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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: 0.7] [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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Macii F, Perez-Arnaiz C, Arrico L, Busto N, Garcia B, Biver T. Alcian blue pyridine variant interaction with DNA and RNA polynucleotides and G-quadruplexes: changes in the binding features for different biosubstrates. J Inorg Biochem 2020; 212:111199. [DOI: 10.1016/j.jinorgbio.2020.111199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
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Katz AM, Tolokh IS, Pabit SA, Baker N, Onufriev AV, Pollack L. Spermine Condenses DNA, but Not RNA Duplexes. Biophys J 2017; 112:22-30. [PMID: 28076812 DOI: 10.1016/j.bpj.2016.11.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 10/25/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022] Open
Abstract
Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.
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Affiliation(s)
- Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Nathan Baker
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia; Department of Physics, Virginia Tech, Blacksburg, Virginia
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
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Lari M, Biver T, Busto N, Lozano HJ, Leal JM, Secco F, García B. Binding of Al(iii) to synthetic RNA and metal-mediated strand aggregation. Dalton Trans 2017; 46:16671-16681. [DOI: 10.1039/c7dt02830j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic curve of the binding of aluminum to RNA and metal-induced strand aggregation.
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Affiliation(s)
- Matteo Lari
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | - Tarita Biver
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Natalia Busto
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | | | - José M. Leal
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | - Fernando Secco
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Begoña García
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
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Haque L, Bhuiya S, Tiwari R, Pradhan AB, Das S. Biophysical insight into the interaction of the bioflavonoid kaempferol with triple and double helical RNA and the dual fluorescence behaviour of kaempferol. RSC Adv 2016. [DOI: 10.1039/c6ra12445c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Binding of kaempferol with triple and double helical RNA.
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Affiliation(s)
- Lucy Haque
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Richa Tiwari
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Suman Das
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
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