgaard List, Nanna, et al.
(author)
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Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder
- 2017
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 139:42, s. 14947-14953
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Journal article (peer-reviewed)abstract
- Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI-DNA interactions.
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| 3. |
- Zhang, Li, et al.
(author)
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pi-Extended perylene diimide double-heterohelicenes as ambipolar organic semiconductors for broadband circularly polarized light detection
- 2021
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In: Nature Communications. - : Nature Research. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Despite great challenges, the development of new molecular structures with multiple and even conflicting characteristics are eagerly pursued for exploring advanced applications. To develop high-performance chiral organic semiconducting molecules, a distorted -system is required for strong coupling with circularly polarized light (CPL), whereas planar pi -stacking systems are necessary for high charge-carrier mobility. To address this dilemma, in this work, we introduce a skeleton merging approach through distortion of a perylene diimide (PDI) core with four fused heteroaromatics to form an ortho-pi -extended PDI double-[7]heterohelicene. PDI double helicene inherits a high dissymmetry factor from the helicene skeleton, and the extended pi -planar system concurrently maintains a high level of charge transport properties. In addition, ortho-pi -extension of the PDI skeleton brings about near-infrared (NIR) light absorption and ambipolar charge transport abilities, endowing the corresponding organic phototransistors with high photoresponsivity of 450 and 120mAW(-1) in p- and n-type modes respectively, along with a high external quantum efficiency (89%) under NIR light irradiations. Remarkably, these multiple characteristics enable high-performance broadband CPL detections up to NIR spectral region with chiral organic semiconductors. In organic semiconducting molecules materials, distorted pi -systems enable strong coupling with circular polarized light while planar pi -stacking systems are necessary for high charge-carrier mobility. Here, the authors address this dilemma by introducing a skeleton merging approach through distortion of a perylene diimide core with four fused heteroaromatics to form a pi -extended double helicene.
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| 4. |
- Caporaletti, Francesca, et al.
(author)
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Design of metalloporphyrins fused to imidazolium rings for binding DNA G-quadruplexes
- 2020
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In: Journal of Porphyrins and Phthalocyanines. - : WORLD SCI PUBL CO INC. - 1088-4246 .- 1099-1409. ; 24:1-3, s. 340-349
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Journal article (peer-reviewed)abstract
- Synthesis and characterization of nickel(II) meso-tetraarylporphyrins fused to imidazolium rings across beta,beta-pyrrolic positions and X-ray structure of the porphyrin where two opposed pyrrole units are fused to an imidazolium ring are presented. The interactions between these mono-, bis-, tris- and tetrakis(imidazolium) porphyrins with human telomeric DNA G-quadruplexes (G4) were investigated using UV-vis absorption spectroscopy, Circular Dichroism (CD) spectroscopy and Fluorescence Resonance Energy Transfer (FRET) melting assay. Possible binding modes between cationic porphyrins and a selected G4 sequence (d[AG(3)(T(2)AG(3))(3)]), and relative stabilities of porphyrin/G4 complexes are discussed. Excepting porphyrins fused to one imidazolium ring, the other derivatives interact with G4 structures and their stabilization strongly depends on the porphyrin structure (number and localization of the imidazolium rings).
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| 5. |
- Di Meo, Florent, et al.
(author)
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DNA electronic circular dichroism on the inter-base pair scale : An experimental-theoretical case study of the at homo-oligonucleotide
- 2015
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:3, s. 355-359
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Journal article (peer-reviewed)abstract
- A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. (Chemical Equation Presented).
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| 6. |
- Rubio-Magnieto, J., et al.
(author)
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Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes
- 2015
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In: Organic and biomolecular chemistry. - : Royal Society of Chemistry. - 1477-0520 .- 1477-0539. ; 13:8, s. 2453-2463
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Journal article (peer-reviewed)abstract
- The molecular recognition of human telomeric G-quadruplexes by a novel cationic π-extended NiII-porphyrin (NiII-TImidP4) is studied in aqueous solutions via (chir)optical spectroscopy, Fluorescence Resonance Energy Transfer (FRET) melting assay, and computational molecular modeling. The results are systematically compared with the recognition by a conventional meso-substituted NiII-porphyrin (NiII-TMPyP4), which allows us to pinpoint the differences in binding modes depending on the G-quadruplex topology. Importantly, FRET melting assays show the higher selectivity of NiII-TImidP4 towards human telomeric G4 than that of NiII-TMPyP4.
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| 7. |
- Rubio-Magnieto, Jenifer, et al.
(author)
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Self-assembly and hybridization mechanisms of DNA with cationic polythiophene
- 2015
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In: Soft Matter. - : Royal Society of Chemistry. - 1744-683X .- 1744-6848. ; 11:2, s. 6460-6471
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Journal article (peer-reviewed)abstract
- The combination of DNA and pi-conjugated polyelectrolytes (CPEs) represents a promising approach to develop DNA hybridization biosensors, with potential applications for instance in the detection of DNA lesions and single-nucleotide polymorphisms. Here we exploit the remarkable optical properties of a cationic poly[3-(6'-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] (CPT) to decipher the self-assembly of DNA and CPT. The ssDNA/ CPT complexes have chiroptical signatures in the CPT absorption region that are strongly dependent on the DNA sequence, which we relate to differences in supramolecular interactions between the thiophene monomers and the various nucleobases. By studying DNA-DNA hybridization and melting processes on preformed ssDNA/ CPT complexes, we observe sequence-dependent mechanisms that can yield DNA-condensed aggregates. Heating-cooling cycles show that non-equilibrium mixtures can form, noticeably depending on the working sequence of the hybridization experiment. These results are of high importance for the use of pi-conjugated polyelectrolytes in DNA hybridization biosensors and in polyplexes.
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| 8. |
- Zhang, L., et al.
(author)
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Naphthodithiophene Diimide Based Chiral π-Conjugated Nanopillar Molecules
- 2021
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In: Angewandte Chemie International Edition. - : John Wiley and Sons Inc. - 1433-7851 .- 1521-3773. ; 60:46, s. 24543-24548
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Journal article (peer-reviewed)abstract
- The synthesis, structures, and properties of [4]cyclonaphthodithiophene diimides ([4]C-NDTIs) are described. NDTIs as important n-type building blocks were catenated in the α-positions of thiophene rings via an unusual electrochemical-oxidation-promoted macrocyclization route. The thiophene–thiophene junction in [4]C-NDTIs results in an ideal pillar shape. This interesting topology, along with appealing electronic and optical properties inherited from the NDTI units, endows the [4]C-NDTIs with both near-infrared (NIR) light absorptions, strong excitonic coupling, and tight encapsulation of C60. Stable orientations of the NDTI units in the nanopillars lead to stable inherent chirality, which enables detailed circular dichroism studies on the impact of isomeric structures on π-conjugation. Remarkably, the [4]C-NDTIs maintain the strong π–π stacking abilities of NDTI units and thus adopt two-dimensional (2D) lattice arrays at the molecular level. These nanopillar molecules have great potential to mimic natural photosynthetic systems for the development of multifunctional organic materials.
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