1
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Falanga AP, Massaro M, Borbone N, Notarbartolo M, Piccialli G, Liotta LF, Sanchez-Espejo R, Viseras Iborra C, Raymo FM, Oliviero G, Riela S. Carrier capability of halloysite nanotubes for the intracellular delivery of antisense PNA targeting mRNA of neuroglobin gene. J Colloid Interface Sci 2024; 663:9-20. [PMID: 38387188 DOI: 10.1016/j.jcis.2024.02.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Peptide nucleic acid (PNA) is a DNA mimic that shows good stability against nucleases and proteases, forming strongly recognized complementary strands of DNA and RNA. However, due to its feeble ability to cross the cellular membrane, PNA activity and its targeting gene action is limited. Halloysite nanotubes (HNTs) are a natural and low-cost aluminosilicate clay. Because of their peculiar ability to cross cellular membrane, HNTs represent a valuable candidate for delivering genetic materials into cells. Herein, two differently charged 12-mer PNAs capable of recognizing as molecular target a 12-mer DNA molecule mimicking a purine-rich tract of neuroglobin were synthetized and loaded onto HNTs by electrostatic attraction interactions. After characterization, the kinetic release was also assessed in media mimicking physiological conditions. Resonance light scattering measurements assessed their ability to bind complementary single-stranded DNA. Furthermore, their intracellular delivery was assessed by confocal laser scanning microscopy on living MCF-7 cells incubated with fluorescence isothiocyanate (FITC)-PNA and HNTs labeled with a probe. The nanomaterials were found to cross cellular membrane and cell nuclei efficiently. Finally, it is worth mentioning that the HNTs/PNA can reduce the level of neuroglobin gene expression, as shown by reverse transcription-quantitative polymerase chain reaction and western blotting analysis.
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Affiliation(s)
- Andrea P Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Marina Massaro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Monica Notarbartolo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Leonarda F Liotta
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN)-CNR, Via Ugo La Malfa 153, Palermo 90146, Italy
| | - Rita Sanchez-Espejo
- University of Granada, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, 18071 Granada, Spain
| | - Cesar Viseras Iborra
- University of Granada, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, 18071 Granada, Spain; Andalusian Institute of Earth Sciences, CSIC-UGR, 18100 Armilla, Granada, Spain
| | - Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables 33146-0431, FL, United States
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Via Sergio Pansini 5, 80131 Napoli, Italy
| | - Serena Riela
- Dipartimento di Scienze Chimiche, Viale Andrea Doria 6, 95125 Catania, Italy.
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2
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Falanga AP, Lupia A, Tripodi L, Morgillo CM, Moraca F, Roviello GN, Catalanotti B, Amato J, Pastore L, Cerullo V, D'Errico S, Piccialli G, Oliviero G, Borbone N. Exploring the DNA 2-PNA heterotriplex formation in targeting the Bcl-2 gene promoter: A structural insight by physico-chemical and microsecond-scale MD investigation. Heliyon 2024; 10:e24599. [PMID: 38317891 PMCID: PMC10839560 DOI: 10.1016/j.heliyon.2024.e24599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Peptide Nucleic Acids (PNAs) represent a promising tool for gene modulation in anticancer treatment. The uncharged peptidyl backbone and the resistance to chemical and enzymatic degradation make PNAs highly advantageous to form stable hybrid complexes with complementary DNA and RNA strands, providing higher stability than the corresponding natural analogues. Our and other groups' research has successfully shown that tailored PNA sequences can effectively downregulate the expression of human oncogenes using antigene, antisense, or anti-miRNA approaches. Specifically, we identified a seven bases-long PNA sequence, complementary to the longer loop of the main G-quadruplex structure formed by the bcl2midG4 promoter sequence, capable of downregulating the expression of the antiapoptotic Bcl-2 protein and enhancing the anticancer activity of an oncolytic adenovirus. Here, we extended the length of the PNA probe with the aim of including the double-stranded Bcl-2 promoter among the targets of the PNA probe. Our investigation primarily focused on the structural aspects of the resulting DNA2-PNA heterotriplex that were determined by employing conventional and accelerated microsecond-scale molecular dynamics simulations and chemical-physical analysis. Additionally, we conducted preliminary biological experiments using cytotoxicity assays on human A549 and MDA-MB-436 adenocarcinoma cell lines, employing the oncolytic adenovirus delivery strategy.
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Affiliation(s)
- Andrea P. Falanga
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Antonio Lupia
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Lorella Tripodi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore S.c.a.r.l., Naples, 80145, Italy
| | - Carmine M. Morgillo
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Federica Moraca
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Giovanni N. Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale Delle Ricerche, Naples, 80131, Italy
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Jussara Amato
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore S.c.a.r.l., Naples, 80145, Italy
| | - Vincenzo Cerullo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
- ImmunoViroTherapy Lab (IVT), Drug Research Program (DRP), Faculty of Pharmacy, University of Helsinki, 00100, Helsinki, Finland
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università Degli Studi di Napoli Federico II, Naples, 80131, Italy
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3
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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4
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Effects of G-Quadruplex-Binding Plant Secondary Metabolites on c-MYC Expression. Int J Mol Sci 2022; 23:ijms23169209. [PMID: 36012470 PMCID: PMC9409388 DOI: 10.3390/ijms23169209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 11/25/2022] Open
Abstract
Guanine-rich DNA sequences tending to adopt noncanonical G-quadruplex (G4) structures are over-represented in promoter regions of oncogenes. Ligands recognizing G4 were shown to stabilize these DNA structures and drive their formation regulating expression of corresponding genes. We studied the interaction of several plant secondary metabolites (PSMs) with G4s and their effects on gene expression in a cellular context. The binding of PSMs with G4s formed by the sequences of well-studied oncogene promoters and telomeric repeats was evaluated using a fluorescent indicator displacement assay. c-MYC G4 folding topology and thermal stability, as well as the PMS influence on these parameters, were demonstrated by UV-spectroscopy and circular dichroism. The effects of promising PSMs on c-MYC expression were assessed using luciferase reporter assay and qPR-PCR in cancer and immortalized cultured cells. The ability of PMS to multi-targeting cell signaling pathways was analyzed by the pathway-focused gene expression profiling with qRT-PCR. The multi-target activity of a number of PSMs was demonstrated by their interaction with a set of G4s mimicking those formed in the human genome. We have shown a direct G4-mediated down regulation of c-MYC expression by sanguinarine, quercetin, kaempferol, and thymoquinone; these effects being modulated by PSM’s indirect influence via cell signaling pathways.
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5
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Exploring the Parallel G-Quadruplex Nucleic Acid World: A Spectroscopic and Computational Investigation on the Binding of the c-myc Oncogene NHE III1 Region by the Phytochemical Polydatin. Molecules 2022; 27:molecules27092997. [PMID: 35566347 PMCID: PMC9099682 DOI: 10.3390/molecules27092997] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Trans-polydatin (tPD), the 3-β-D-glucoside of the well-known nutraceutical trans-resveratrol, is a natural polyphenol with documented anti-cancer, anti-inflammatory, cardioprotective, and immunoregulatory effects. Considering the anticancer activity of tPD, in this work, we aimed to explore the binding properties of this natural compound with the G-quadruplex (G4) structure formed by the Pu22 [d(TGAGGGTGGGTAGGGTGGGTAA)] DNA sequence by exploiting CD spectroscopy and molecular docking simulations. Pu22 is a mutated and shorter analog of the G4-forming sequence known as Pu27 located in the promoter of the c-myc oncogene, whose overexpression triggers the metabolic changes responsible for cancer cells transformation. The binding of tPD with the parallel Pu22 G4 was confirmed by CD spectroscopy, which showed significant changes in the CD spectrum of the DNA and a slight thermal stabilization of the G4 structure. To gain a deeper insight into the structural features of the tPD-Pu22 complex, we performed an in silico molecular docking study, which indicated that the interaction of tPD with Pu22 G4 may involve partial end-stacking to the terminal G-quartet and H-bonding interactions between the sugar moiety of the ligand and deoxynucleotides not included in the G-tetrads. Finally, we compared the experimental CD profiles of Pu22 G4 with the corresponding theoretical output obtained using DichroCalc, a web-based server normally used for the prediction of proteins’ CD spectra starting from their “.pdb” file. The results indicated a good agreement between the predicted and the experimental CD spectra in terms of the spectral bands’ profile even if with a slight bathochromic shift in the positive band, suggesting the utility of this predictive tool for G4 DNA CD investigations.
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6
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Cesaro E, Falanga AP, Catapano R, Greco F, Romano S, Borbone N, Pastore A, Marzano M, Chiurazzi F, D’Errico S, Piccialli G, Oliviero G, Costanzo P, Grosso M. Exploring a peptide nucleic acid-based antisense approach for CD5 targeting in chronic lymphocytic leukemia. PLoS One 2022; 17:e0266090. [PMID: 35358273 PMCID: PMC8970396 DOI: 10.1371/journal.pone.0266090] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
We herein report an innovative antisense approach based on Peptide Nucleic Acids (PNAs) to down-modulate CD5 expression levels in chronic lymphocytic leukemia (CLL). Using bioinformatics tools, we selected a 12-mer tract of the CD5 mRNA as the molecular target and synthesized the complementary and control PNA strands bearing a serine phosphate dipeptide tail to enhance their water solubility and bioavailability. The specific recognition of the 12-mer DNA strand, corresponding to the target mRNA sequence by the complementary PNA strand, was confirmed by non-denaturing polyacrylamide gel electrophoresis, thermal difference spectroscopy, circular dichroism (CD), and CD melting studies. Cytofluorimetric assays and real-time PCR analysis demonstrated the downregulation of CD5 expression due to incubation with the anti-CD5 PNA at RNA and protein levels in Jurkat cell line and peripheral blood mononuclear cells from B-CLL patients. Interestingly, we also observed that transfection with the anti-CD5 PNA increases apoptotic response induced by fludarabine in B-CLL cells. The herein reported results suggest that PNAs could represent a potential candidate for the development of antisense therapeutic agents in CLL.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukocytes, Mononuclear
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacology
- Peptide Nucleic Acids/chemistry
- RNA, Messenger/genetics
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Affiliation(s)
- Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | | | - Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
| | - Arianna Pastore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Maria Marzano
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Federico Chiurazzi
- Department of Clinical and Experimental Medicine, Division of Hematology, University of Naples Federico II, Napoli, Italy
| | - Stefano D’Errico
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
- * E-mail:
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
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7
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Periyalagan A, Hong IS. A novel synthetic method of peptide nucleic acid (
PNA
) oligomers using Boc/
Cbz‐protected PNA
trimer blocks in the solution phase. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alagarsamy Periyalagan
- Department of Chemistry College of Natural Science, Kongju National University Chungnam Republic of Korea
| | - In Seok Hong
- Department of Chemistry College of Natural Science, Kongju National University Chungnam Republic of Korea
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8
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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9
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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10
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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11
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Paul R, Dutta D, Das T, Debnath M, Dash J. G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells. Chemistry 2021; 27:8590-8599. [PMID: 33851760 DOI: 10.1002/chem.202100907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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12
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Comegna M, Conte G, Falanga AP, Marzano M, Cernera G, Di Lullo AM, Amato F, Borbone N, D'Errico S, Ungaro F, d'Angelo I, Oliviero G, Castaldo G. Assisting PNA transport through cystic fibrosis human airway epithelia with biodegradable hybrid lipid-polymer nanoparticles. Sci Rep 2021; 11:6393. [PMID: 33737583 PMCID: PMC7973768 DOI: 10.1038/s41598-021-85549-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is characterized by an airway obstruction caused by a thick mucus due to a malfunctioning Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. The sticky mucus restricts drugs in reaching target cells limiting the efficiency of treatments. The development of new approaches to enhance drug delivery to the lungs represents CF treatment's main challenge. In this work, we report the production and characterization of hybrid core–shell nanoparticles (hNPs) comprising a PLGA core and a dipalmitoylphosphatidylcholine (DPPC) shell engineered for inhalation. We loaded hNPs with a 7-mer peptide nucleic acid (PNA) previously considered for its ability to modulate the post-transcriptional regulation of the CFTR gene. We also investigated the in vitro release kinetics of hNPs and their efficacy in PNA delivery across the human epithelial airway barrier using an ex vivo model based on human primary nasal epithelial cells (HNEC) from CF patients. Confocal analyses and hNPs transport assay demonstrated the ability of hNPs to overcome the mucus barrier and release their PNA cargo within the cytoplasm, where it can exert its biological function.
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Affiliation(s)
- Marika Comegna
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Gemma Conte
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | | | - Maria Marzano
- Institute of Crystallography, National Research Council, 70126, Bari, Italy
| | - Gustavo Cernera
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Antonella Miriam Di Lullo
- ENT Section, Department of Neuroscience, Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131, Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Francesca Ungaro
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Ivana d'Angelo
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy.
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
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13
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Bioconjugation of a PNA Probe to Zinc Oxide Nanowires for Label-Free Sensing. NANOMATERIALS 2021; 11:nano11020523. [PMID: 33670746 PMCID: PMC7923052 DOI: 10.3390/nano11020523] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/04/2022]
Abstract
Zinc oxide nanowires (ZnONWs) are largely used in biosensing applications due to their large specific surface area, photoluminescence emission and electron mobility. In this work, the surfaces of ZnONWs are modified by covalent bioconjugation of a peptidic nucleic acid (PNA) probe whose sequence is properly chosen to recognize a complementary DNA (cDNA) strand corresponding to a tract of the CD5 mRNA, the main prognostic marker of chronic lymphatic leukemia. The interaction between PNA and cDNA is preliminarily investigated in solution by circular dichroism, CD melting, and polyacrylamide gel electrophoresis. After the immobilization of the PNA probe on the ZnONW surface, we demonstrate the ability of the PNA-functionalized ZnONW platform to detect cDNA in the μM range of concentration by electrical, label-free measurements. The specificity of the sensor is also verified against a non-complementary DNA sequence. These preliminary results highlight the potential application of PNA-bioconjugated ZnONWs to label-free biosensing of tumor markers.
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14
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Kumar S, Choudhary D, Patra A, Bhavesh NS, Vivekanandan P. Analysis of G-quadruplexes upstream of herpesvirus miRNAs: evidence of G-quadruplex mediated regulation of KSHV miR-K12-1-9,11 cluster and HCMV miR-US33. BMC Mol Cell Biol 2020; 21:67. [PMID: 32972365 PMCID: PMC7513282 DOI: 10.1186/s12860-020-00306-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND G-quadruplexes regulate gene expression, recombination, packaging and latency in herpesviruses. Herpesvirus-encoded miRNAs have been linked to important biological functions. The presence and the biological role of G-quadruplexes have not been studied in the regulatory regions of virus miRNA. We hypothesized that herpesvirus-encoded miRNAs are regulated by G-quadruplexes in their promoters. RESULTS We analyzed the 1 kb regulatory regions of all herpesvirus-encoded miRNAs for the presence of putative quadruplex-forming sequences (PQS). Over two-third (67%) of the regulatory regions of herpesvirus miRNAs had atleast 1 PQS. The 200 bp region of the promoter proximal to herpesvirus miRNA is particularly enriched for PQS. We chose to study the G-quadruplex motifs in the promoters of miR-K12 cluster in Kaposi's sarcoma-associated Herpesvirus (KSHV miR-K12-1-9,11) and the miR-US33 encoded by Human Cytomegalovirus (HCMV miR-US33). Biophysical characterization indicates that the G-quadruplex motifs in the promoters of the KSHV miR-K12 cluster and the HCMV miR-US33 form stable intramolecular G-quadruplexes in vitro. Mutations disrupting the G-quadruplex motif in the promoter of the KSHV miR-K12 cluster significantly inhibits promoter activity, while those disrupting the motif in the promoter of HCMV miR-US33 significantly enhance the promoter activity as compared to that of the respective wild-type promoter. Similarly, the addition of G-quadruplex binding ligands resulted in the modulation of promoter activity of the wild-type promoters (with intact G-quadruplex) but not the mutant promoters (containing quadruplex-disrupting mutations). CONCLUSION Our findings highlight previously unknown mechanisms of regulation of virus-encoded miRNA and also shed light on new roles for G-quadruplexes in herpesvirus biology.
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Affiliation(s)
- Shivani Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Divya Choudhary
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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15
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Su Y, Edwards PJB, Stetsenko DA, Filichev VV. The Importance of Phosphates for DNA G-Quadruplex Formation: Evaluation of Zwitterionic G-Rich Oligodeoxynucleotides. Chembiochem 2020; 21:2455-2466. [PMID: 32281223 DOI: 10.1002/cbic.202000110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/09/2020] [Indexed: 12/21/2022]
Abstract
A quaternary ammonium butylsulfonyl phosphoramidate group (N+) was designed to replace all the phosphates in a G-rich oligodeoxynucleotide d(TG4 T), resulting in a formally charge-neutral zwitterionic N+TG4 T sequence. We evaluated the effects of N+phosphate modifications on the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes (G4) formed by TG4 T and compared them to the properties of the recently published phosphoryl guanidine d(TG4 T) (PG-TG4 T). Using size-exclusion chromatography, we established that, unlike PG-TG4 T, which exists as a mixture of complexes of different molecularity in solution, N+TG4 T forms an individual tetramolecular complex. In contrast to PG modifications that destabilized G4s, the presence of N+ modifications increased thermal stability relative to unmodified [d(TG4 T)]4 . The initial stage of assembly of N+TG4 T proceeded faster in the presence of Na+ than K+ ions and, similarly to PG-TG4 T, was independent of the salt concentration. However, after complex formation exceeded 75 %, N+TG4 T in solution with Na+ showed slower association than with K+ . N+TG4 T could also form G4s in solution with Li+ ions at a very low strand concentration (10 μM); something that has never been reported for the native d(TG4 T). Charge-neutral PG-G4s can invade preformed native G4s, whereas no invasion was observed between N+and native G4s, possibly due to the increased thermal stability of [N+TG4 T]4 . The N+ modification makes d(TG4 T) fully resistant to enzymatic digestion, which could be useful for intracellular application of N+-modified DNA or RNA.
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Affiliation(s)
- Yongdong Su
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Dmitry A Stetsenko
- Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1142, New Zealand
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16
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Sengupta P, Banerjee N, Roychowdhury T, Dutta A, Chattopadhyay S, Chatterjee S. Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells. Nucleic Acids Res 2019; 46:9932-9950. [PMID: 30239898 PMCID: PMC6212778 DOI: 10.1093/nar/gky824] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022] Open
Abstract
c-MYC proto-oncogene harbours a transcription-inhibitory quadruplex-forming scaffold (Pu27) upstream P1 promoter providing anti-neoplastic therapeutic target. Previous reports showed the binding profile of human Cathelicidin peptide (LL37) and telomeric G-quadruplex. Here, we truncated the quadruplex-binding domain of LL37 to prepare a small library of peptides through site-specific amino acid substitution. We investigated the intracellular selectivity of peptides for Pu27 over other oncogenic quadruplexes and their role in c-MYC promoter repression by dual-luciferase assays. We analysed their thermodynamics of binding reactions with c-MYC quadruplex isomers (Pu27, Myc22, Pu19) by Isothermal Titration Calorimetry. We discussed how amino acid substitutions and peptide helicity enhanced/weakened their affinities for c-MYC quadruplexes and characterized specific non-covalent inter-residual interactions determining their selectivity. Solution NMR structure indicated that KR12C, the best peptide candidate, selectively stabilized the 5′-propeller loop of c-MYC quadruplex by arginine-driven electrostatic-interactions at the sugar-phosphate backbone while KR12A peptide destabilized the quadruplex inducing a single-stranded hairpin-like conformation. Chromatin immunoprecipitations envisaged that KR12C and KR12A depleted and enriched Sp1 and NM23-H2 (Nucleoside diphosphate kinase) occupancy at Pu27 respectively supporting their regulation in stabilizing and unfolding c-MYC quadruplex in MCF-7 cells. We deciphered that selective arresting of c-MYC transcription by KR12C triggered apoptotic-signalling pathway via VEGF-A-BCL-2 axis.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Tanaya Roychowdhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Samit Chattopadhyay
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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17
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Falanga AP, Cerullo V, Marzano M, Feola S, Oliviero G, Piccialli G, Borbone N. Peptide Nucleic Acid-Functionalized Adenoviral Vectors Targeting G-Quadruplexes in the P1 Promoter of Bcl-2 Proto-Oncogene: A New Tool for Gene Modulation in Anticancer Therapy. Bioconjug Chem 2019; 30:572-582. [PMID: 30620563 DOI: 10.1021/acs.bioconjchem.8b00674] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The B-cell lymphoma 2 (Bcl-2) gene encodes for an antiapoptotic protein associated with the onset of many human tumors. Several oligonucleotides (ONs) and ON analogues are under study as potential tools to counteract the Bcl-2 expression. Among these are Peptide Nucleic Acids (PNAs). The absence of charges on PNA backbones allows the formation of PNA/DNA complexes provided with higher stability than the corresponding natural DNA/DNA counterparts. To date, the use of PNAs in antigene or antisense strategies is strongly limited by their inability to efficiently cross the cellular membranes. With the aim of downregulating the expression of Bcl-2, we propose here a novel antigene approach which uses oncolytic adenoviral vectors (OAds) as a new cancer cell-targeted PNA delivery system. The ability of oncolytic Ad5D24 vectors to selectively infect and kill cancer cells was exploited to transfect with high efficiency and selectivity a short cytosine-rich PNA complementary to the longest loop of the main G-quadruplex formed by the 23-base-long bcl2midG4 sequence located 52-30 bp upstream of the P1 promoter of Bcl-2 gene. Physico-chemical and biological investigations confirmed the ability of the PNA-conjugated Ad5D24 vectors to load and transfect their PNA cargo into human A549 and MDA-MB-436 cancer cell lines, as well as the synergistic (OAd+PNA) cytotoxic effect against the same cell lines. This approach holds promise for safer chemotherapy because of reduced toxicity to healthy tissues and organs.
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Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | - Vincenzo Cerullo
- Department of Molecular Medicine and Medical Biotechnologies , University of Naples Federico II , Via Sergio Pansini 5 , 80131 Naples , Italy
| | - Maria Marzano
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | | | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies , University of Naples Federico II , Via Sergio Pansini 5 , 80131 Naples , Italy
| | - Gennaro Piccialli
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | - Nicola Borbone
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
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18
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Su Y, Fujii H, Burakova EA, Chelobanov BP, Fujii M, Stetsenko DA, Filichev VV. Neutral and Negatively Charged Phosphate Modifications Altering Thermal Stability, Kinetics of Formation and Monovalent Ion Dependence of DNA G-Quadruplexes. Chem Asian J 2019; 14:1212-1220. [PMID: 30600926 DOI: 10.1002/asia.201801757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/22/2018] [Indexed: 12/18/2022]
Abstract
The effect of phosphate group modifications on formation and properties of G-quadruplexes (G4s) has not been investigated in detail. Here, we evaluated the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes formed by oligodeoxynucleotides d(G4 T), d(TG4 T) and d(TG5 T), in which all phosphates were replaced with N-methanesulfonyl (mesyl) phosphoramidate or phosphoryl guanidine groups resulting in either negatively charged or neutral DNA sequences, respectively. We established that all modified sequences were able to form G-quadruplexes of parallel topology; however, the presence of modifications led to a decrease in thermal stability relative to unmodified G4s. In contrast to negatively charged G4s, assembly of neutral G4 DNA species was faster in the presence of sodium ions than potassium ions, and was independent of the salt concentration used. Formation of mixed G4s composed of both native and neutral G-rich strands has been detected using native gel electrophoresis, size-exclusion chromatography and ESI-MS. In summary, our results indicate that the phosphate modifications studied are compatible with G-quadruplex formation, which could be used for the design of biologically active compounds.
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Affiliation(s)
- Yongdong Su
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Hirofumi Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Ekaterina A Burakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Boris P Chelobanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Masayuki Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
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19
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Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis. Molecules 2017; 22:molecules22071144. [PMID: 28698463 PMCID: PMC6152032 DOI: 10.3390/molecules22071144] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3’UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3’UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression.
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20
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Oyaghire SN, Cherubim CJ, Telmer CA, Martinez JA, Bruchez MP, Armitage BA. RNA G-Quadruplex Invasion and Translation Inhibition by Antisense γ-Peptide Nucleic Acid Oligomers. Biochemistry 2016; 55:1977-88. [PMID: 26959335 DOI: 10.1021/acs.biochem.6b00055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the abilities of three complementary γ-peptide nucleic acid (γPNA) oligomers to invade an RNA G-quadruplex and potently inhibit translation of a luciferase reporter transcript containing the quadruplex-forming sequence (QFS) within its 5'-untranslated region. All three γPNA oligomers bind with low nanomolar affinities to an RNA oligonucleotide containing the QFS. However, while all probes inhibit translation with low to midnanomolar IC50 values, the γPNA designed to hybridize to the first two G-tracts of the QFS and adjacent 5'-overhanging nucleotides was 5-6 times more potent than probes directed to either the 3'-end or internal regions of the target at 37 °C. This position-dependent effect was eliminated after the probes and target were preincubated at an elevated temperature prior to translation, demonstrating that kinetic effects exert significant control over quadruplex invasion and translation inhibition. We also found that antisense γPNAs exhibited similarly potent effects against luciferase reporter transcripts bearing QFS motifs having G2, G3, or G4 tracts. Finally, our results indicate that γPNA oligomers exhibit selectivity and/or potency higher than those of other antisense molecules such as standard PNA and 2'-OMe RNA previously reported to target G-quadruplexes in RNA.
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Affiliation(s)
- Stanley N Oyaghire
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Collin J Cherubim
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Cheryl A Telmer
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Joe A Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Marcel P Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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21
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Kormuth KA, Woolford JL, Armitage BA. Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes. Biochemistry 2016; 55:1749-57. [PMID: 26950608 DOI: 10.1021/acs.biochem.6b00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potential guanine (G) quadruplex-forming sequences (QFSs) found throughout the genomes and transcriptomes of organisms have emerged as biologically relevant structures. These G-quadruplexes represent novel opportunities for gene regulation at the DNA and RNA levels. Recently, the definition of functional QFSs has been expanding to include a variety of unconventional motifs, including relatively long loop sequences (i.e., >7 nucleotides) separating adjacent G-tracts. We have identified a QFS within the 25S rDNA gene from Saccharomyces cerevisae that features a long loop separating the two 3'-most G-tracts. An oligonucleotide based on this sequence, QFS3, folds into a stable G-quadruplex in vitro. We have studied the interaction between QFS3 and several loop mutants with a small, homologous (G-rich) peptide nucleic acid (PNA) oligomer that is designed to form a DNA/PNA heteroquadruplex. The PNA successfully invades the DNA quadruplex target to form a stable heteroquadruplex, but with surprisingly high PNA:DNA ratios based on surface plasmon resonance and mass spectrometric results. A model for high stoichiometry PNA-DNA heteroquadruplexes is proposed, and the implications for quadruplex targeting by G-rich PNA are discussed.
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Affiliation(s)
- Karen A Kormuth
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - John L Woolford
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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22
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Gupta P, Rastede EE, Appella DH. Multivalent LKγ-PNA oligomers bind to a human telomere DNA G-rich sequence to form quadruplexes. Bioorg Med Chem Lett 2015; 25:4757-4760. [PMID: 26259805 PMCID: PMC5603266 DOI: 10.1016/j.bmcl.2015.07.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 12/15/2022]
Abstract
We report G-quadruplex formation between peptide nucleic acids (PNAs) composed of (L)Kγ-PNA-G monomers and a known portion of human telomeric DNA that adopts three G3 tracts via intramolecular hydrogen bonding. The resulting complex is a bimolecular PNA-DNA heteroquadruplex. In this Letter, we show that introduction of a γ-modification and addition of a peptide ligand does not disrupt the heteroquadruplex. Although the unmodified PNA1 forms a quadruplex with itself, the γ-substituted PNAs (PNA2-PNA6) do not form G-quadruplexes on their own, at even high concentrations. The selectivity of these PNAs could influence the design of new quadruplex-targeting molecules or allow the quadruplex structure to be used as a scaffold for multivalent display of protein binding ligands.
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Affiliation(s)
- Pankaj Gupta
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA
| | | | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA.
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23
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Gaynutdinov TI, Englund EA, Appella DH, Onyshchenko MI, Neumann RD, Panyutin IG. G-quadruplex formation between G-rich PNA and homologous sequences in oligonucleotides and supercoiled plasmid DNA. Nucleic Acid Ther 2015; 25:78-84. [PMID: 25650982 DOI: 10.1089/nat.2014.0517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Guanine (G)-rich DNA sequences can adopt four-stranded quadruplex conformations that may play a role in the regulation of genetic processes. To explore the possibility of targeted molecular recognition of DNA sequences with short G-rich peptide nucleic acids (PNA) and to assess the strand arrangement in such complexes, we used PNA and DNA with the Oxytricha nova telomeric sequence d(G4T4G4) as a model. PNA probes were complexed with DNA targets in the following forms: single-stranded oligonucleotides, a loop of DNA in a hairpin conformation, and as supercoiled plasmid with the (G4T4G4)/(C4A4C4) insert. Gel-shift mobility assays demonstrated formation of stable hybrid complexes between the homologous G4T4G4 PNA and DNA with multiple modes of binding. Chemical and enzymatic probing revealed sequence-specific and G-quadruplex dependent binding of G4T4G4 PNA to dsDNA. Spectroscopic and electrophoretic analysis of the complex formed between PNA and the synthetic DNA hairpin containing the G4T4G4 loop showed that the stoichiometry of a prevailing complex is three PNA strands per one DNA strand. We speculate how this new PNA-DNA complex architecture can help to design more selective, quadruplex-specific PNA probes.
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Affiliation(s)
- Timur I Gaynutdinov
- 1 Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health , Bethesda, Maryland
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24
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Sequencing and G-quadruplex folding of the canine proto-oncogene KIT promoter region: might dog be used as a model for human disease? PLoS One 2014; 9:e103876. [PMID: 25084283 PMCID: PMC4118953 DOI: 10.1371/journal.pone.0103876] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/03/2014] [Indexed: 12/05/2022] Open
Abstract
Downregulation of gene expression by induction of non-canonical DNA structures at promotorial level is a novel attractive anticancer strategy. In human, two guanine-rich sequences (h_kit1 and h_kit2) were identified in the promotorial region of oncogene KIT. Their stabilization into G-quadruplex structures can find applications in the treatment of leukemias, mastocytosis, gastrointestinal stromal tumor, and lung carcinomas which are often associated to c-kit mis-regulation. Also the most common skin cancer in domestic dog, mast cell tumor, is linked to a mutation and/or to an over-expression of c-kit, thus supporting dog as an excellent animal model. In order to assess if the G-quadruplex mediated mechanism of regulation of c-kit expression is conserved among the two species, herein we cloned and sequenced the canine KIT promoter region and we compared it with the human one in terms of sequence and conformational equilibria in physiologically relevant conditions. Our results evidenced a general conserved promotorial sequence between the two species. As experimentally confirmed, this grants that the conformational features of the canine kit1 sequence are substantially shared with the human one. Conversely, two isoforms of the kit2 sequences were identified in the analyzed dog population. In comparison with the human counterpart, both of them showed an altered distribution among several folded conformations.
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Exploitation of a very small peptide nucleic acid as a new inhibitor of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. BIOMED RESEARCH INTERNATIONAL 2014; 2014:610718. [PMID: 24829907 PMCID: PMC4009323 DOI: 10.1155/2014/610718] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
Computational techniques, and in particular molecular dynamics (MD) simulations, have been successfully used as a complementary technique to predict and analyse the structural behaviour of nucleic acids, including peptide nucleic acid- (PNA-) RNA hybrids. This study shows that a 7-base long PNA complementary to the seed region of miR-509-3p, one of the miRNAs involved in the posttranscriptional regulation of the CFTR disease-gene of Cystic Fibrosis, and bearing suitable functionalization at its N- and C-ends aimed at improving its resistance to nucleases and cellular uptake, is able to revert the expression of the luciferase gene containing the 3′UTR of the gene in A549 human lung cancer cells, in agreement with the MD results that pointed at the formation of a stable RNA/PNA heteroduplex notwithstanding the short sequence of the latter. The here reported results widen the interest towards the use of small PNAs as effective anti-miRNA agents.
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Amato F, Tomaiuolo R, Borbone N, Elce A, Amato J, D'Errico S, De Rosa G, Mayol L, Piccialli G, Oliviero G, Castaldo G. Design, synthesis and biochemical investigation, by in vitro luciferase reporter system, of peptide nucleic acids as new inhibitors of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00257h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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D'Atri V, Borbone N, Amato J, Gabelica V, D'Errico S, Piccialli G, Mayol L, Oliviero G. DNA-based nanostructures: The effect of the base sequence on octamer formation from d(XGGYGGT) tetramolecular G-quadruplexes. Biochimie 2013; 99:119-28. [PMID: 24316277 DOI: 10.1016/j.biochi.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]
Abstract
In a previous work we have demonstrated that the DNA sequence CGGTGGT folds into a higher order G-quadruplex structure (2Q), obtained by the 5'-5' stacking of two unusual G(:C):G(:C):G(:C):G(:C) planar octads belonging to two identical tetra-stranded parallel quadruplexes, when annealed in the presence of ammonium or potassium ions. In the present paper, we discuss the role played by the title nucleosides X and Y (where X and Y stand for A, C, G, or T) on the formation and stability of 2Q structures formed by the XGGYGGT oligodeoxynucleotides. We found that the above mentioned dimerization pathway is not peculiar to the CGGTGGT sequence, but is possible for all the remaining CGGYGGT sequences (with Y = A, C, or G). Furthermore, we have found that the TGGAGGT sequence, despite the absence of the 5'-ending C, is also capable of forming a 2Q-like higher order quadruplex by using a slightly different dimerization interface, as characterized by NMR spectroscopy. To the best of our knowledge, this is the first characterization of a quadruplex multimer formed by an oligodeoxynucleotide presenting a thymine at its 5'-end. Examples of such structures were observed previously only in crystals and in the presence of non-physiological cations. Our results expand the repertoire of DNA quadruplex nanostructures of chosen length and add further complexity to the structural polymorphism of G-rich DNA sequences.
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Affiliation(s)
- Valentina D'Atri
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Jussara Amato
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Valérie Gabelica
- Univ. Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France; INSERM, U869, ARNA laboratory, F-33000 Bordeaux, France
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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Amato J, Stellato MI, Pizzo E, Petraccone L, Oliviero G, Borbone N, Piccialli G, Orecchia A, Bellei B, Castiglia D, Giancola C. PNA as a potential modulator of COL7A1 gene expression in dominant dystrophic epidermolysis bullosa: a physico-chemical study. MOLECULAR BIOSYSTEMS 2013; 9:3166-74. [PMID: 24121392 DOI: 10.1039/c3mb70283a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dominant diseases are single gene disorders occurring in the heterozygous state. The mutated allele exerts a dominant effect because it produces an abnormal polypeptide that interferes with the function of the normal allele product. Peptide Nucleic Acids (PNAs) offer a route for a potential therapy for dominant diseases by selectively silencing the allele carrying the dominant mutation. Here, we have synthesized and studied the properties of a 15-mer PNA fully complementary to the site of the c.5272-38T>A sequence variation, which identifies a recurrent mutant COL7A1 allele causing dominant dystrophic epidermolysis bullosa (DDEB), a mendelian disease characterized by skin blistering. The PNA was conjugated with four lysine residues at the C-terminus and a fluorescent probe at the N-terminus. Physico-chemical results proved the formation of a stable, selective PNA/mutant-DNA heteroduplex in vitro. Intriguingly, when transfected into normal human fibroblasts, the PNA correctly localized in the cell nucleus. Our results open new therapeutic possibilities for patients with DDEB.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
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Gupta A, Lee LL, Roy S, Tanious FA, Wilson WD, Ly DH, Armitage BA. Strand invasion of DNA quadruplexes by PNA: comparison of homologous and complementary hybridization. Chembiochem 2013; 14:1476-84. [PMID: 23868291 PMCID: PMC3856695 DOI: 10.1002/cbic.201300263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Indexed: 12/18/2022]
Abstract
Molecular recognition of DNA quadruplex structures is envisioned to be a strategy for regulating gene expression at the transcriptional level and for in situ analysis of telomere structure and function. The recognition of DNA quadruplexes by peptide nucleic acid (PNA) oligomers is presented here, with a focus on comparing complementary, heteroduplex-forming and homologous, heteroquadruplex-forming PNAs. Surface plasmon resonance and optical spectroscopy experiments demonstrated that the efficacy of a recognition mode depended strongly on the target. Homologous PNA readily invades a quadruplex derived from the promoter regulatory region found upstream of the MYC proto-oncogene to form a heteroquadruplex at high potassium concentration mimicking the intracellular environment, whereas complementary PNA exhibits virtually no hybridization. In contrast, complementary PNA is superior to the homologous in hybridizing to a quadruplex modeled on the human telomere sequence. The results are discussed in terms of the different structural morphologies of the quadruplex targets and the implications for in vivo recognition of quadruplexes by PNAs.
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Affiliation(s)
- Anisha Gupta
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Ling-Ling Lee
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Subhadeep Roy
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Farial A. Tanious
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
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Liang J, Wu YL, Chen BJ, Zhang W, Tanaka Y, Sugiyama H. The C-kit receptor-mediated signal transduction and tumor-related diseases. Int J Biol Sci 2013; 9:435-43. [PMID: 23678293 PMCID: PMC3654492 DOI: 10.7150/ijbs.6087] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 04/15/2013] [Indexed: 02/04/2023] Open
Abstract
As an important member of tyrosine kinase family, c-kit receptor causes specific expression of certain genes, regulates cell differentiation and proliferation, resists cell apoptosis, and plays a key role in tumor occurrence, development, migration and recurrence through activating the downstream signaling molecules following interaction with stem cell factor (SCF). The abnormality of SCF/c-kit signaling pathway is closely related to some certain tumors. The discovery of c-kit receptor-targeted drugs has promoted clinical-related cancer's diagnosis and treatment. In this paper, we review recent research progress on c-kit receptor-mediated signal transduction and its potential therapeutic application as a target in tumor-related diseases.
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Affiliation(s)
- Jing Liang
- Department of Biopharmaceutical Science, College of Pharmaceutical Sciences, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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De Stefano L, Oliviero G, Amato J, Borbone N, Piccialli G, Mayol L, Rendina I, Terracciano M, Rea I. Aminosilane functionalizations of mesoporous oxidized silicon for oligonucleotide synthesis and detection. J R Soc Interface 2013; 10:20130160. [PMID: 23536541 DOI: 10.1098/rsif.2013.0160] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Direct solid phase synthesis of peptides and oligonucleotides (ONs) requires high chemical stability of the support material. In this work, we have investigated the passivation ability of porous oxidized silicon multilayered structures by two aminosilane compounds, 3-aminopropyltriethoxysilane and 3-aminopropyldimethylethoxysilane (APDMES), for optical label-free ON biosensor fabrication. We have also studied by spectroscopic reflectometry the hybridization between a 13 bases ON, directly grown on the aminosilane modified porous oxidized silicon by in situ synthesis, and its complementary sequence. Even if the results show that both devices are stable to the chemicals (carbonate/methanol) used, the porous silica structure passivated by APDMES reveals higher functionalization degree due to less steric hindrance of pores.
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Affiliation(s)
- Luca De Stefano
- National Council of Research, Institute for Microelectronics and Microsystems, Via P. Castellino 111, Naples, Italy
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G-ruption: the third international meeting on G-quadruplex and G-assembly. Biochimie 2012; 94:2475-83. [PMID: 22974982 DOI: 10.1016/j.biochi.2012.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/04/2012] [Indexed: 12/31/2022]
Abstract
A three and a half day conference focusing on nucleic acid structures called G-quadruplexes (G4s) and other guanine-based assemblies was held in Sorrento, Italy (June 28-July 1, 2011) and featured 35 invited talks and over 89 posters. The G-quadruplex field continues to expand at an explosive rate with the emergence of new connections to biology, chemistry, physics, and nanotechnology. Following the trend established by the previous two international G4 meetings, the conference touched upon all these areas and facilitated productive exchanges of ideas between researchers from all over the world.
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Panyutin IG, Onyshchenko MI, Englund EA, Appella DH, Neumann RD. Targeting DNA G-quadruplex structures with peptide nucleic acids. Curr Pharm Des 2012; 18:1984-91. [PMID: 22376112 DOI: 10.2174/138161212799958440] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 11/22/2022]
Abstract
Regulation of genetic functions based on targeting DNA or RNA sequences with complementary oligonucleotides is especially attractive in the post-genome era. Oligonucleotides can be rationally designed to bind their targets based on simple nucleic acid base pairing rules. However, the use of natural DNA and RNA oligonucleotides as targeting probes can cause numerous off-target effects. In addition, natural nucleic acids are prone to degradation in vivo by various nucleases. To address these problems, nucleic acid mimics such as peptide nucleic acids (PNA) have been developed. They are more stable, show less off-target effects, and, in general, have better binding affinity to their targets. However, their high affinity to DNA can reduce their sequence-specificity. The formation of alternative DNA secondary structures, such as the G-quadruplex, provides an extra level of specificity as targets for PNA oligomers. PNA probes can target the loops of G-quadruplex, invade the core by forming PNA-DNA guanine-tetrads, or bind to the open bases on the complementary cytosine-rich strand. Not only could the development of such G-quadruplex-specific probes allow regulation of gene expression, but it will also provide a means to clarify the biological roles G-quadruplex structures may possess.
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Rahman KM, Tizkova K, Reszka AP, Neidle S, Thurston DE. Identification of novel telomeric G-quadruplex-targeting chemical scaffolds through screening of three NCI libraries. Bioorg Med Chem Lett 2012; 22:3006-10. [PMID: 22421021 DOI: 10.1016/j.bmcl.2012.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/26/2022]
Abstract
Thirteen compounds with diverse chemical structures have been identified as selective telomeric G-quadruplex-binding ligands through screening the NCI Diversity Set II, the NCI Natural Products Set II and the NCI Mechanistic Diversity Set libraries containing a total of 2307 members against a human telomeric G-quadruplex using a FRET-based DNA melting assay. These compounds show significant selectivity towards a telomeric G-quadruplex compared to duplex DNA, fall within a molecular weight range of 327-533, and are generally consistent with the Lipinski Rule of Five for drug-likeness. Thus they provide new chemical scaffolds for the development of novel classes of G-quadruplex-targeting agents.
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Petraccone L, Fotticchia I, Cummaro A, Pagano B, Ginnari-Satriani L, Haider S, Randazzo A, Novellino E, Neidle S, Giancola C. The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: Biophysical and molecular modeling studies. Biochimie 2011; 93:1318-27. [DOI: 10.1016/j.biochi.2011.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 05/19/2011] [Indexed: 12/24/2022]
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