RT info:eu-repo/semantics/article
T1 Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes
A1 Macii, Francesca
A1 Cupellini, Lorenzo
A1 Stifano, Mariassunta
A1 Santolaya, Javier
A1 Pérez Arnáiz, Cristina
A1 Pucci, Andrea
A1 Barone, Giampaolo
A1 García Ruiz, Begoña
A1 Busto Vázquez, Natalia
A1 Biver, Tarita
K1 Density functional theory
K1 Intercalation
K1 Sitting atop
K1 Molecular dynamics
K1 Aggregation
K1 Química física
K1 Chemistry, Physical and theoretical
AB 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.
PB Elsevier
SN 1386-1425
YR 2021
FD 2021-11
LK http://hdl.handle.net/10259/5815
UL http://hdl.handle.net/10259/5815
LA eng
NO “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)
DS Repositorio Institucional de la Universidad de Burgos
RD 23-nov-2024