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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures. ChemistryOpen 2022; 11:e202200090. [PMID: 35608081 PMCID: PMC9127747 DOI: 10.1002/open.202200090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 04/22/2022] [Indexed: 12/27/2022] Open
Abstract
DNA G-quadruplexes (G4s) are key structures for the development of targeted anticancer therapies. In this context, ligands selectively interacting with G4s can represent valuable anticancer drugs. Aiming at speeding up the identification of G4-targeting synthetic or natural compounds, we developed an affinity chromatography-based assay, named G-quadruplex on Oligo Affinity Support (G4-OAS), by synthesizing G4-forming sequences on commercially available polystyrene OAS. Then, due to unspecific binding of several hydrophobic ligands on nude OAS, we moved to Controlled Pore Glass (CPG). We thus conceived an ad hoc functionalized, universal support on which both the on-support elongation and deprotection of the G4-forming oligonucleotides can be performed, along with the successive affinity chromatography-based assay, renamed as G-quadruplex on Controlled Pore Glass (G4-CPG) assay. Here we describe these assays and their applications to the screening of several libraries of chemically different putative G4 ligands. Finally, ongoing studies and outlook of our G4-CPG assay are reported.
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Affiliation(s)
- Chiara Platella
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Ettore Napolitano
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Claudia Riccardi
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Domenica Musumeci
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
- Institute of Biostructures and BioimagesCNRVia Tommaso De Amicis, 9580145NaplesItaly
| | - Daniela Montesarchio
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
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Miskiewicz J, Sarzynska J, Szachniuk M. How bioinformatics resources work with G4 RNAs. Brief Bioinform 2020; 22:5902714. [PMID: 32898859 PMCID: PMC8138894 DOI: 10.1093/bib/bbaa201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Quadruplexes (G4s) are of interest, which increases with the number of identified G4 structures and knowledge about their biomedical potential. These unique motifs form in many organisms, including humans, where their appearance correlates with various diseases. Scientists store and analyze quadruplexes using recently developed bioinformatic tools—many of them focused on DNA structures. With an expanding collection of G4 RNAs, we check how existing tools deal with them. We review all available bioinformatics resources dedicated to quadruplexes and examine their usefulness in G4 RNA analysis. We distinguish the following subsets of resources: databases, tools to predict putative quadruplex sequences, tools to predict secondary structure with quadruplexes and tools to analyze and visualize quadruplex structures. We share the results obtained from processing specially created RNA datasets with these tools. Contact: mszachniuk@cs.put.poznan.pl Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Joanna Miskiewicz
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
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Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT. A Minimal Sequence for Left-Handed G-Quadruplex Formation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS; Ecole Normale Supérieure Paris-Saclay; 94235 Cachan France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
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Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT. A Minimal Sequence for Left-Handed G-Quadruplex Formation. Angew Chem Int Ed Engl 2019; 58:2331-2335. [PMID: 30481397 DOI: 10.1002/anie.201812628] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Indexed: 12/20/2022]
Abstract
Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.
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Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay, 94235, Cachan, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G-Quadruplex Folding. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G‐Quadruplex Folding. Angew Chem Int Ed Engl 2015; 54:11716-9. [DOI: 10.1002/anie.201505348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
- EN‐FIST Center of Excellence, 1000 Ljubljana (Slovenia)
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana (Slovenia)
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Dickerhoff J, Weisz K. Flipping a G-tetrad in a unimolecular quadruplex without affecting its global fold. Angew Chem Int Ed Engl 2015; 54:5588-91. [PMID: 25775974 DOI: 10.1002/anie.201411887] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/22/2015] [Indexed: 11/07/2022]
Abstract
A unimolecular G-quadruplex with a hybrid-type topology and propeller, diagonal, and lateral loops was examined for its ability to undergo structural changes upon specific modifications. Substituting 2'-deoxy-2'-fluoro analogues with a propensity to adopt an anti glycosidic conformation for two or three guanine deoxyribonucleosides in syn positions of the 5'-terminal G-tetrad significantly alters the CD spectral signature of the quadruplex. An NMR analysis reveals a polarity switch of the whole tetrad with glycosidic conformational changes detected for all four guanine nucleosides in the modified sequence. As no additional rearrangement of the overall fold occurs, a novel type of G-quadruplex is formed with guanosines in the four columnar G-tracts lined up in either an all-syn or an all-anti glycosidic conformation.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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Dickerhoff J, Weisz K. Flipping a G-Tetrad in a Unimolecular Quadruplex Without Affecting Its Global Fold. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Xu B, Zhao C, Chen Y, Tateishi-Karimata H, Ren J, Sugimoto N, Qu X. Methyl Substitution Regulates the Enantioselectivity of Supramolecular Complex Binding to Human Telomeric G-Quadruplex DNA. Chemistry 2014; 20:16467-72. [DOI: 10.1002/chem.201404854] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 01/23/2023]
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Ma'ani Hessari N, Spindler L, Troha T, Lam WC, Drevenšek-Olenik I, Webba da Silva M. Programmed Self-Assembly of a Quadruplex DNA Nanowire. Chemistry 2014; 20:3626-30. [DOI: 10.1002/chem.201300692] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 12/02/2013] [Indexed: 12/30/2022]
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Ferreira R, Alvira M, Aviñó A, Gómez-Pinto I, González C, Gabelica V, Eritja R. Synthesis and structural characterization of stable branched DNA g-quadruplexes using the trebler phosphoramidite. ChemistryOpen 2012; 1:106-14. [PMID: 24551498 PMCID: PMC3922461 DOI: 10.1002/open.201200009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 01/17/2023] Open
Abstract
Guanine (G)-rich sequences can form a noncanonical four-stranded structure known as the G-quadruplex. G-quadruplex structures are interesting because of their potential biological properties and use in nanosciences. Here, we describe a method to prepare highly stable G-quadruplexes by linking four G-rich DNA strands to form a monomolecular G-quadruplex. In this method, one strand is synthesized first, and then a trebler molecule is added to simultaneously assemble the remaining three strands. This approach allows the introduction of specific modifications in only one of the strands. As a proof of concept, we prepared a quadruplex where one of the chains includes a change in polarity. A hybrid quadruplex is observed in ammonium acetate solutions, whereas in the presence of sodium or potassium, a parallel G-quadruplex structure is formed. In addition to the expected monomolecular quadruplexes, we observed the presence of dimeric G-quadruplex structures. We also applied the method to prepare G-quadruplexes containing a single 8-aminoguanine substitution and found that this single base stabilizes the G-quadruplex structure when located at an internal position.
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Affiliation(s)
- Rubén Ferreira
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) Jordi Girona 18-26, 08034 Barcelona (Spain) ; Department of Chemistry and Molecular Pharmacology, Institute for Research in Biomedicine (IRB Barcelona) Baldiri i Reixac 10, 08028 Barcelona (Spain)
| | - Margarita Alvira
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) Jordi Girona 18-26, 08034 Barcelona (Spain) ; Department of Chemistry and Molecular Pharmacology, Institute for Research in Biomedicine (IRB Barcelona) Baldiri i Reixac 10, 08028 Barcelona (Spain)
| | - Anna Aviñó
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) Jordi Girona 18-26, 08034 Barcelona (Spain) ; Department of Chemistry and Molecular Pharmacology, Institute for Research in Biomedicine (IRB Barcelona) Baldiri i Reixac 10, 08028 Barcelona (Spain)
| | - Irene Gómez-Pinto
- Departmento de Química Física Biológica, Instituto de Química Física 'Rocasolano' CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Carlos González
- Departmento de Química Física Biológica, Instituto de Química Física 'Rocasolano' CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Valérie Gabelica
- Department of Chemistry, University of Liège Allée de la Chimie Building B6c, 4000 Liège (Belgium)
| | - Ramon Eritja
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) Jordi Girona 18-26, 08034 Barcelona (Spain) ; Department of Chemistry and Molecular Pharmacology, Institute for Research in Biomedicine (IRB Barcelona) Baldiri i Reixac 10, 08028 Barcelona (Spain)
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Abstract
Circular dichroism (CD) is a widespread technique for studying the polymorphism of G-quadruplexes. In this chapter the CD spectral features characteristic of different folding topologies of G4-DNA are analyzed in terms of the sequence of the syn or anti glycosidic bond angle (GBA) within a quadruplex stem. Depending on the GBA sequence, the chiral disposition of two stacked guanines, adjacent along a strand, is different and this leads to a predictable contribution to the overall CD spectrum. The CD spectra of a series of G-quadruplexes, chosen as prototypal of the most common strand folding, are illustrated. The validity and the prediction power of the approach is corroborated by the analysis of CD spectra of structurally modified G4-DNA either with chemically modified guanines or polarity inversion site (5'-5' or 3'-3') along the strands or additional nucleobases contributing to the stacking.
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Karsisiotis AI, Hessari NM, Novellino E, Spada GP, Randazzo A, Webba da Silva M. Topological Characterization of Nucleic Acid G-Quadruplexes by UV Absorption and Circular Dichroism. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105193] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Karsisiotis AI, Hessari NM, Novellino E, Spada GP, Randazzo A, Webba da Silva M. Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew Chem Int Ed Engl 2011; 50:10645-8. [PMID: 21928459 DOI: 10.1002/anie.201105193] [Citation(s) in RCA: 325] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Indexed: 11/07/2022]
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Pradhan D, Hansen LH, Vester B, Petersen M. Selection of G-quadruplex folding topology with LNA-modified human telomeric sequences in K+ solution. Chemistry 2011; 17:2405-13. [PMID: 21264960 DOI: 10.1002/chem.201001961] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 11/21/2011] [Indexed: 12/28/2022]
Abstract
G-rich nucleic acid oligomers can form G-quadruplexes built by G-tetrads stacked upon each other. Depending on the nucleotide sequence, G-quadruplexes fold mainly with two topologies: parallel, in which all G-tracts are oriented parallel to each other, or antiparallel, in which one or more G-tracts are oriented antiparallel to the other G-tracts. In the former topology, all glycosidic bond angles conform to anti conformations, while in the latter topology they adopt both syn and anti conformations. It is of interest to understand the molecular forces that govern G-quadruplex folding. Here, we approach this problem by examining the impact of LNA (locked nucleic acid) modifications on the folding topology of the dimeric model system of the human telomere sequence. In solution, this DNA G-quadruplex forms a mixture of G-quadruplexes with antiparallel and parallel topologies. Using CD and NMR spectroscopies, we show that LNA incorporations can modulate this equilibrium in a rational manner and we establish a relationship between incorporation of LNA nucleotides in syn and/or anti positions and the shift of the equilibrium to obtain exclusively the parallel G-quadruplex. The change in topology is driven by a combination of the C3'-endo puckering of LNA nucleotides and their preference for the anti glycosidic conformation. In addition, the parallel LNA-modified G-quadruplexes are thermally stabilised by about 11 °C relative to their DNA counterparts.
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Affiliation(s)
- Devranjan Pradhan
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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