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Fang J, Zheng L, Liu Y, Peng Y, Yang Q, Huang Y, Zhang J, Luo L, Shen D, Tan Y, Lu X, Feng G. Smart G-quadruplex hydrogels: From preparations to comprehensive applications. Int J Biol Macromol 2023; 247:125614. [PMID: 37414320 DOI: 10.1016/j.ijbiomac.2023.125614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/18/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
In recent years, the accelerated development of G-quadruplexes and hydrogels has driven the development of intelligent biomaterials. Based on the excellent biocompatibility and special biological functions of G-quadruplexes, and the hydrophilicity, high-water retention, high water content, flexibility and excellent biodegradability of hydrogels, G-quadruplex hydrogels are widely used in various fields by combining the dual advantages of G-quadruplexes and hydrogels. Here, we provide a systematic and comprehensive classification of G-quadruplex hydrogels in terms of preparation strategies and applications. This paper reveals how G-quadruplex hydrogels skillfully utilize the special biological functions of G-quadruplexes and the skeleton structure of hydrogels, and expounds its applications in the fields of biomedicine, biocatalysis, biosensing and biomaterials. In addition, we deeply analyze the challenges in preparation, applications, stability and safety of G-quadruplex hydrogels, as well as potential future development directions.
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Affiliation(s)
- Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lijuan Zheng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yan Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yuxin Peng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Qinghui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yuewen Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Jiali Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lixin Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Dunkai Shen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yuyan Tan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xuefen Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Guangfu Feng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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2
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Sannikova NE, Kolokolov MI, Khlynova TA, Chubarov AS, Polienko YF, Fedin MV, Krumkacheva OA. Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study. Phys Chem Chem Phys 2023; 25:22455-22466. [PMID: 37581249 DOI: 10.1039/d3cp01775c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable importance in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience structural changes as a result of ligand interactions and light exposure. Understanding these modifications is essential to uncover the fundamental biological roles of the complexes and optimize their therapeutic potential. The structural diversity of G4s makes it challenging to study their complexes with ligands, necessitating the use of various complementary methods to fully understand these interactions. In this study, we introduce, for the first time, the application of laser-induced dipolar EPR as a method to characterize G-quadruplex DNA complexes containing photosensitizers and to investigate light-induced structural modifications in these systems. To demonstrate the feasibility of this approach, we studied complexes of the human telomeric G-quadruplex (HTel-22) with cationic 5,10,15,20-tetrakis(1-methyl-4-pyridinio) porphyrin tetra(p-toluenesulfonate) (TMPyP4). In addition to showcasing a new methodology, we also aimed to provide insights into the mechanisms underlying photoinduced HTel-22/TMPyP4 structural changes, thereby aiding in the advancement of approaches targeting G4s in photodynamic therapy. EPR revealed G-quadruplex unfolding and dimer formation upon light exposure. Our findings demonstrate the potential of EPR spectroscopy for examining G4 complexes with photosensitizers and contribute to a better understanding of G4s' interactions with ligands under light.
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Affiliation(s)
- Natalya E Sannikova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Mikhail I Kolokolov
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Tamara A Khlynova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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3
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Libera V, Ripanti F, Petrillo C, Sacchetti F, Ramos-Soriano J, Galan MC, Schirò G, Paciaroni A, Comez L. Stability of Human Telomeric G-Quadruplexes Complexed with Photosensitive Ligands and Irradiated with Visible Light. Int J Mol Sci 2023; 24:ijms24109090. [PMID: 37240437 DOI: 10.3390/ijms24109090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Guanine-rich DNA sequences can fold into non-canonical nucleic acid structures called G-quadruplexes (G4s). These nanostructures have strong implications in many fields, from medical science to bottom-up nanotechnologies. As a result, ligands interacting with G4s have attracted great attention as candidates in medical therapies, molecular probe applications, and biosensing. In recent years, the use of G4-ligand complexes as photopharmacological targets has shown significant promise for developing novel therapeutic strategies and nanodevices. Here, we studied the possibility of manipulating the secondary structure of a human telomeric G4 sequence through the interaction with two photosensitive ligands, DTE and TMPyP4, whose response to visible light is different. The effect of these two ligands on G4 thermal unfolding was also considered, revealing the occurrence of peculiar multi-step melting pathways and the different attitudes of the two molecules on the quadruplex stabilization.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Javier Ramos-Soriano
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Maria Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Giorgio Schirò
- CNRS, CEA, IBS, c/o University Grenoble Alpes, 38400 Grenoble, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
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Roy A, Basu D, Bose D, Dutta A, Dastidar SG, Chatterjee S. Identification and characterization of a flexile G-quadruplex in the distal promoter region of stemness gene REX1. Int J Biol Macromol 2023; 231:123263. [PMID: 36649868 DOI: 10.1016/j.ijbiomac.2023.123263] [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: 10/25/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
We have identified a parallel G-quadruplex (R1WT) in the distal promoter region (-821 base-pairs upstream of the TSS) of the pluripotent gene REX1. Through biophysical and biochemical approach, we have characterized the G-quadruplex (GQ) as a potential molecular switch that may control REX1 promoter activity to determine the transcriptional fate. Small- molecule interactive study of the monomeric form of R1WT (characterized as R1mut2) with TMPyP4 and BRACO-19 revealed GQ destabilization upon interaction with TMPyP4 and stabilization upon interaction with BRACO-19. This distinctive drug interactivity suggests the in cellulo R1WT to be a promising drug target. The endogenous existence of R1WT was confirmed by BG4 antibody derived chromatin immunoprecipitation experiment. Here in, we also report the endogenous interaction of GQ specific transcription factors (TFs) with R1WT region in the human chromatin of cancer cell. The wild-type G-quadruplex was found to interact with four important transcription factors, (i) specificity protein (Sp1) (ii) non-metastatic cell 2 (NM23-H2): a diphosphatase (iii) cellular nucleic acid binding protein (CNBP) and (iv) heterogenous nuclear ribonucleoprotein K (hnRNPK) in the REX1 promoter. In contrast, nucleolin protein (NCL) binding was found to be low to the said G-quadruplex. The flexibility of R1WT between folded and unfolded states, obtained from experimental and computational analysis strongly suggests R1WT to be an important gene regulatory element in the genome. It controls promoter DNA relaxation with the coordinated interaction of transcription factors, the deregulation of which seeds stemness characteristic in cancer cells for further metastatic progression.
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Affiliation(s)
- Ananya Roy
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Debadrita Basu
- Department of Bioinformatics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Department of Bioinformatics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India.
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Bertini L, Libera V, Ripanti F, Natali F, Paolantoni M, Orecchini A, Nucara A, Petrillo C, Comez L, Paciaroni A. Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes. Int J Mol Sci 2023; 24:ijms24054280. [PMID: 36901712 PMCID: PMC10001961 DOI: 10.3390/ijms24054280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Francesca Natali
- CNR-IOM and INSIDE@ILL c/o OGG, 71 avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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6
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Bertini L, Libera V, Ripanti F, Seydel T, Paolantoni M, Orecchini A, Petrillo C, Comez L, Paciaroni A. Role of fast dynamics in the complexation of G-quadruplexes with small molecules. Phys Chem Chem Phys 2022; 24:29232-29240. [PMID: 36445842 DOI: 10.1039/d2cp03602a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) formed by the human telomeric sequence AG3 (TTAG3)3 (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy. .,Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) 71 avenue des Martyrs, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
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7
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Libera V, Bianchi F, Rossi B, D’Amico F, Masciovecchio C, Petrillo C, Sacchetti F, Paciaroni A, Comez L. Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding. Int J Mol Sci 2022; 23:ijms23095123. [PMID: 35563512 PMCID: PMC9100830 DOI: 10.3390/ijms23095123] [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: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Federico Bianchi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Francesco D’Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Claudio Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- Correspondence: (A.P.); (L.C.)
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (A.P.); (L.C.)
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