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Gangemi CMA, Alaimo S, Pulvirenti A, García-Viñuales S, Milardi D, Falanga AP, Fragalà ME, Oliviero G, Piccialli G, Borbone N, Ferro A, D'Urso A, Croce CM, Purrello R. Endogenous and artificial miRNAs explore a rich variety of conformations: a potential relationship between secondary structure and biological functionality. Sci Rep 2020; 10:453. [PMID: 31949213 PMCID: PMC6965629 DOI: 10.1038/s41598-019-57289-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022] Open
Abstract
Mature microRNAs are short non-coding RNA sequences which upon incorporation into the RISC ribonucleoprotein complex, play a crucial role in regulation of gene expression. However, miRNAs can exist within the cell also as free molecules fulfilling their biological activity. Therefore, it is emerging that in addition to sequence even the structure adopted by mature miRNAs might play an important role to reach the target. Indeed, we analysed by several spectroscopic techniques the secondary structures of two artificial miRNAs selected by computational tool (miR-Synth) as best candidates to silence c-MET and EGFR genes and of two endogenous miRNAs (miR-15a and miR-15b) having the same seed region, but different biological activity. Our results demonstrate that both endogenous and artificial miRNAs can arrange in several 3D-structures which affect their activity and selectivity toward the targets.
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Affiliation(s)
- C M A Gangemi
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - S Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy
| | - A Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy
| | | | - D Milardi
- Istituto di Cristallografia CNR, Via P. Gaifami 9, 95126, Catania, Italy
| | - A P Falanga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Napoli, Italy
| | - M E Fragalà
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131, Napoli, Italy
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, D. Montesano 49, 80131, Napoli, Italy
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, D. Montesano 49, 80131, Napoli, Italy
| | - A Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy c/o Department of Mathematics and Computer Science, Viale A. Doria 6, 95125, Catania, Italy.
| | - A D'Urso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - C M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - R Purrello
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
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Nici F, Oliviero G, Falanga AP, D'Errico S, Marzano M, Musumeci D, Montesarchio D, Noppen S, Pannecouque C, Piccialli G, Borbone N. Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides. Org Biomol Chem 2019. [PMID: 29543291 DOI: 10.1039/c7ob02346d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties. The here reported results demonstrate that only the DMT-substituted TEL-ODN 2 is effective in protecting human MT-4 cell cultures from HIV infection (76% max protection), notwithstanding all the three new aptamers proved to be capable of forming stable higher order dimeric G4s when annealed in K+-containing buffer, thus suggesting that the recognition of a hydrophobic pocket on the target glycoprotein by the aptamers represents a main structural feature for triggering their anti-HIV activity.
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Affiliation(s)
- F Nici
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli, Italy
| | - A P Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - S D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - M Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - D Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - D Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - S Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - C Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
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D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
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Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
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Scuotto M, Persico M, Bucci M, Vellecco V, Borbone N, Morelli E, Oliviero G, Novellino E, Piccialli G, Cirino G, Varra M, Fattorusso C, Mayol L. Outstanding effects on antithrombin activity of modified TBA diastereomers containing an optically pure acyclic nucleotide analogue. Org Biomol Chem 2015; 12:5235-42. [PMID: 24920241 DOI: 10.1039/c4ob00149d] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Herein, we report optically pure modified acyclic nucleosides as ideal probes for aptamer modification. These new monomers offer unique advantages in exploring the role played in thrombin inhibition by a single residue modification at key positions of the TBA structure.
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Affiliation(s)
- M Scuotto
- Dipartimento di Farmacia, via D. Montesano 49, 80131 Napoli, Italy.
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