2026-04-19T17:04:22Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/58152023-11-04T23:42:12Zcom_10259_4365com_10259_5086com_10259_2604col_10259_4366

Macii, Francesca 83aa6ac0-e1f1-4ef9-8d5f-6e700cc20253 500 Cupellini, Lorenzo 79abbdb6-36df-4c8b-b95a-53dfe5d9a16c 500 Stifano, Mariassunta 5ff2f4b2-e51d-4c4f-bc5f-8c1ff7fe1f07 500 Santolaya, Javier ac73c679-73ee-420a-b52e-e67a1b6502d7 500 Pérez Arnáiz, Cristina 435 500 0000-0002-1468-9860 Pucci, Andrea 067566dd-8f8d-44e4-9882-d5fb75b72c13 500 Barone, Giampaolo 2502c306-a514-4e96-9cd8-7a3b547ae347 500 García Ruiz, Begoña 217 500 0000-0002-0817-1651 Busto Vázquez, Natalia 83 500 0000-0001-9637-1209 Biver, Tarita 686e3c46-a69c-4fbe-9b7a-e05265bbac4e 500 2021-06-24T08:51:21Z 2021-06-24T08:51:21Z 2021-11 1386-1425 http://hdl.handle.net/10259/5815 10.1016/j.saa.2021.119914 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. “la Caixa” Foundation (LCF/PR/PR12/11070003), Ministerio de Ciencia, Innovación y Universidades-FEDER (RTI2018-102040-B-100) and Junta de Castilla y León-FEDER (BU305P18). LC acknowledges funding by the European Research Council, under the grant ERC-AdG-786714 (LIFETimeS) application/pdf eng Elsevier Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2021, V. 260, 119914 https://doi.org/10.1016/j.saa.2021.119914 info:eu-repo/grantAgreement/FundaciónLaCaixa/LCF/PR/PR12/11070003 info:eu-repo/grantAgreement/MICINN/RTI2018-102040-B-100 info:eu-repo/grantAgreement/JCyL/BU305P18 info:eu-repo/grantAgreement/ERC/ERC-AdG-786714 Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess Density functional theory Intercalation Sitting atop Molecular dynamics Aggregation Química física Chemistry, Physical and theoretical Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 260 119914 THUMBNAIL Macii-sapambs_2021.pdf.jpg Macii-sapambs_2021.pdf.jpg IM Thumbnail image/jpeg 4409 https://riubu.ubu.es/bitstream/10259/5815/4/Macii-sapambs_2021.pdf.jpg d17e18723ab7ba2c8ac79f211c9fa30e MD5 4 LICENSE license.txt license.txt text/plain; charset=utf-8 999 https://riubu.ubu.es/bitstream/10259/5815/3/license.txt b295bcbce42e2caabeb0c623d3860c06 MD5 3 CC-LICENSE license_rdf license_rdf application/rdf+xml; charset=utf-8 805 https://riubu.ubu.es/bitstream/10259/5815/2/license_rdf 4460e5956bc1d1639be9ae6146a50347 MD5 2 ORIGINAL Macii-sapambs_2021.pdf Macii-sapambs_2021.pdf application/pdf 1228877 https://riubu.ubu.es/bitstream/10259/5815/1/Macii-sapambs_2021.pdf 66e67b603d9bdeca9cec0458848af9a6 MD5 1 10259/5815 oai:riubu.ubu.es:10259/5815 2023-11-05 00:42:12.961 Repositorio Institucional de la Universidad de Burgos bubrep@ubu.es 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