1
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Benigno D, Navarro N, Aviñó A, Esposito V, Galeone A, Virgilio A, Fàbrega C, Eritja R. Aptamer-Drug conjugates for a targeted and synergistic anticancer Response: Exploiting T30923-5-fluoro-2'-deoxyuridine (INT-FdU) derivatives. Eur J Pharm Biopharm 2024:114354. [PMID: 38852755 DOI: 10.1016/j.ejpb.2024.114354] [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: 03/26/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
One of the most appealing approaches for cancer treatment is targeted therapy, which is based on the use of drugs able to target cancer cells without affecting normal ones. This strategy lets to overcome the major limitation of conventional chemotherapy, namely the lack of specificity of anticancer drugs, which often leads to severe side effects, decreasing the therapy effectiveness. Delivery of cell-killing substances to tumor cells is one-way targeted drug therapy can work. Generally, monoclonal antibodies are combined with chemotherapeutic drugs, allowing cellular uptake through the binding to their targets on the surface of cancer cells. Aptamer-drug conjugates represent a promising alternative solution to antibodies to minimize off-target effects, considering the remarkable selective binding capabilities of aptamers. In this study, to enhance the therapeutic efficacy of the antineoplastic agent 5-fluoro-2'-deoxyuridine (FdU) in various cancer cells, we focused on the development of a novel conjugate using the antiproliferative aptamer T30923 (INT) as a drug vehicle. Three derivatives composed of T30923 conjugated with a different number of FdU units were synthesized, and their structural and biological properties were thoroughly characterized, highlighting their potential for targeted and synergistic anticancer responses.
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Affiliation(s)
- Daniela Benigno
- Department of Pharmacy, University of Naples Federico II, Napoli 80131, Italy
| | - Natalia Navarro
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Nucleic Acids Chemistry Group, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain
| | - Anna Aviñó
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Nucleic Acids Chemistry Group, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Napoli 80131, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Napoli 80131, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Napoli 80131, Italy.
| | - Carme Fàbrega
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Nucleic Acids Chemistry Group, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain.
| | - Ramon Eritja
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Nucleic Acids Chemistry Group, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain.
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2
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El Deeb S, Al-Harrasi A, Khan A, Al-Broumi M, Al-Thani G, Alomairi M, Elumalai P, Sayed RA, Ibrahim AE. Microscale thermophoresis as a powerful growing analytical technique for the investigation of biomolecular interaction and the determination of binding parameters. Methods Appl Fluoresc 2022; 10. [PMID: 35856854 DOI: 10.1088/2050-6120/ac82a6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022]
Abstract
The in vitro panel of technologies to address biomolecular interactions are in play, however microscale thermophoresis is continuously increasing in use to represent a key player in this arena. This review highlights the usefulness of microscale thermophoresis in the determination of molecular and biomolecular affinity interactions. This work reviews the literature from January 2016 to January 2022 about microscale thermophoresis. It gives a summarized overview about both the state-of the art and the development in the field of microscale thermophoresis. The principle of microscale thermophoresis is also described supported with self-created illustrations. Moreover, some recent advances are mentioned that showing application of the technique in investigating biomolecular interactions in different fields. Finally, advantages as well as drawbacks of the technique in comparison with other competing techniques are summarized.
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Affiliation(s)
- Sami El Deeb
- Technische Universitat Braunschweig, Braunschweig, Braunschweig, Niedersachsen, 38106, GERMANY
| | | | - Ajmal Khan
- University of Nizwa, Nizwa, Nizwa, 616, OMAN
| | | | | | | | | | - Rania A Sayed
- Pharmaceutical analytical chemistry department, Zagazig University, Zagazig, Zagazig, 44519, EGYPT
| | - Adel Ehab Ibrahim
- Pharmaceutical Analytical Chemistry, Port Said University, Port Said, Port Said, 42526, EGYPT
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3
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Virgilio A, Pecoraro A, Benigno D, Russo A, Russo G, Esposito V, Galeone A. Antiproliferative Effects of the Aptamer d(GGGT) 4 and Its Analogues with an Abasic-Site Mimic Loop on Different Cancer Cells. Int J Mol Sci 2022; 23:ijms23115952. [PMID: 35682635 PMCID: PMC9181107 DOI: 10.3390/ijms23115952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/24/2022] Open
Abstract
In this paper, we study the T30923 antiproliferative potential and the contribution of its loop residues in six different human cancer cell lines by preparing five T30923 variants using the single residue replacement approach of loop thymidine with an abasic site mimic (S). G-rich oligonucleotides (GRO) show interesting anticancer properties because of their capability to adopt G-quadruplex structures (G4s), such as the G4 HIV-1 integrase inhibitor T30923. Considering the multi-targeted effects of G4-aptamers and the limited number of cancer cell lines tested, particularly for T30923, it should be important to find a suitable tumor line, in addition to considering that the effects also strictly depend on G4s. CD, NMR and non-denaturating polyacrylamide gel electrophoresis data clearly show that all modified ODNs closely resemble the dimeric structure of parallel G4s’ parent aptamer, keeping the resistance in biological environments substantially unchanged, as shown by nuclease stability assay. The antiproliferative effects of T30923 and its variants are tried in vitro by MTT assays, showing interesting cytotoxic activity, depending on time and dose, for all G4s, especially in MDA-MB-231 cells with a reduction in cell viability approximately up to 30%. Among all derivatives, QS12 results are the most promising, showing more pronounced cytotoxic effects both in MDA-MB-231 and Hela cells, with a decrease in cell viability from 70% to 60%. In summary, the single loop residue S substitution approach may be useful for designing antiproliferative G4s, considering that most of them, characterized by single residue loops, may be able to bind different targets in several cancer cell pathways. Generally, this approach could be of benefit by revealing some minimal functional structures, stimulating further studies aimed at the development of novel anticancer drugs.
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4
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Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules 2022; 12:biom12050648. [PMID: 35625576 PMCID: PMC9138358 DOI: 10.3390/biom12050648] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.
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5
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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6
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Virgilio A, Benigno D, Pecoraro A, Russo A, Russo G, Esposito V, Galeone A. Exploring New Potential Anticancer Activities of the G-Quadruplexes Formed by [(GTG 2T(G 3T) 3] and Its Derivatives with an Abasic Site Replacing Single Thymidine. Int J Mol Sci 2021; 22:ijms22137040. [PMID: 34208896 PMCID: PMC8268168 DOI: 10.3390/ijms22137040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
In this paper, we report our investigations on five T30175 analogues, prepared by replacing sequence thymidines with abasic sites (S) one at a time, in comparison to their natural counterpart in order to evaluate their antiproliferative potential and the involvement of the residues not belonging to the central core of stacked guanosines in biological activity. The collected NMR (Nuclear Magnetic Resonance), CD (Circular Dichroism), and PAGE (Polyacrylamide Gel Electrophoresis) data strongly suggest that all of them adopt G-quadruplex (G4) structures strictly similar to that of the parent aptamer with the ability to fold into a dimeric structure composed of two identical G-quadruplexes, each characterized by parallel strands, three all-anti-G-tetrads and four one-thymidine loops (one bulge and three propeller loops). Furthermore, their antiproliferative (MTT assay) and anti-motility (wound healing assay) properties against lung and colorectal cancer cells were tested. Although all of the oligodeoxynucleotides (ODNs) investigated here exhibited anti-proliferative activity, the unmodified T30175 aptamer showed the greatest effect on cell growth, suggesting that both its characteristic folding in dimeric form and its presence in the sequence of all thymidines are crucial elements for antiproliferative activity. This straightforward approach is suitable for understanding the critical requirements of the G-quadruplex structures that affect antiproliferative potential and suggests its application as a starting point to facilitate the reasonable development of G-quadruplexes with improved anticancer properties.
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7
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Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol. Mikrochim Acta 2020; 187:505. [PMID: 32815083 DOI: 10.1007/s00604-020-04471-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.
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8
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Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA. G-quadruplex structures bind to EZ-Tn5 transposase. Biochimie 2020; 177:190-197. [PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
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Affiliation(s)
- Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Eng Wee Chua
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Jennifer Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.
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9
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Esposito V, Esposito F, Pepe A, Gomez Monterrey I, Tramontano E, Mayol L, Virgilio A, Galeone A. Probing the Importance of the G-Quadruplex Grooves for the Activity of the Anti-HIV-Integrase Aptamer T30923. Int J Mol Sci 2020; 21:ijms21165637. [PMID: 32781637 PMCID: PMC7460552 DOI: 10.3390/ijms21165637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
In this paper, we report studies concerning four variants of the G-quadruplex forming anti-HIV-integrase aptamer T30923, in which specific 2′-deoxyguanosines have been singly replaced by 8-methyl-2′-deoxyguanosine residues, with the aim to exploit the methyl group positioned in the G-quadruplex grooves as a steric probe to investigate the interaction aptamer/target. Although, the various modified aptamers differ in the localization of the methyl group, NMR, circular dichroism (CD), electrophoretic and molecular modeling data suggest that all of them preserve the ability to fold in a stable dimeric parallel G-quadruplex complex resembling that of their natural counterpart T30923. However, the biological data have shown that the T30923 variants are characterized by different efficiencies in inhibiting the HIV-integrase, thus suggesting the involvement of the G-quadruplex grooves in the aptamer/target interaction.
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Affiliation(s)
- Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (V.E.); (I.G.M.); (L.M.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09045 Monserrato (CA), Italy; (F.E.); (E.T.)
| | - Antonietta Pepe
- Department of Science, University of Basilicata, 85100 Potenza, Italy;
| | - Isabel Gomez Monterrey
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (V.E.); (I.G.M.); (L.M.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09045 Monserrato (CA), Italy; (F.E.); (E.T.)
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (V.E.); (I.G.M.); (L.M.)
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (V.E.); (I.G.M.); (L.M.)
- Correspondence: (A.V.); (A.G.)
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (V.E.); (I.G.M.); (L.M.)
- Correspondence: (A.V.); (A.G.)
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10
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Bošković F, Zhu J, Chen K, Keyser UF. Monitoring G-Quadruplex Formation with DNA Carriers and Solid-State Nanopores. NANO LETTERS 2019; 19:7996-8001. [PMID: 31577148 DOI: 10.1021/acs.nanolett.9b03184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G-quadruplexes (Gqs) are guanine-rich DNA structures formed by single-stranded DNA. They are of paramount significance to gene expression regulation, but also drug targets for cancer and human viruses. Current ensemble and single-molecule methods require fluorescent labels, which can affect Gq folding kinetics. Here we introduce, a single-molecule Gq nanopore assay (smGNA) to detect Gqs and kinetics of Gq formation. We use ∼5 nm solid-state nanopores to detect various Gq structural variants attached to designed DNA carriers. Gqs can be identified by localizing their positions along designed DNA carriers, establishing smGNA as a tool for Gq mapping. In addition, smGNA allows for discrimination of (un)folded Gq structures, provides insights into single-molecule kinetics of Gq folding, and probes quadruplex-to-duplex structural transitions. smGNA can elucidate the formation of Gqs at the single-molecule level without labeling and has potential implications on the study of these structures both in single-stranded DNA and in genomic samples.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , JJ Thompson Avenue , Cambridge CB3 0HE , United Kingdom
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11
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Facile detection of melamine by a FAM-aptamer-G-quadruplex construct. Anal Bioanal Chem 2019; 411:2521-2530. [PMID: 30863884 DOI: 10.1007/s00216-019-01688-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/26/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022]
Abstract
The development of a novel method for melamine detection that uses a FAM-aptamer-G-quadruplex construct due to the efficient quenching ability of an aptamer-linked G-quadruplex is reported herein. The construct, which is labeled with the fluorescent dye 6-carboxyfluorescein (FAM), consists of two parts: a melamine-binding aptamer and a G-rich sequence that can form a G-quadruplex structure. Because of the specific recognition of melamine by the T-rich aptamer, this aptamer folds into a hairpin structure in the presence of melamine, which draws the G-quadruplex closer to the FAM fluorophore, leading to the quenching of the fluorescence of FAM. Thus, a highly sensitive and selective fluorescence strategy for assaying melamine was established. Under optimal conditions, the fluorescence quenching is proportional to the concentration of melamine within the range 10-90 nM, and the method has a detection limit of 6.32 nM. Further application of the method to plastic cup samples suggested that it permitted recoveries of between 97.15% ± 1.02 and 101.92% ± 2.07. The detected amounts of melamine spiked into the plastic cup samples and the corresponding amounts measured by HPLC were in good accordance, indicating that this fluorescent method is reliable and practical. Owing to its high sensitivity, excellent selectivity, and convenient procedure, this strategy represents a promising alternative method of melamine screening. Graphical abstract.
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12
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Yoon S, Rossi JJ. Aptamers: Uptake mechanisms and intracellular applications. Adv Drug Deliv Rev 2018; 134:22-35. [PMID: 29981799 PMCID: PMC7126894 DOI: 10.1016/j.addr.2018.07.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/06/2018] [Accepted: 07/04/2018] [Indexed: 01/10/2023]
Abstract
The structural flexibility and small size of aptamers enable precise recognition of cellular elements for imaging and therapeutic applications. The process by which aptamers are taken into cells depends on their targets but is typically clathrin-mediated endocytosis or macropinocytosis. After internalization, most aptamers are transported to endosomes, lysosomes, endoplasmic reticulum, Golgi apparatus, and occasionally mitochondria and autophagosomes. Intracellular aptamers, or “intramers,” have versatile functions ranging from intracellular RNA imaging, gene regulation, and therapeutics to allosteric modulation, which we discuss in this review. Immune responses to therapeutic aptamers and the effects of G-quadruplex structure on aptamer function are also discussed.
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13
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Mercurio FA, Pirone L, Di Natale C, Marasco D, Pedone EM, Leone M. Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2. Bioorg Chem 2018; 80:602-610. [PMID: 30036816 DOI: 10.1016/j.bioorg.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Abstract
Sam (Sterile alpha motif) domains represent small helical protein-protein interaction modules which play versatile functions in different cellular processes. The Sam domain from the EphA2 receptor binds the Sam domain of the lipid phosphatase Ship2 and this interaction modulates receptor endocytosis and degradation primarily generating pro-oncogenic effects in cell. To identify molecule antagonists of the EphA2-Sam/Ship2-Sam complex with anti-cancer activity, we focused on hydrocarbon helical stapled peptides. EphA2-Sam and one of its interactors (i.e., the first Sam domain of the adaptor protein Odin) were used as model systems for peptide design. Increase in helicity in the stapled peptides, with respect to the corresponding linear/native-like regions, was proved by structural studies conducted through CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance). Interestingly, interaction assays by means of NMR, SPR (Surface Plasmon Resonance) and MST (MicroScale Thermophoresis) techniques led to the discovery of a novel ligand of Ship2-Sam.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | | | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy; University of Naples Federico II, Department of Pharmacy, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy.
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14
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Samokhvalov AV, Safenkova IV, Eremin SA, Zherdev AV, Dzantiev BB. Measurement of (Aptamer–Small Target) KD Using the Competition between Fluorescently Labeled and Unlabeled Targets and the Detection of Fluorescence Anisotropy. Anal Chem 2018; 90:9189-9198. [DOI: 10.1021/acs.analchem.8b01699] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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15
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Improvement of the activity of the anti-HIV-1 integrase aptamer T30175 by introducing a modified thymidine into the loops. Sci Rep 2018; 8:7447. [PMID: 29749406 PMCID: PMC5945619 DOI: 10.1038/s41598-018-25720-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/24/2018] [Indexed: 11/12/2022] Open
Abstract
In this paper, we report our investigations on analogues of the anti-human immunodeficiency virus type 1 (HIV-1) integrase (IN) aptamer T30175 in which the individual thymidines forming the loops were replaced by 5-hydroxymethyl-2′-deoxyuridine residues (H). Circular dichroism, nuclear magnetic resonance and gel electrophoresis investigations clearly indicated that all the modified aptamers preserve the ability to form the original 5′-5′ end-stacked head-to-head dimeric G-quadruplex structure, in which each G-quadruplex adopts a parallel arrangement and is characterized by three G-tetrads, three propeller loops and one bulge-loop. All the modified aptamers were tested in an IN inhibition LEDGF-independent assay. While the modified aptamers INTB-H13 and INTB-H17 showed IC50 values comparable with that of the parent aptamer (INTB-nat), analogues INTB-H2, INTB-H5 and, to a lesser extent, INTB-H9 showed a higher ability to inhibit the HIV IN than the unmodified aptamer. Molecular modelling studies evaluating the aptamer/HIV IN interaction highlighted the ability of the modified thymidines to establish several contacts with the target protein. All the data point to the importance of loops in the aptamer/target interaction and suggest that the site-specific replacement of loop residues with commercially available analogues can be considered a straightforward strategy to improve the biological activities of several G-quadruplex aptamers.
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16
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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The essential player in adipogenesis GRP78 is a novel KCTD15 interactor. Int J Biol Macromol 2018; 115:469-475. [PMID: 29665387 DOI: 10.1016/j.ijbiomac.2018.04.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 01/08/2023]
Abstract
KCTD15 is a member of the K+ Channel Tetramerization Domain family, implicated in crucial physio-pathological processes. Recent evidences suggest that KCTD15 is an obesity-linked protein in humans and its Drosophila homologue is involved in food uptake. KCTD15 molecular mechanism in these processes is still unknown. To fill this gap, KCTD15 was biophysically characterized showing a folded, pentameric region endowed with a remarkable thermal stability. Notably, the C-terminal domain significantly contributes to the stabilization of the BTB N-terminal domain. The availability of large amount of stable recombinant protein also made possible a functional proteomic approach in 3T3-L1 cells to search for novel KCTD15 interactors. These investigations led to the discovery that GRP78 is a KCTD15 partner in all the adipogenesis phases. Our data clearly prove the physical interaction of the two proteins and also indicate that GRP78 plays an active role in the stabilization of KCTD15. Furthermore, the presence in Drosophila of a GRP78 homologue corroborates the physiological role played by the complex KCTD15-GRP78 in the adipogenesis process and indicates that it is evolutionarily conserved. Present results also suggest that KCTD15 may be a new target for obesity control.
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18
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Huang S, Liang Y, Cui J, Xie J, Liu Y, Hu B, Xiao Q. Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT) 4 G-quadruplex aptamer. Steroids 2018; 132:46-55. [PMID: 29458054 DOI: 10.1016/j.steroids.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/19/2022]
Abstract
Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)4 G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)4 G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Yu Liang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Jianguo Cui
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China.
| | - Jiangning Xie
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Yi Liu
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Baoqing Hu
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Qi Xiao
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China.
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Shao C, Liu Y, Qi J, Su Y, Chen Y, Xu H, Lin Z, Guan H. Real-time detection of the interaction between alpha-fetoprotein and its ssDNA aptamer by dual polarization interferometry. NEW J CHEM 2018. [DOI: 10.1039/c8nj04200d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A real-time and label-free strategy to understand the interaction between biomarkers and ssDNA aptamers.
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Affiliation(s)
- Chenggang Shao
- The Department of Gastroenterology and Hepatology
- The First Affiliated Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
- Center of Scientific Research
| | - Yuxin Liu
- Center of Scientific Research
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Jinxia Qi
- Center of Scientific Research
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Yu Su
- Center of Scientific Research
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Yonghui Chen
- Center of Scientific Research
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Huaguo Xu
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Zhenkun Lin
- Center of Scientific Research
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Huaqin Guan
- The Department of Gastroenterology and Hepatology
- The First Affiliated Hospital of Wenzhou Medical University
- Wenzhou
- P. R. China
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20
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Mercurio FA, Di Natale C, Pirone L, Iannitti R, Marasco D, Pedone EM, Palumbo R, Leone M. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors. Sci Rep 2017; 7:17474. [PMID: 29234063 PMCID: PMC5727260 DOI: 10.1038/s41598-017-17684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Concetta Di Natale
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Roberta Iannitti
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.,Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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22
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Mercurio FA, Marasco D, Di Natale C, Pirone L, Costantini S, Pedone EM, Leone M. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues. Chembiochem 2016; 17:2179-2188. [DOI: 10.1002/cbic.201600413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Flavia A. Mercurio
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
- Department of Pharmacy; University of Naples “Federico II”; Via Mezzocannone 16 80134 Naples Italy
| | - Concetta Di Natale
- Department of Biology; University of Naples “Federico II”; Via Cinthia 4 80126 Naples Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Susan Costantini
- CROM; IRCCS-Istituto Nazionale Tumori “Fondazione G. Pascale”; Via Mariano Semmola 52 80131 Naples Italy
| | - Emilia M. Pedone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
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