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Das P, Ngo KH, Winnerdy FR, Maity A, Bakalar B, Mechulam Y, Schmitt E, Phan AT. Bulges in left-handed G-quadruplexes. Nucleic Acids Res 2021; 49:1724-1736. [PMID: 33503265 PMCID: PMC7897477 DOI: 10.1093/nar/gkaa1259] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/03/2022] Open
Abstract
G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Khac Huy Ngo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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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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Esposito V, Russo A, Amato T, Varra M, Vellecco V, Bucci M, Russo G, Virgilio A, Galeone A. Backbone modified TBA analogues endowed with antiproliferative activity. Biochim Biophys Acta Gen Subj 2016; 1861:1213-1221. [PMID: 27663232 DOI: 10.1016/j.bbagen.2016.09.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/13/2016] [Accepted: 09/16/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The thrombin binding aptamer (TBA) is endowed with antiproliferative properties but its potential development is counteracted by the concomitant anticoagulant activity. METHODS Five oligonucleotides (ODNs) based on TBA sequence (GGTTGGTGTGGTTGG) and containing l-residues or both l-residues and inversion of polarity sites have been investigated by NMR and CD techniques for their ability to form G-quadruplex structures. Furthermore, their anticoagulant (PT assay) and antiproliferative properties (MTT assay), and their resistance in fetal bovine serum have been tested. RESULTS CD and NMR data suggest that the investigated ODNs are able to form right- and left-handed G-quadruplex structures. All ODNs do not retain the anticoagulant activity characteristic of TBA but are endowed with a significant antiproliferative activity against two cancerous cell lines. Their resistance in biological environment after six days is variable, depending on the ODN. CONCLUSIONS A comparison between results and literature data suggests that the antiproliferative activity of the TBA analogues investigated could depends on two factors: a) biological pathways and targets different from those already identified or proposed for other antiproliferative G-quadruplex aptamers, and b) the contribution of the guanine-based degradation products. GENERAL SIGNIFICANCE Modified TBA analogues containing l-residues and inversion of polarity sites lose the anticoagulant activity but gain antiproliferative properties against two cancer cell lines. 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)
- Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Teresa Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
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Fu B, Huang J, Chen Y, Wang Y, Xue T, Xu G, Wang S, Zhou X. Right-handed and left-handed G-quadruplexes have the same DNA sequence: distinct conformations induced by an organic small molecule and potassium. Chem Commun (Camb) 2016; 52:10052-5. [PMID: 27452654 DOI: 10.1039/c6cc04866h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Herein, we report two distinct G-quadruplex conformations of the same G-rich oligonucleotide, regulated by a small molecule. This is the first report in which both right- and left-handed G-quadruplex conformations have been obtained from the same sequence. We discriminated these two distinct conformations and investigated their kinetics and thermodynamics.
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Affiliation(s)
- Boshi Fu
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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Abstract
Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.
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Unusual Chair-Like G-Quadruplex Structures: Heterochiral TBA Analogues Containing Inversion of Polarity Sites. J CHEM-NY 2015. [DOI: 10.1155/2015/473051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochiral oligodeoxynucleotides based on the thrombin binding aptamer sequence, namely, 5′gg3′-3′TT5′-5′ggtgtgg3′-3′TT5′-5′gg3′ (H1), 5′gg3′-3′TT5′-5′gg3′-3′TGT5′-5′gg3′-3′TT5′-5′gg3′ (H2), and 5′gGTTGgtgtgGTTGg3′ (H3), where lower case letters indicate L-residues, have been investigated in their ability to fold in G-quadruplex structures through a combination of gel electrophoresis, circular dichroism, and UV spectroscopy techniques. InH1andH2inversions of polarity sites have been introduced to control the strand direction in the loop regions. Collected data suggest that all modified sequences are able to fold in chair-like G-quadruplexes mimicking the originalTBAstructure.
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Yuan L, Tian T, Chen Y, Zhang Z, Zhou X. An L-DNA G-quadruplex: application for peroxidase DNAzyme. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:589-98. [PMID: 24138498 DOI: 10.1080/15257770.2013.838260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
L-DNA is the mirror-image form of natural D-DNA. We demonstrate that one left-handed G-rich sequence can form an L-DNA intramolecular G-quadruplex. Further investigation revealed that a DNAzyme formed by an L-nucleotide G-quadruplex exhibited peroxidase catalytic efficiency. The enhancement of the color change of the oxygenation product ABTS(•-) caused by L-nucleotide G-quadruplex formation could be clearly observed with naked eyes. This research provides a new concept for the application of the L-DNA peroxidase DNAzyme complex in nuclease-containing biological systems.
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Affiliation(s)
- Libo Yuan
- a College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei , P. R. China
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Zhou J, Rosu F, Amrane S, Korkut DN, Gabelica V, Mergny JL. Assembly of chemically modified G-rich sequences into tetramolecular DNA G-quadruplexes and higher order structures. Methods 2014; 67:159-68. [DOI: 10.1016/j.ymeth.2014.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/20/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022] Open
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Virgilio A, Varra M, Scuotto M, Capuozzo A, Irace C, Mayol L, Esposito V, Galeone A. Expanding the potential of G-quadruplex structures: formation of a heterochiral TBA analogue. Chembiochem 2014; 15:652-5. [PMID: 24520055 DOI: 10.1002/cbic.201300775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Indexed: 11/11/2022]
Abstract
In order to expand the potential applications of G-quadruplex structures, we explored the ability of heterochiral oligodeoxynucleotides based on the thrombin-binding aptamer (TBA) sequence to fold into similar complexes, with particular focus on their resistance in biological environments. A combination of CD and NMR techniques was used. Similarly to TBA, the ODN ggTTggtgtggTTgg (lower case letters indicate L residues) is able to fold into a chair-like antiparallel G-quadruplex structure, but has a slightly higher thermal stability. The discovery that heterochiral ODNs are able to form stable G-quadruplex structures opens up new possibilities for their development in several fields, as aptamers, sensors and, as recently shown, as catalysts for enantioselective reactions.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli (Italy)
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Virgilio A, Esposito V, Mangoni A, Mayol L, Galeone A. A novel equilibrium relating to the helix handedness in G-quadruplexes formed by heterochiral oligonucleotides with an inversion of polarity site. Chem Commun (Camb) 2013; 49:7935-7. [PMID: 23900626 DOI: 10.1039/c3cc44607g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Investigations of heterochiral oligodeoxynucleotides 5'-TD1GD2GD3-3'-3'-GL3GL2TL1-5' (L33) and 3'-TD1GD2GD3-5'-5'-GL3GL2TL1-3' (L55) forming quadruplex structures are reported. Data indicate the presence of enantiomeric left- and right-handed quadruplex helices. In the case of L55, NMR experiments point to an unusual equilibrium between them.
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Affiliation(s)
- Antonella Virgilio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131 Naples, Italy.
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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