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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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2
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Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
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Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
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3
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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] [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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Marzano M, Falanga AP, D'Errico S, Pinto B, Roviello GN, Piccialli G, Oliviero G, Borbone N. New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes. Molecules 2019; 24:molecules24030654. [PMID: 30759875 PMCID: PMC6384581 DOI: 10.3390/molecules24030654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/13/2023] Open
Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG₄T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG₄T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC⁻size-exclusion chromatography (HPLC⁻SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG₄T)₄. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.
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Affiliation(s)
- Maria Marzano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Brunella Pinto
- Dipartimento di Chimica, Università degli Studi di Milano, via Camillo Golgi 19, 20133 Milano, Italy.
| | | | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, via Sergio Pansini 5, 80131 Napoli, Italy.
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
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5
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Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
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6
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Oliviero G, Stornaiuolo M, D'Atri V, Nici F, Yousif AM, D'Errico S, Piccialli G, Mayol L, Novellino E, Marinelli L, Grieco P, Carotenuto A, Noppen S, Liekens S, Balzarini J, Borbone N. Screening Platform toward New Anti-HIV Aptamers Set on Molecular Docking and Fluorescence Quenching Techniques. Anal Chem 2016; 88:2327-34. [PMID: 26810800 DOI: 10.1021/acs.analchem.5b04268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
By using a new rapid screening platform set on molecular docking simulations and fluorescence quenching techniques, three new anti-HIV aptamers targeting the viral surface glycoprotein 120 (gp120) were selected, synthesized, and assayed. The use of the short synthetic fluorescent peptide V35-Fluo mimicking the V3 loop of gp120, as the molecular target for fluorescence-quenching binding affinity studies, allowed one to measure the binding affinities of the new aptamers for the HIV-1 gp120 without the need to obtain and purify the full recombinant gp120 protein. The almost perfect correspondence between the calculated Kd and the experimental EC50 on HIV-infected cells confirmed the reliability of the platform as an alternative to the existing methods for aptamer selection and measuring of aptamer-protein equilibria.
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Affiliation(s)
- Giorgia Oliviero
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Mariano Stornaiuolo
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Valentina D'Atri
- University of Bordeaux , IECB, ARNA laboratory, Pessac, 33600, France.,INSERM , U869, ARNA laboratory, Bordeaux, 33000, France
| | - Fabrizia Nici
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ali Munaim Yousif
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Stefano D'Errico
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Gennaro Piccialli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy.,CNR , Institute of Protein Biochemistry, Napoli, 80131, Italy
| | - Luciano Mayol
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ettore Novellino
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Luciana Marinelli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Paolo Grieco
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Alfonso Carotenuto
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Sam Noppen
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Sandra Liekens
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Jan Balzarini
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Nicola Borbone
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
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7
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Grijalvo S, Alagia A, Gargallo R, Eritja R. Cellular uptake studies of antisense oligonucleotides using G-quadruplex-nanostructures. The effect of cationic residue on the biophysical and biological properties. RSC Adv 2016. [DOI: 10.1039/c6ra15336d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cellular uptake studies of G-quadruplex constructs having the Tetrahymena telomeric repeat sequence d(TGGGGT) modified with amino and guanidinium residues at the 3′-termini and an antisense oligonucleotide at 5′-termini were studied.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
| | - Adele Alagia
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
| | - Raimundo Gargallo
- University of Barcelona
- Department of Chemical Engineering and Analytical Chemistry
- E-08028 Barcelona
- Spain
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC)
- E-08034 Barcelona
- Spain
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine (CIBER-BBN)
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8
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Hui WQB, Sherman JC. Self-assembly of a thymine quartet and quadruplex via an organic template. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Musumeci D, Roviello GN, Montesarchio D. An overview on HMGB1 inhibitors as potential therapeutic agents in HMGB1-related pathologies. Pharmacol Ther 2013; 141:347-57. [PMID: 24220159 DOI: 10.1016/j.pharmthera.2013.11.001] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/25/2013] [Indexed: 12/13/2022]
Abstract
HMGB1 (High-Mobility Group Box-1) is a nuclear protein that acts as an architectural chromatin-binding factor involved in the maintenance of nucleosome structure and regulation of gene transcription. It can be released into the extracellular milieu from immune and non-immune cells in response to various stimuli. Extracellular HMGB1 contributes to the pathogenesis of numerous chronic inflammatory and autoimmune diseases, including sepsis, rheumatoid arthritis, atherosclerosis, chronic kidney disease, systemic lupus erythematosus (SLE), as well as cancer pathogenesis. Interaction of released HMGB1 with the cell-surface receptor for advanced glycation end products (RAGE) is one of the main signaling pathways triggering these diseases. It has been also demonstrated that the inhibition of the HMGB1-RAGE interaction represents a promising approach for the modulation of the inflammatory and tumor-facilitating activity of HMGB1. In this review we describe various approaches recently proposed in the literature to inhibit HMGB1 and the related inflammatory processes, especially focusing on the block of RAGE-HMGB1 signaling. Several strategies are based on molecules which mainly interact with RAGE as competitive antagonists of HMGB1. As an alternative, encouraging results have been obtained with HMGB1-targeting, leading to the identification of compounds that directly bind to HMGB1, ranging from small natural or synthetic molecules, such as glycyrrhizin and gabexate mesilate, to HMGB1-specific antibodies, peptides, proteins as well as bent DNA-based duplexes. Future perspectives are discussed in the light of the overall body of knowledge acquired by a large number of research groups operating in different but related fields.
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Affiliation(s)
- Domenica Musumeci
- Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", via Cintia 21, Complesso Universitario di Monte Sant'Angelo, I-80126 Napoli, Italy.
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, I-80134 Napoli, Italy
| | - Daniela Montesarchio
- Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", via Cintia 21, Complesso Universitario di Monte Sant'Angelo, I-80126 Napoli, Italy
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10
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Multitasking Water-Soluble Synthetic G-Quartets: From Preferential RNA-Quadruplex Interaction to Biocatalytic Activity. Chemistry 2013; 19:12739-47. [DOI: 10.1002/chem.201300791] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Indexed: 01/21/2023]
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11
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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12
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D'Atri V, Oliviero G, Amato J, Borbone N, D'Errico S, Mayol L, Piccialli V, Haider S, Hoorelbeke B, Balzarini J, Piccialli G. New anti-HIV aptamers based on tetra-end-linked DNA G-quadruplexes: effect of the base sequence on anti-HIV activity. Chem Commun (Camb) 2013; 48:9516-8. [PMID: 22898884 DOI: 10.1039/c2cc34399a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This communication reports on the synthesis and biophysical, biological and SAR studies of a small library of new anti-HIV aptamers based on the tetra-end-linked G-quadruplex structure. The new aptamers showed EC(50) values against HIV-1 in the range of 0.04-0.15 μM as well as affinities for the HIV-1 gp120 envelope in the same order of magnitude.
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Affiliation(s)
- Valentina D'Atri
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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13
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Borbone N, Bucci M, Oliviero G, Morelli E, Amato J, D'Atri V, D'Errico S, Vellecco V, Cirino G, Piccialli G, Fattorusso C, Varra M, Mayol L, Persico M, Scuotto M. Investigating the role of T7 and T12 residues on the biological properties of thrombin-binding aptamer: enhancement of anticoagulant activity by a single nucleobase modification. J Med Chem 2012; 55:10716-28. [PMID: 23126678 DOI: 10.1021/jm301414f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An acyclic pyrimidine analogue, containing a five-member cycle fused on the pyrimidine ring, was synthesized and introduced at position 7 or 12 of the 15-mer oligodeoxynucleotide GGTTGGTGTGGTTGG, known as thrombin-binding aptamer (TBA). Characterization by 1H NMR and CD spectroscopies of the resulting aptamers, TBA-T7b and TBA-T12b, showed their ability to fold into the typical antiparallel chairlike G-quadruplex structure formed by TBA. The apparent CD melting temperatures indicated that the introduction of the acyclic residue, mainly at position 7, improves the thermal stability of resulting G-quadruplexes with respect to TBA. The anticoagulant activity of the new molecules was then valued in PT assay, and it resulted that TBA-T7b is more potent than TBA in prolonging clotting time. On the other hand, in purified fibrinogen assay the thrombin inhibitory activity of both modified sequences was lower than that of TBA using human enzyme, whereas the potency trend was again reversed using bovine enzyme. Obtained structure-activity relationships were investigated by structural and computational studies. Taken together, these results reveal the active role of TBA residues T7 and T12 and the relevance of some amino acids located in the anion binding exosite I of the protein in aptamer-thrombin interaction.
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Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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Hui BWQ, Sherman JC. A Template-Assembled Synthetic U-Quadruplex. Chembiochem 2012; 13:1865-8. [DOI: 10.1002/cbic.201200442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Indexed: 01/23/2023]
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15
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Hui BWQ, Sherman JC. Synthesis and characterization of a template-assembled synthetic U-quartet. Chem Commun (Camb) 2012; 48:109-11. [DOI: 10.1039/c1cc15608j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Rusciano G, De Luca AC, Pesce G, Sasso A, Oliviero G, Amato J, Borbone N, D'Errico S, Piccialli V, Piccialli G, Mayol L. Label-free probing of G-quadruplex formation by surface-enhanced Raman scattering. Anal Chem 2011; 83:6849-55. [PMID: 21780762 DOI: 10.1021/ac201783h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, we establish the use of surface-enhanced Raman scattering (SERS) as a label-free analytical technique for the direct detection of G-quadruplex formation. In particular, we demonstrate that SERS analysis allows the evaluation of the relative stability of G quadruplexes that differ for the number of G tetrads and investigate several structural features of quadruplexes, such as the orientation of glycosidic bonds, the identification of distortions in the sugar-phosphate backbone, and the degree of hydrogen-bond solvation. Herein, the fluctuation of the SERS spectra, due to the specific interaction of vibrational modes with the SERS-active substrate, is quantitatively analyzed before and after quadruplex formation. The results of this study suggest a perpendicular orientation of the quadruplexes (with or without the 3'-tetra end linker) with respect to the silver colloidal surface, which opens new perspectives for the use of SERS as a label-free analytical tool for the study of the binding mode between quadruplexes and their ligands.
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Affiliation(s)
- Giulia Rusciano
- Dipartimento di Scienze Fisiche, Complesso Universitario, Universitá di Napoli Federico II, Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy.
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17
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Nikan M, Bare GA, Sherman JC. Synthesis of a water-soluble triazole-linked cavitand–guanosine conjugate. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Oliviero G, Amato J, Borbone N, D'Errico S, Galeone A, Mayol L, Haider S, Olubiyi O, Hoorelbeke B, Balzarini J, Piccialli G. Tetra-end-linked oligonucleotides forming DNA G-quadruplexes: a new class of aptamers showing anti-HIV activity. Chem Commun (Camb) 2010; 46:8971-3. [PMID: 20972507 DOI: 10.1039/c0cc02866e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biophysical and biological properties of unprecedented anti-HIV aptamers are presented. The most active aptamer (1L) shows a significant affinity to the HIV protein gp120.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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19
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Sannohe Y, Sugiyama H. Overview of formation of G-quadruplex structures. ACTA ACUST UNITED AC 2010; Chapter 17:Unit 17.2.1-17. [PMID: 20201027 DOI: 10.1002/0471142700.nc1702s40] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There are many structures that can be adopted by nucleic acids other than the Watson-Crick duplex. In particular, a noncanonical four-stranded topology, called a G-quadruplex, is of great interest because of its roles in key biological processes such as the maintenance of telomeres and regulation of gene transcription. This review describes the condition for forming the G-quadruplex structure, G-quadruplex-forming sequences, and methods for studying the structures.
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Oliviero G, Borbone N, Amato J, D'Errico S, Galeone A, Piccialli G, Varra M, Mayol L. Synthesis of quadruplex-forming tetra-end-linked oligonucleotides: effects of the linker size on quadruplex topology and stability. Biopolymers 2009; 91:466-77. [PMID: 19189376 DOI: 10.1002/bip.21153] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
G-quadruplexes are characteristic structural arrangements of guanine-rich DNA sequences that abound in regions with relevant biological significance. These structures are highly polymorphic differing in the number and polarity of the strands, loop composition, and conformation. Furthermore, the cation species present in solution strongly influence the topology of the G-quadruplexes. Recently, we reported the synthesis and structural studies of new G-quadruplex forming oligodeoxynucleotides (ODNs) in which the 3'- and/or the 5'-ends of four ODN strands are linked together by a non-nucleotidic tetra-end-linker (TEL). These TEL-ODN analogs having the sequence TGGGGT are able to form parallel G-quadruplexes characterized by a remarkable high thermal stability. We report here an investigation about the influence of the reduction of the TEL size on the molecularity, topology, and stability of the resulting TEL-G-quadruplexes using a combination of circular dichroism (CD), CD melting, (1)H NMR spectroscopy, gel electrophoresis, and molecular modeling data. We found that all TEL-(TGGGGT)(4) analogs, regardless the TEL size and the structural orientation of the ODN branches, formed parallel TEL-G-quadruplexes. The molecular modeling studies appear to be consistent with the experimental CD and NMR data revealing that the G-quadruplexes formed by TEL-ODNs having the longer TEL (L1-4) are more stable than the corresponding G-quadruplexes having the shorter TEL (S1-4). The relative stability of S1-4 was also reported. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 466-477, 2009.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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21
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Franceschin M. G‐Quadruplex DNA Structures and Organic Chemistry: More Than One Connection. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801196] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza – Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy, Fax: +39‐06‐4991‐3841
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22
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Borbone N, Oliviero G, Amato J, D'Errico S, Galeone A, Piccialli G, Mayol L. Synthesis and characterization of tetra-end linked oligonucleotides capable of forming monomolecular G-quadruplexes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1231-6. [PMID: 18066758 DOI: 10.1080/15257770701528172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The chemical synthesis of two new G-rich Tetra-End-Linked-oligodeoxyribonucleotides (TEL-ODNs) as well as (1)H-NMR and CD spectra of the corresponding monomolecular quadruplexes (IVa and IVb) has been reported. The new TEL-ODNs, characterized by the presence of short branches in the linker moiety, could be very useful for the achievement of monomolecular quadruplexes with predetermined strand orientation.
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Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli Federico II, via Domenico Montesano 49, Naples 80131, Italy.
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25
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Oliviero G, Amato J, Borbone N, Galeone A, Petraccone L, Varra M, Piccialli G, Mayol L. Synthesis and characterization of monomolecular DNA G-quadruplexes formed by tetra-end-linked oligonucleotides. Bioconjug Chem 2006; 17:889-98. [PMID: 16848394 DOI: 10.1021/bc060009b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanine-rich DNA sequences are widely dispersed in the eukaryotic genome and are abundant in regions with relevant biological significance. They can form quadruplex structures stabilized by guanine quartets. These structures differ for number and strand polarity, loop composition, and conformation. We report here the syntheses and the structural studies of a set of interconnected d(TG(4)T) fragments which are tethered, with different orientations, to a tetra-end-linker in an attempt to force the formation of specific four-stranded DNA quadruplex structures. Two synthetic strategies have been used to obtain oligodeoxyribonucleotide (ODN) strands linked with their 3'- or 5'-ends to each of the four arms of the linker. The first approach allowed the synthesis of tetra-end-linked ODN (TEL-ODN) containing the four ODN strands with a parallel orientation, while the latter synthetic pathway led to the synthesis of TEL-ODNs each containing antiparallel ODN pairs. The influence of the linker at 3'- or 5'-ODN, on the quadruplex typology and stability, in the presence of sodium or potassium ions, has been investigated by circular dichroism (CD), CD thermal denaturation, (1)H NMR experiments at variable temperature, and molecular modeling. All synthesized TEL-ODNs formed parallel G-quadruplex structures. Particularly, the TEL-ODN containing all parallel ODN tracts formed very stable parallel G-quadruplex complexes, whereas the TEL-ODNs containing antiparallel ODN pairs led to relatively less stable parallel G-quadruplexes. The molecular modeling data suggested that the above antiparallel TEL-ODNs can adopt parallel G-quadruplex structures thanks to a considerable folding of the tetra-end-linker around the whole quadruplex scaffold.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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26
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Petraccone L, Martino L, Duro I, Oliviero G, Borbone N, Piccialli G, Giancola C. Physico-chemical analysis of G-quadruplex containing bunch-oligonucleotides. Int J Biol Macromol 2006; 40:242-7. [PMID: 16979232 DOI: 10.1016/j.ijbiomac.2006.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 07/28/2006] [Accepted: 07/28/2006] [Indexed: 11/29/2022]
Abstract
A growing number of evidences suggest that DNA G-quadruplex structures play an important role in many relevant biological processes. The introduction of chemical modifications in quadruplex structures could enhance the in vivo biological activity. The correlation between the physico-chemical properties and chemical modifications represents an essential step toward the de novo design of quadruplex forming oligonucleotides for biomedical applications. We report the physico-chemical characterisation of a quadruplex formed by a bunch of four d(TG4T) oligonucleotides whose 3'-ends are linked together by a tetra-branched linker. The study was performed by circular dichroism, gel electrophoresis and molecular modelling techniques. The data indicate an high stability for this kind of quadruplex and add some information on the role of the tetra-branched linker on the quadruplex stability.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Farmaceutiche, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
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27
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Oliviero G, Amato J, Borbone N, Galeone A, Varra M, Piccialli G, Mayol L. Synthesis and characterization of DNA quadruplexes containing T-tetrads formed by bunch-oligonucleotides. Biopolymers 2006; 81:194-201. [PMID: 16235233 DOI: 10.1002/bip.20399] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The solid phase syntheses of the bunch oligonucleotides and based on the sequences of the natural oligodeoxynucleotides (ODNs) d(TG2TG2C) and d(CG2TG2T), respectively, attached to a non-nucleotidic tetrabranched linker, are reported. Bunch-ODNs and were shown to form more stable monomolecular parallel G-quadruplexes and when compared with their tetramolecular counterparts [d(TG2TG2C)]4 and [d(CG2TG2T)]4, respectively. The structure and stability of all the synthesized complexes have been investigated by circular dichroism (CD), CD thermal denaturation experiments, and 1H-NMR (nuclear magnetic resonance) experiments at variable temperatures. Particularly, the spectroscopic data confirmed that 1 adopts a T-tetrad containing parallel-stranded quadruplex structure as in the tetramolecular complex.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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Oliviero G, Amato J, Borbone N, Galeone A, Varra M, Piccialli G, Mayol L. Unusual monomolecular DNA quadruplex structures using bunch-oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:739-41. [PMID: 16248027 DOI: 10.1081/ncn-200060048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The chemical synthesis of several G-rich bunch-oligonucleotides and the structural characterization of the corresponding monomolecular G-quadruplexes (I-IV) have been reported. The synthetic method allow the achievement of monomolecular DNA quadruplex structures having unusual and predeterminable oligodeoxyribonucleotide (ODN) strand orientation.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli Federico II, Napoli, Italy.
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29
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Borbone N, Oliviero G, Galeone A, Piccialli G, Varra M, Mayol L. A bunch-oligonucleotide forming stable monomolecular quadruplex containing a T-tetrad. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:443-6. [PMID: 16247967 DOI: 10.1081/ncn-200059989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The chemical synthesis of bunch-ODN I and II prone to form quadruplex structures containing G-and T-tetrads has been reported. Structural studies were performed by 1H-NMR and CD melting experiments.
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Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Napoli, Italy.
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