2024-03-29T15:27:15Zhttps://riubu.ubu.es/oai/requestoai:riubu.ubu.es:10259/58152023-11-04T23:42:12Zcom_10259_4365com_10259_5086com_10259_2604col_10259_4366
Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes
Macii, Francesca
Cupellini, Lorenzo
Stifano, Mariassunta
Santolaya, Javier
Pérez Arnáiz, Cristina
Pucci, Andrea
Barone, Giampaolo
García Ruiz, Begoña
Busto Vázquez, Natalia
Biver, Tarita
Density functional theory
Intercalation
Sitting atop
Molecular dynamics
Aggregation
Química física
Chemistry, Physical and theoretical
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)
2021-06-24T08:51:21Z
2021-06-24T08:51:21Z
2021-11
info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
1386-1425
http://hdl.handle.net/10259/5815
10.1016/j.saa.2021.119914
eng
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
application/pdf
Elsevier
https://riubu.ubu.es/bitstream/10259/5815/4/Macii-sapambs_2021.pdf.jpg
Hispana
TEXT
http://creativecommons.org/licenses/by-nc-nd/4.0/
RIUBU. Repositorio Institucional de la Universidad de Burgos
http://hdl.handle.net/10259/5815