https://hdl.handle.net/10259/4883 Mon, 27 Apr 2026 13:55:58 GMT 2026-04-27T13:55:58Z https://hdl.handle.net/10259/4882 Fishing for G-Quadruplexes in solution with a perylene diimide derivative labeled with biotins Busto Vázquez, Natalia; Calvo Gredilla, Patricia; Santolaya, Javier; Leal Villalba, José María; Guédin, Aurore .; Barone, Giampaolo; Torroba Pérez, Tomás; Mergny, Jean-Louis; García Ruiz, Begoña A new fluorescent, non‐cytotoxic perylene diimide derivative with two biotins at the peri position, PDI2B, has been synthesized. This molecule is able to interact selectively with G‐quadruplexes with scarce or no affinity towards single‐ or double‐stranded DNA. These features have made it possible to design a simple, effective, safe, cheap, and selective method for fishing G‐quadruplex structures in solution by use of PDI2B and streptavidin coated magnetic beads. The new cyclic method reported leads to the recovery of more than 80 % of G‐quadruplex structures from solution, even in the presence of an excess of single‐stranded or duplex DNA as competitors. Moreover, PDI2B is a G4 ligand that can display higher thermal stabilization and greater affinity for 2‐ over 3‐tetrad quadruplexes, which constitutes a novel type of behavior. Wed, 01 Aug 2018 00:00:00 GMT https://hdl.handle.net/10259/4882 2018-08-01T00:00:00Z https://hdl.handle.net/10259/4798 Role of Seroalbumin in the Cytotoxicity of cis-Dichloro Pt(II) Complexes with (N^N)-Donor Ligands Bearing Functionalized Tails Pérez Arnáiz, Cristina; Leal, Jorge .; Busto Vázquez, Natalia; Carrión, María C. .; Rubio Antolin, Ana Rosa; Ortiz, Imanol .; Barone, Giampaolo; Díaz de Greñu Puertas, Borja; Santolaya, Javier; Leal Villalba, José María; Vaquero Gutiérrez, Mónica; Jalón Sotés, Félix Ángel; Manzano, Blanca R. .; García Ruiz, Begoña Given the potent anticancer properties of cisdiamminedichloroplatinum( II) and knowing its mode of action, we synthesized four new cis-[PtCl2(N^N)] organoplatinum complexes, two with N-substituted pbi ligands (pbiR = 1-R-2-(2-pyridyl)benzimidazole) (namely, 1 and 2) and two more with 4,4′-disubstituted bpy ligands (bpy = 2,2′-bipyridine) (namely, 3 and 4). We explored their cytotoxicity and ability to bind to deoxyguanosine monophosphate (dGMP), DNA, and albumin models. By 1H NMR and UV−vis spectroscopies, circular dichroism, agarose gel electrophoresis, differential scanning calorimetry measurements, and density functional theory calculations, we verified that only 3 can form aquacomplex species after dimethyl sulfoxide solvation; surprisingly, 1, 2, and 3 can bind covalently to DNA, whereas 4 can form a noncovalent complex. Interestingly, only complexes 1 and 4 exhibit good cytotoxicity against human ovarian carcinoma (HeLa) cell line, whereas 2 and 3 are inactive. Although lung carcinoma (A549) cells are more resistant to the four platinum complexes than HeLa cells, when the protein concentration in the extracellular media is lower, the cytotoxicity becomes substantially enhanced. By native electrophoresis of bovine seroalbumin (BSA) and inductively coupled plasma mass spectrometry uptake studies we bear out, on one hand, that 2 and 3 can interact strongly with BSA and its cellular uptake is negligible and, on the other hand, that 1 and 4 can interact with BSA only weakly, its cellular uptake being higher by several orders. These results point up the important role of the protein binding features on their biological activity and cellular uptake of cis-“PtCl2” derivatives. Our results are valuable in the future rational design of new platinum complexes with improved biological properties, as they expose the importance not only of their DNA binding abilities but also of additional factors such as protein binding. Mon, 21 May 2018 00:00:00 GMT https://hdl.handle.net/10259/4798 2018-05-21T00:00:00Z https://hdl.handle.net/10259/4746 Kinetic evidence for interaction of TMPyP4 with two different G-quadruplex conformations of human telomeric DNA Pérez Arnáiz, Cristina; Busto Vázquez, Natalia; Santolaya, Javier; Leal Villalba, José María; Barone, Giampaolo; García Ruiz, Begoña Background: Stabilization of G-quadruplex helices by small ligands has attracted growing attention because they inhibit the activity of the enzyme telomerase, which is overexpressed in> 80% cancer cells. TMPyP4, one of the most studied G-quadruplex ligands, is used as a model to show that the ligands can exhibit different binding features with different conformations of a human telomeric specific sequence. Methods: UV–Vis, FRET melting Assay, Isothermal Titration Calorimetry, Time-resolved Fluorescence lifetime, T-Jump and Molecular Dynamics. Results: TMPyP4 yields two different complexes with two Tel22 telomeric conformations in the presence of Na+ or K+. T-Jump kinetic experiments show that the rates of formation and dissociation of these complexes in the ms time scale differ by one order of magnitude. MD simulations reveal that, in K+ buffer, “hybrid 1” conformation yields kinetic constants on interaction with TMPyP4 one order lower than “hybrid 2”. The binding involves π–π stacking with external loop bases. Conclusions: For the first time we show that for a particular buffer TMPyP4 interacts in a kinetically different way with the two Tel22 conformations even if the complexes formed are thermodynamically indistinguishable. General significance: G-quadruplexes, endowed with technological applications and potential impact on regulation mechanisms, define a new research field. The possibility of building different conformations from same sequence is a complex issue that confers G-quadruplexes very interesting features. The obtaining of reliable kinetic data constitutes an efficient tool to determine reaction mechanisms between conformations and small molecules. Thu, 01 Mar 2018 00:00:00 GMT https://hdl.handle.net/10259/4746 2018-03-01T00:00:00Z https://hdl.handle.net/10259/4282 Selectivity of a thiosemicarbazonatocopper(II) complex towards duplex RNA. Relevant noncovalent interactions both in solid state and solution Gil García, Rubén; Ugalde, María; Busto Vázquez, Natalia; Lozano Ordóñez, Héctor J.; Leal Villalba, José María; Pérez, Begoña; Madariaga, Gotzon; Insausti, Maite; Lezama, Luis; Sanz Díez, Roberto; Gómez Sainz, Lidia M.; García Ruiz, Begoña; García Tojal, Javier Thiosemicarbazones and their metal derivatives have long been screened as antitumor agents, and their interactions with DNA have been analysed. Herein, we describe the synthesis and characterization of compounds containing [CuL]+ entities (HL = pyridine-2-carbaldehyde thiosemicarbazone) and adenine, cytosine or 9-methylguanine, and some of their corresponding nucleotides. For the first time, crystal structures of adenine- and 9-methylguanine-containing thiosemicarbazone complexes are reported. To the best of our knowledge, the first study on the affinity thiosemicarbazone–RNA is also provided here. Experimental and computational studies have shown that [CuL(OH2)]+ entities at low concentration intercalate into dsRNA poly(rA)·poly(rU) through strong hydrogen bonds involving uracil residues and π–π stacking interactions. In fact, noncovalent interactions are present both in the solid state and in solution. This behaviour diverges from that observed with DNA duplexes and creates an optimistic outlook in achieving selective binding to RNA for subsequent possible medical applications. Thu, 01 Dec 2016 00:00:00 GMT https://hdl.handle.net/10259/4282 2016-12-01T00:00:00Z