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Macii F, Cupellini L, Stifano M, Santolaya J, Pérez-Arnaiz C, Pucci A, Barone G, García B, Busto N, Biver T. Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119914. [PMID: 34015745 DOI: 10.1016/j.saa.2021.119914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Francesca Macii
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Mariassunta Stifano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Javier Santolaya
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Cristina Pérez-Arnaiz
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Andrea Pucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Begoña García
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Busto
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
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