1
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Ji J, Sharma A, Pokhrel P, Karna D, Pandey S, Zheng YR, Mao H. Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400485. [PMID: 38678502 DOI: 10.1002/smll.202400485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/04/2024] [Indexed: 05/01/2024]
Abstract
8-oxoguanines (8-oxoG) in cells form compromised G-quadruplexes (GQs), which may vary GQ mediated gene regulations. By mimicking molecularly crowded cellular environment using 40% DMSO or sucrose, here it is found that oxidized human telomeric GQs have stabilities close to the wild-type (WT) GQs. Surprisingly, while WT GQs show negative formation cooperativity between a Pt(II) binder and molecularly crowded environment, positive cooperativity is observed for oxidized GQ formation. Single-molecule mechanical unfolding reveals that 8-oxoG sequence formed more diverse and flexible structures with faster folding/unfolding transition kinetics, which facilitates the Pt(II) ligand to bind the best-fit structures with positive cooperativity. These findings offer new understanding on structures and properties of oxidized G-rich species in crowded environments. They also provide insights into the design of better ligands to target oxidized G-rich structures formed under oxidative cell stress.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Arpit Sharma
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yao-Rong Zheng
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
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2
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Jurkowski M, Kogut M, Sappati S, Czub J. Why Are Left-Handed G-Quadruplexes Scarce? J Phys Chem Lett 2024; 15:3142-3148. [PMID: 38477716 PMCID: PMC10961827 DOI: 10.1021/acs.jpclett.3c03589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.
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Affiliation(s)
- Michał Jurkowski
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Mateusz Kogut
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Subrahmanyam Sappati
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
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3
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Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [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: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
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Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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4
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Zalar M, Wang B, Plavec J, Šket P. Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure. Int J Mol Sci 2023; 24:13437. [PMID: 37686239 PMCID: PMC10487854 DOI: 10.3390/ijms241713437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The G4C2 hexanucleotide repeat expansion in the c9orf72 gene is a major genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), with the formation of G-quadruplexes directly linked to the development of these diseases. Cations play a crucial role in the formation and structure of G-quadruplexes. In this study, we investigated the impact of biologically relevant potassium ions on G-quadruplex structures and utilized 15N-labeled ammonium cations as a substitute for K+ ions to gain further insights into cation binding and exchange dynamics. Through nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we demonstrate that the single d(G4C2) repeat, in the presence of 15NH4+ ions, adopts a tetramolecular G-quadruplex with an all-syn quartet at the 5'-end. The movement of 15NH4+ ions through the central channel of the G-quadruplex, as well as to the bulk solution, is governed by the vacant cation binding site, in addition to the all-syn quartet at the 5'-end. Furthermore, the addition of K+ ions to G-quadruplexes folded in the presence of 15NH4+ ions induces stacking of G-quadruplexes via their 5'-end G-quartets, leading to the formation of stable higher-ordered species.
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Affiliation(s)
- Matja Zalar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
- EN-FIST Center of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
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5
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Mizunuma M, Suzuki M, Kobayashi T, Hara Y, Kaneko A, Furukawa K, Chuman Y. Development of Mn 2+-Specific Biosensor Using G-Quadruplex-Based DNA. Int J Mol Sci 2023; 24:11556. [PMID: 37511324 PMCID: PMC10380348 DOI: 10.3390/ijms241411556] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Metal ions are used in various situations in living organisms and as a part of functional materials. Since the excessive intake of metal ions can cause health hazards and environmental pollution, the development of new molecules that can monitor metal ion concentrations with high sensitivity and selectivity is strongly desired. DNA can form various structures, and these structures and their properties have been used in a wide range of fields, including materials, sensors, and drugs. Guanine-rich sequences respond to metal ions and form G-quadruplex structures and G-wires, which are the self-assembling macromolecules of G-quadruplex structures. Therefore, guanine-rich DNA can be applied to a metal ion-detection sensor and functional materials. In this study, the IRDAptamer library originally designed based on G-quadruplex structures was used to screen for Mn2+, which is known to induce neurodegenerative diseases. Circular dichroism and fluorescence analysis using Thioflavin T showed that the identified IRDAptamer sequence designated MnG4C1 forms a non-canonical G-quadruplex structure in response to low concentrations of Mn2+. A serum resistance and thermostability analysis revealed that MnG4C1 acquired stability in a Mn2+-dependent manner. A Förster resonance energy transfer (FRET) system using fluorescent molecules attached to the termini of MnG4C1 showed that FRET was effectively induced based on Mn2+-dependent conformational changes, and the limit of detection (LOD) was 0.76 µM for Mn2+. These results suggested that MnG4C1 can be used as a novel DNA-based Mn2+-detecting molecule.
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Affiliation(s)
- Masataka Mizunuma
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Mirai Suzuki
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Tamaki Kobayashi
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yuki Hara
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Atsushi Kaneko
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Kazuhiro Furukawa
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
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6
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Chen EV, Nicoludis JM, Powell BM, Li KS, Yatsunyk LA. Crystal structure of a three-tetrad, parallel, K +-stabilized human telomeric G-quadruplex at 1.35 Å resolution. Acta Crystallogr F Struct Biol Commun 2023; 79:144-150. [PMID: 37223975 PMCID: PMC10231262 DOI: 10.1107/s2053230x23003977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
The crystal structure of the G-rich human telomeric DNA Tel22 has been determined at 1.35 Å resolution in space group P6. Tel22 forms a non-canonical DNA structure called the G-quadruplex. The space group and unit-cell parameters are comparable to those in the crystal structures with PDB codes 6ip3 (1.40 Å resolution) and 1kf1 (2.15 Å resolution). The G-quadruplexes are highly similar in all of the structures. However, this structure of Tel22 displays clear density for polyethylene glycol and two potassium ions, which are located outside the ion channel in the G-quadruplex and play an important role in stabilizing the crystal contacts. In addition, 111 water molecules were identified (compared with 79 and 68 in PDB entries 6ip3 and 1kf1, respectively) that participate in intricate and extensive networks providing high stability to the G-quadruplex.
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Affiliation(s)
- E. V. Chen
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - J. M. Nicoludis
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - B. M. Powell
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - K. S. Li
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - L. A. Yatsunyk
- Chemistry and Biochemistry, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
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7
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Nishio T, Masaoka T, Yoshikawa Y, Sadakane K, Kenmotsu T, Schiessel H, Yoshikawa K. Markedly Different Effects of Monovalent Cations on the Efficiency of Gene Expression. Adv Biol (Weinh) 2023; 7:e2200164. [PMID: 36328593 DOI: 10.1002/adbi.202200164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/20/2022] [Indexed: 11/06/2022]
Abstract
The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system is examined using a luciferase assay. It is found that the potency for all ions analyzed here is in the order Rb+ > K+ > Cs+ > Na+ ≈ Li+ > (CH3 )4 N+ , where Rb+ is most efficient at promoting TX-TL and the ions of Li+ , Na+ , and (CH3 )4 N+ exhibit an inhibitory effect. Similar promotion/inhibition effects are observed for cell-free TL alone with an mRNA template.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Tomoya Masaoka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics Institute for Advanced Study, Kyoto University, Kyoto, 606-8501, Japan
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8
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Iwaniuk EE, Adebayo T, Coleman S, Villaros CG, Nesterova IV. Activatable G-quadruplex based catalases for signal transduction in biosensing. Nucleic Acids Res 2023; 51:1600-1607. [PMID: 36727464 PMCID: PMC9976883 DOI: 10.1093/nar/gkad031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
Discovery of oxidative catalysis with G-quadruplex•hemin constructs prompted a range of exciting developments in the field of biosensor design. Thus, G-quadruplex based DNAzymes with peroxidase activity found a niche as signal transduction modules in a wide range of analytical applications. The ability of nucleic acid scaffolds to recognise a variety of practically meaningful markers and to translate the recognition events into conformational changes powers numerous sensor design possibilities. In this work, we establish a catalase activity of G-quadruplex•hemin scaffolds. Catalase activated hydrogen peroxide decomposition generates molecular oxygen that forms bubbles. Observation of bubbles is a truly equipment free signal readout platform that is highly desirable in limited resources or do-it-yourself environments. We take a preliminary insight into a G-quadruplex structure-folding topology-catalase activity correlation and establish efficient operating conditions. Further, we demonstrate the platform's potential as a signal transduction modality for reporting on biomolecular recognition using an oligonucleotide as a proof-of-concept target. Ultimately, activatable catalases based on G-quadruplex•hemin scaffolds promise to become valuable contributors towards accessible molecular diagnostics applications.
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Affiliation(s)
- Elzbieta E Iwaniuk
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Thuwebat Adebayo
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Caitlin G Villaros
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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9
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Alangari M, Demir B, Gultakti CA, Oren EE, Hihath J. Mapping DNA Conformations Using Single-Molecule Conductance Measurements. Biomolecules 2023; 13:129. [PMID: 36671514 PMCID: PMC9855376 DOI: 10.3390/biom13010129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
DNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. In this report, we examine the origin of multiple conductance peaks that can occur during single-molecule break-junction (SMBJ)-based conductance measurements on DNA. We demonstrate that these peaks originate from the presence of multiple DNA conformations within the solutions, in particular, double-stranded B-form DNA (dsDNA) and G-quadruplex structures. Using a combination of circular dichroism (CD) spectroscopy, computational approaches, sequence and environmental controls, and single-molecule conductance measurements, we disentangle the conductance information and demonstrate that specific conductance values come from specific conformations of the DNA and that the occurrence of these peaks can be controlled by controlling the local environment. In addition, we demonstrate that conductance measurements are uniquely sensitive to identifying these conformations in solutions and that multiple configurations can be detected in solutions over an extremely large concentration range, opening new possibilities for examining low-probability DNA conformations in solutions.
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Affiliation(s)
- Mashari Alangari
- Department of Electrical Engineering, Engineering College, University of Ha’il, Ha’il 55476, Saudi Arabia
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA 95616, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA 95616, USA
- Biodesign Center for Bioelectronics, School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
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10
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Teng Y, Zhu M, Chi Y, Li L, Jin Y. Can G-quadruplex become a promising target in HBV therapy? Front Immunol 2022; 13:1091873. [PMID: 36591216 PMCID: PMC9797731 DOI: 10.3389/fimmu.2022.1091873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The chronic infection with hepatitis B virus (HBV) is an important health problem that affects millions of people worldwide. Current therapies for HBV always suffer from a poor response rate, common side effects, and the need for lifelong treatment. Novel therapeutic targets are expected. Interestingly, non-canonical structures of nucleic acids play crucial roles in the regulation of gene expression. Especially the formation of G-quadruplexes (G4s) in G-rich strands has been demonstrated to affect many bioprocesses including replication, transcription, and translation, showing great potential as targets in anticancer and antiviral therapies. In this review, we summarize recent antiviral studies about G4s and discuss the potential roles of G4 structures in antiviral therapy for HBV.
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Affiliation(s)
- Ye Teng
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ming Zhu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuan Chi
- Pharmaceutical Department, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Lijing Li
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
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11
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Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques. Int J Mol Sci 2022; 23:ijms23105761. [PMID: 35628571 PMCID: PMC9144967 DOI: 10.3390/ijms23105761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.
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12
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Yadav K, Sardana D, Shweta H, Clovis NS, Sen S. Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA. J Phys Chem B 2022; 126:1668-1681. [PMID: 35170968 DOI: 10.1021/acs.jpcb.1c09349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.
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Affiliation(s)
- Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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13
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Molnár OR, Végh A, Somkuti J, Smeller L. Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3. Sci Rep 2021; 11:23243. [PMID: 34853392 PMCID: PMC8636512 DOI: 10.1038/s41598-021-02689-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Specific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.
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Affiliation(s)
- Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - András Végh
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.,Department of Ophthalmology, Semmelweis University, Budapest, 1085, Hungary
| | - Judit Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.
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14
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Qiao H, Asayama S. Guanidinopropyl end‐modified poly(ethylene glycol) to form highly compact plasmid
DNA
mono‐ion complexes by thermal treatment. POLYM ADVAN TECHNOL 2021. [DOI: 10.1002/pat.5530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Haibo Qiao
- Department of Applied Chemistry Tokyo Metropolitan University Tokyo Japan
| | - Shoichiro Asayama
- Department of Applied Chemistry Tokyo Metropolitan University Tokyo Japan
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15
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Figueiredo J, Santos T, Miranda A, Alexandre D, Teixeira B, Simões P, Lopes-Nunes J, Cruz C. Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs. Molecules 2021; 26:6164. [PMID: 34684745 PMCID: PMC8540333 DOI: 10.3390/molecules26206164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem-loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem-loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA-mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.
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Affiliation(s)
| | | | | | | | | | | | | | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Hen-rique, 6200-506 Covilhã, Portugal; (J.F.); (T.S.); (A.M.); (D.A.); (B.T.); (P.S.); (J.L.-N.)
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16
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Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
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Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
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17
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Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation. BIOTECH 2021; 10:biotech10040020. [PMID: 35822794 PMCID: PMC9245464 DOI: 10.3390/biotech10040020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
G-quadruplexes are four-stranded nucleic acid structures occurring in the genomes of all living organisms and viruses. It is increasingly evident that these structures play important molecular roles; generally, by modulating gene expression and overall genome integrity. For a long period, G-quadruplexes have been studied specifically in the context of human promoters, telomeres, and associated diseases (cancers, neurological disorders). Several of the proteins for binding G-quadruplexes are known, providing promising targets for influencing G-quadruplex-related processes in organisms. Nonetheless, in plants, only a small number of G-quadruplex binding proteins have been described to date. Thus, we aimed to bioinformatically inspect the available protein sequences to find the best protein candidates with the potential to bind G-quadruplexes. Two similar glycine and arginine-rich G-quadruplex-binding motifs were described in humans. The first is the so-called “RGG motif”-RRGDGRRRGGGGRGQGGRGRGGGFKG, and the second (which has been recently described) is known as the “NIQI motif”-RGRGRGRGGGSGGSGGRGRG. Using this general knowledge, we searched for plant proteins containing the above mentioned motifs, using two independent approaches (BLASTp and FIMO scanning), and revealed many proteins containing the G4-binding motif(s). Our research also revealed the core proteins involved in G4 folding and resolving in green plants, algae, and the key plant model organism, Arabidopsis thaliana. The discovered protein candidates were annotated using STRINGdb and sorted by their molecular and physiological roles in simple schemes. Our results point to the significant role of G4-binding proteins in the regulation of gene expression in plants.
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18
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Pavlova AV, Kubareva EA, Monakhova MV, Zvereva MI, Dolinnaya NG. Impact of G-Quadruplexes on the Regulation of Genome Integrity, DNA Damage and Repair. Biomolecules 2021; 11:1284. [PMID: 34572497 PMCID: PMC8472537 DOI: 10.3390/biom11091284] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
DNA G-quadruplexes (G4s) are known to be an integral part of the complex regulatory systems in both normal and pathological cells. At the same time, the ability of G4s to impede DNA replication plays a critical role in genome integrity. This review summarizes the results of recent studies of G4-mediated genomic and epigenomic instability, together with associated DNA damage and repair processes. Although the underlying mechanisms remain to be elucidated, it is known that, among the proteins that recognize G4 structures, many are linked to DNA repair. We analyzed the possible role of G4s in promoting double-strand DNA breaks, one of the most deleterious DNA lesions, and their repair via error-prone mechanisms. The patterns of G4 damage, with a focus on the introduction of oxidative guanine lesions, as well as their removal from G4 structures by canonical repair pathways, were also discussed together with the effects of G4s on the repair machinery. According to recent findings, there must be a delicate balance between G4-induced genome instability and G4-promoted repair processes. A broad overview of the factors that modulate the stability of G4 structures in vitro and in vivo is also provided here.
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Affiliation(s)
- Anzhela V. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Mayya V. Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
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19
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Carrino S, Hennecker CD, Murrieta AC, Mittermaier A. Frustrated folding of guanine quadruplexes in telomeric DNA. Nucleic Acids Res 2021; 49:3063-3076. [PMID: 33693924 PMCID: PMC8034632 DOI: 10.1093/nar/gkab140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/22/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Human chromosomes terminate in long, single-stranded, DNA overhangs of the repetitive sequence (TTAGGG)n. Sets of four adjacent TTAGGG repeats can fold into guanine quadruplexes (GQ), four-stranded structures that are implicated in telomere maintenance and cell immortalization and are targets in cancer therapy. Isolated GQs have been studied in detail, however much less is known about folding in long repeat sequences. Such chains adopt an enormous number of configurations containing various arrangements of GQs and unfolded gaps, leading to a highly frustrated energy landscape. To better understand this phenomenon, we used mutagenesis, thermal melting, and global analysis to determine stability, kinetic, and cooperativity parameters for GQ folding within chains containing 8–12 TTAGGG repeats. We then used these parameters to simulate the folding of 32-repeat chains, more representative of intact telomeres. We found that a combination of folding frustration and negative cooperativity between adjacent GQs increases TTAGGG unfolding by up to 40-fold, providing an abundance of unfolded gaps that are potential binding sites for telomeric proteins. This effect was most pronounced at the chain termini, which could promote telomere extension by telomerase. We conclude that folding frustration is an important and largely overlooked factor controlling the structure of telomeric DNA.
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Affiliation(s)
- Simone Carrino
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Ana C Murrieta
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.,School of Engineering and Sciences, Instituto Tecnológico y de Estudios Superiores De Monterrey, Av. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849, Monterrey, Nuevo León, México
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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20
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Mustafa G, Shiekh S, Gc K, Abeysirigunawardena S, Balci H. Interrogating accessibility of telomeric sequences with FRET-PAINT: evidence for length-dependent telomere compaction. Nucleic Acids Res 2021; 49:3371-3380. [PMID: 33693934 PMCID: PMC8034622 DOI: 10.1093/nar/gkab067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/23/2021] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
Single-stranded telomeric overhangs are ∼200 nucleotides long and can form tandem G-quadruplex (GQ) structures, which reduce their accessibility to nucleases and proteins that activate DNA damage response. Whether these tandem GQs further stack to form compact superstructures, which may provide better protection for longer telomeres, is not known. We report single-molecule measurements where the accessibility of 24-144 nucleotide long human telomeric DNA molecules is interrogated by a short PNA molecule that is complementary to a single GGGTTA repeat, as implemented in the FRET-PAINT method. Binding of the PNA strand to available GGGTTA sequences results in discrete FRET bursts which were analyzed in terms of their dwell times, binding frequencies, and topographic distributions. The binding frequencies were greater for binding to intermediate regions of telomeric DNA compared to 3'- or 5'-ends, suggesting these regions are more accessible. Significantly, the binding frequency per telomeric repeat monotonically decreased with increasing telomere length. These results are consistent with telomeres forming more compact structures at longer lengths, reducing accessibility of these critical genomic sites.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Keshav Gc
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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21
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Hossain KA, Jurkowski M, Czub J, Kogut M. Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2526-2536. [PMID: 34025941 PMCID: PMC8114077 DOI: 10.1016/j.csbj.2021.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Because of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type G4s using all-atom molecular dynamics simulations. By computing binding free energies, we found that the two main G4-interacting subdomains of DHX36, DSM and OB, separately exhibit high G4 affinity but they act cooperatively to recognize two distinctive features of parallel G4s: the exposed planar face of a guanine tetrad and the unique backbone conformation of a continuous guanine tract, respectively. Our results also show that DSM-mediated interactions are the main contributor to the binding free energy and rely on making extensive van der Waals contacts between the GXXXG motifs and hydrophobic residues of DSM and a flat guanine plane. Accordingly, the sterically more accessible 5'-G-tetrad allows for more favorable van der Waals and hydrophobic interactions which leads to the preferential binding of DSM to the 5'-side. In contrast to DSM, OB binds to G4 mostly through polar interactions by flexibly adapting to the 5'-terminal guanine tract to form a number of strong hydrogen bonds with the backbone phosphate groups. We also identified a third DHX36/G4 interaction site formed by the flexible loop missing in the crystal structure.
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Affiliation(s)
- Kazi Amirul Hossain
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Michal Jurkowski
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Mateusz Kogut
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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22
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Jana J, Mohr S, Vianney YM, Weisz K. Structural motifs and intramolecular interactions in non-canonical G-quadruplexes. RSC Chem Biol 2021; 2:338-353. [PMID: 34458788 PMCID: PMC8341446 DOI: 10.1039/d0cb00211a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Guanine(G)-rich DNA or RNA sequences can assemble or intramolecularly fold into G-quadruplexes formed through the stacking of planar G·G·G·G tetrads in the presence of monovalent cations. These secondary nucleic acid structures have convincingly been shown to also exist within a cellular environment exerting important regulatory functions in physiological processes. For identifying nucleic acid segments prone to quadruplex formation, a putative quadruplex sequence motif encompassing closely spaced tracts of three or more guanosines is frequently employed for bioinformatic search algorithms. Depending on the number and type of intervening residues as well as on solution conditions, such sequences may fold into various canonical G4 topologies with continuous G-columns. On the other hand, a growing number of sequences capable of quadruplex formation feature G-deficient guanine tracts, escaping the conservative consensus motif. By folding into non-canonical quadruplex structures, they adopt unique topologies depending on their specific sequence context. These include G-columns with only two guanines, bulges, snapback loops, D- and V-shaped loops as well as interlocked structures. This review focuses on G-quadruplex species carrying such distinct structural motifs. It evaluates characteristic features of their non-conventional scaffold and highlights principles of stabilizing interactions that also allow for their folding into stable G-quadruplex structures.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Swantje Mohr
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
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23
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Nishio M, Tsukakoshi K, Ikebukuro K. G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing. Biosens Bioelectron 2021; 178:113030. [PMID: 33524709 DOI: 10.1016/j.bios.2021.113030] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 12/20/2022]
Abstract
G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. While G4s have some functions in vivo, there are many reports of developed applications that use G4s. As various conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others.
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Affiliation(s)
- Maui Nishio
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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24
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Reddy Sannapureddi RK, Mohanty MK, Gautam AK, Sathyamoorthy B. Characterization of DNA G-quadruplex Topologies with NMR Chemical Shifts. J Phys Chem Lett 2020; 11:10016-10022. [PMID: 33179931 DOI: 10.1021/acs.jpclett.0c02969] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
G-quadruplexes are nucleic acid motifs formed by stacking of guanosine-tetrad pseudoplanes. They perform varied biological roles, and their distinctive structural features enable diverse applications. High-resolution structural characterization of G-quadruplexes is often time-consuming and expensive, calling for effective methods. Herein, we develop NMR chemical shifts and machine learning-based methodology that allows direct, rapid, and reliable analysis of canonical three-plane DNA G-quadruplexes sans isotopic enrichment. We show, for the first time, that each unique topology enforces a specific distribution of glycosidic torsion angles. Newly acquired carbon chemical shifts are exquisite probes for the dihedral angle distribution and provide immediate and unambiguous backbone topology assignment. The support vector machine learning methodology aids resonance assignment by providing plane indices for tetrad-forming guanosines. We further demonstrate the robustness by successful application of the methodology to a sequence that folds in two dissimilar topologies under different ionic conditions, providing its first atomic-level characterization.
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Affiliation(s)
| | - Manish Kumar Mohanty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Anoop Kumar Gautam
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
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25
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Jana J, Weisz K. A Thermodynamic Perspective on Potential G-Quadruplex Structures as Silencer Elements in the MYC Promoter. Chemistry 2020; 26:17242-17251. [PMID: 32761687 PMCID: PMC7839732 DOI: 10.1002/chem.202002985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Indexed: 01/10/2023]
Abstract
Multiple G‐tracts within the promoter region of the c‐myc oncogene may fold into various G‐quadruplexes with the recruitment of different tracts and guanosine residues for the G‐core assembly. Thermodynamic profiles for the folding of wild‐type and representative truncated as well as mutated sequences were extracted by comprehensive DSC experiments. The unique G‐quadruplex involving consecutive G‐tracts II–V with formation of two one‐nucleotide and one central two‐nucleotide propeller loop, previously proposed to be the biologically most relevant species, was found to be the most stable fold in terms of its Gibbs free energy of formation at ambient temperatures. Its stability derives from its short propeller loops but also from the favorable type of loop residues. Whereas quadruplex folds with long propeller loops are significantly disfavored, a snap‐back loop structure formed by incorporating a 3’‐terminal guanosine into the empty position of a tetrad seems highly competitive based on its thermodynamic stability. However, its destabilization by extending the 3’‐terminus questions the significance of such a species under in vivo conditions.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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26
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Vianney YM, Preckwinkel P, Mohr S, Weisz K. Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands. Chemistry 2020; 26:16910-16922. [PMID: 32975874 PMCID: PMC7756412 DOI: 10.1002/chem.202003540] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Indexed: 12/23/2022]
Abstract
A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q-D hybrids with a very high affinity in the order Ka ≈107 m-1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Pit Preckwinkel
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Swantje Mohr
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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27
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Comez L, Bianchi F, Libera V, Longo M, Petrillo C, Sacchetti F, Sebastiani F, D'Amico F, Rossi B, Gessini A, Masciovecchio C, Amenitsch H, Sissi C, Paciaroni A. Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study. Phys Chem Chem Phys 2020; 22:11583-11592. [PMID: 32400802 DOI: 10.1039/d0cp01483d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - V Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - M Longo
- JCNS Forschungszentrum Jülich GmbH at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany
| | - C Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sebastiani
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - F D'Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - B Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - A Gessini
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - H Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - C Sissi
- Dipartimento di Scienze del Farmaco, Via Marzolo 5, 35131 Padova, Italy and Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, University of Padova, Italy
| | - A Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
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28
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Development of Specific Inhibitors for Oncogenic Phosphatase PPM1D by Using Ion-Responsive DNA Aptamer Library. Catalysts 2020. [DOI: 10.3390/catal10101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
(1) Background: Ser/Thr protein phosphatase PPM1D is an oncogenic protein. In normal cells, however, PPM1D plays essential roles in spermatogenesis and immune response. Hence, it is necessary to develop novel PPM1D inhibitors without side effects on normal cells. Stimuli-responsive molecules are suitable for the spatiotemporal regulation of inhibitory activity. (2) Methods: In this study, we designed an ion-responsive DNA aptamer library based on G-quadruplex DNA that can change its conformation and function in response to monovalent cations. (3) Results: Using this library, we identified the PPM1D specific inhibitor M1D-Q5F aptamer. The M1D-Q5F aptamer showed anti-cancer activity against breast cancer MCF7 cells. Interestingly, the induction of the structural change resulting in the formation of G-quadruplex upon stimulation by monovalent cations led to the enhancement of the inhibitory activity and binding affinity of M1D-Q5F. (4) Conclusions: These data suggest that the M1D-Q5F aptamer may act as a novel stimuli-responsive anti-cancer agent.
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29
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Smirnov IP, Kolganova NA, Surzhikov SA, Grechishnikova IV, Novikov RA, Timofeev EN. Folding topology, structural polymorphism, and dimerization of intramolecular DNA G-quadruplexes with inverted polarity strands and non-natural loops. Int J Biol Macromol 2020; 162:1972-1981. [PMID: 32800956 DOI: 10.1016/j.ijbiomac.2020.08.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 01/27/2023]
Abstract
Synthetically modified DNA G-quadruplexes (GQs) have great potential in the development of designer molecules for a wide range of applications. Identification of the role of various structural elements in the folding and final topology of artificial GQs is necessary to predict their secondary structure. We report here the results of spectroscopic and electrophoretic studies of GQ scaffolds formed by G-rich sequences comprising four G3-tracts of different polarity connected by either a single-nucleotide thymine loop or a non-natural tetraethyleneglycol loop. Depending on G-strand polarities, loop arrangement and the presence of extra 5'-base G-rich oligonucleotides form monomeric, dimeric, or multimeric species of different topologies. In most cases, oligonucleotides were able to fold into stable parallel or hybrid GQs. However, certain specific arrangements of loops and G-tracts resulted in a diverse mixture of low stable structures. Comparative analysis of topology, stability, and structural heterogeneity of different G-rich sequences suggests the important role of loop type and arrangement, G3-tract polarities, and the presence of 5'-capping residues in the outcome of the folding process. The results also imply that the formation of anti-parallel G-hairpin intermediates is a key event in major favourable folding pathways.
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Affiliation(s)
- Igor P Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Natalia A Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina V Grechishnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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30
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Ferenc G, Váradi Z, Kupihár Z, Paragi G, Kovács L. Analytical and Structural Studies for the Investigation of Oxidative Stress in Guanine Oligonucleotides. Int J Mol Sci 2020; 21:E4981. [PMID: 32679695 PMCID: PMC7404036 DOI: 10.3390/ijms21144981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
DNA damage plays a decisive role in epigenetic effects. The detection and analysis of DNA damages, like the most common change of guanine (G) to 8-oxo-7,8-dihydroguanine (OG), is a key factor in cancer research. It is especially true for G quadruplex structure (GQ), which is one of the best-known examples of a non-canonical DNA arrangement. In the present work, we provided an overview on analytical methods in connection with the detection of OG in oligonucleotides with GQ-forming capacity. Focusing on the last five years, novel electrochemical tools, like dedicated electrodes, were overviewed, as well as different optical methods (fluorometric assays, resonance light scattering or UV radiation) along with hyphenated detection and structural analysis methods (CD, NMR, melting temperature analysis and nanopore detection) were also applied for OG detection. Additionally, GQ-related computational simulations were also summarized. All these results emphasize that OG detection and the analysis of the effect of its presence in higher ordered structures like GQ is still a state-of-the-art research line with continuously increasing interest.
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Affiliation(s)
- Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary;
| | - Zoltán Váradi
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
| | - Zoltán Kupihár
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, Dóm tér 8, 6720 Szeged, Hungary
- Institute of Physics, University of Pécs, Ifjúság útja 6, 7624 Pécs, Hungary
| | - Lajos Kovács
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
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31
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Effects of Molecular Crowding on G-Quadruplex-hemin Mediated Peroxidase Activity. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-0018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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33
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Benabou S, Mazzini S, Aviñó A, Eritja R, Gargallo R. A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor. Sci Rep 2019; 9:15807. [PMID: 31676783 PMCID: PMC6825181 DOI: 10.1038/s41598-019-52311-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023] Open
Abstract
Some lung and ovarian tumors are connected to the loss of expression of SMARCA4 gene. In its promoter region, a 44-nucleotides long guanine sequence prone to form G-quadruplex structures has been studied by means of spectroscopic techniques (circular dichroism, molecular absorption and nuclear magnetic resonance), size exclusion chromatography and multivariate analysis. The results have shown that the central 21-nucleotides long sequence comprising four guanine tracts of disparate length is able to fold into a pH-dependent ensemble of G-quadruplex structures. Based on acid-base titrations and melting experiments of wild and mutated sequences, the formation of a C·C+ base pair between cytosine bases present at the two lateral loops is shown to promote a reduction in conformational heterogeneity, as well as an increase in thermal stability. The formation of this base pair is characterized by a pKa value of 7.1 ± 0.2 at 20 °C and 150 mM KCl. This value, higher than those usually found in i-motif structures, is related to the additional stability provided by guanine tetrads in the G-quadruplex. To our knowledge, this is the first thermodynamic description of this base pair in loops of antiparallel G-quadruplex structures.
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Affiliation(s)
- Sanae Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain.
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34
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Kotar A, Rigo R, Sissi C, Plavec J. Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure. Nucleic Acids Res 2019; 47:2641-2653. [PMID: 30590801 PMCID: PMC6411839 DOI: 10.1093/nar/gky1269] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/16/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In the promoter of c-KIT proto-oncogene, whose deregulation has been implicated in many cancers, three G-rich regions (kit1, kit* and kit2) are able to fold into G-quadruplexes. While kit1 and kit2 have been studied in depth, little information is available on kit* folding behavior despite its key role in regulation of c-KIT transcription. Notably, kit* contains consensus sites for SP1 and AP2 transcription factors. Herein, a set of complementary spectroscopic and biophysical methods reveals that kit*, d[GGCGAGGAGGGGCGTGGCCGGC], adopts a chair type antiparallel G-quadruplex with two G-quartets at physiological relevant concentrations of KCl. Heterogeneous ensemble of structures is observed in the presence of Na+ and NH4+ ions, which however stabilize pre-folded structure. In the presence of K+ ions stacking interactions of adenine and thymine residues on the top G-quartet contribute to structural stability together with a G10•C18 base pair and a fold-back motif of the five residues at the 3′-terminal under the bottom G-quartet. The 3′-tail enables formation of a bimolecular pre-folded structure that drives folding of kit* into a single G-quadruplex. Intriguingly, kinetics of kit* G-quadruplex formation matches timescale of transcriptional processes and might demonstrate interplay of kinetic and thermodynamic factors for understanding regulation of c-KIT proto-oncogene expression.
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Affiliation(s)
- Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.,EN-FIST Center of Excellence, 1000 Ljubljana, Slovenia
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35
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Bednářová K, Kejnovská I, Vorlíčková M, Renčiuk D. Guanine Substitutions Prevent Conformational Switch from Antiparallel to Parallel G-Quadruplex. Chemistry 2019; 25:13422-13428. [PMID: 31453656 DOI: 10.1002/chem.201903015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/08/2019] [Indexed: 12/20/2022]
Abstract
Guanine quadruplexes, recently reported to form in vivo, represent a broad spectrum of non-canonical conformations of nucleic acids. The actual conformation might differ between water solutions and crowding or dehydrating solutions that better reflect the conditions in the cell. Here we show, using spectroscopic techniques, that most guanine substitutions prevent the conformational switch from antiparallel or hybrid forms to parallel ones when induced by dehydrating agents. The inhibitory effect does not depend on the position of the substitution, but, interestingly, on the type of substitution and, to some extent, on its destabilising potential. A parallel form might be induced in some cases by ligands such as N-methyl mesoporphyrin IX and even this ligand-induced switch is inhibited by guanine substitution. The ability or inability to have a conformation switch, based on actual conditions, might significantly influence potential conformation-dependent quadruplex interactions.
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Affiliation(s)
- Klára Bednářová
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Iva Kejnovská
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Michaela Vorlíčková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Daniel Renčiuk
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
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36
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Paul A, Musetti C, Nanjunda R, Wilson WD. Biosensor-Surface Plasmon Resonance: Label-Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions. Methods Mol Biol 2019; 2035:63-85. [PMID: 31444744 DOI: 10.1007/978-1-4939-9666-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
Abstract
Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real-time equilibrium and kinetic characterization for quadruplex DNA interactions and requires small amounts of materials and no external probe. A detailed protocol for quadruplex-DNA interaction analyses with a variety of binding molecules using biosensor-SPR methods is presented. Explanations of the SPR method with basic fundamentals for use and analysis of results are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples. Details of experimental design, quantitative and qualitative data analyses, and presentation are described. Some specific examples of small molecule-DNA quadruplex interactions are presented with results evaluated by both kinetic and steady-state SPR methods.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Caterina Musetti
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Department of Screening, Profiling and Mechanistic Biology, Platform Technology and Science, Glaxo Smith Kline, Collegeville, PA, USA
| | - Rupesh Nanjunda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Janssen Research and Development, Spring House, PA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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37
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Somkuti J, Adányi M, Smeller L. Self-crowding influences the temperature - pressure stability of the human telomere G-quadruplex. Biophys Chem 2019; 254:106248. [PMID: 31470349 DOI: 10.1016/j.bpc.2019.106248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023]
Abstract
We measured the effect of crowded environment on G-quadruplex structures, formed by guanine rich DNA sequences. Fluorescence and infrared spectroscopy were used to determine the temperature stability of G-quadruplex structure formed by the human telomere sequence. We determined the T-p phase diagram of Htel aptamer up to 1 GPa at different self-crowding conditions. The unfolding volume change was determined from the pressure induced shift of the unfolding temperature of the quadruplex form. The unfolding volume change decreased in magnitude, and even its sign changed from negative (-19 ml/mol) to positive (7 ml/mol) under self-crowded conditions. The possible explanations are the appearance of the parallel GQ structure at high concentration or the fact that the volume decrease caused by the released central K+ ion during the unfolding is less significant in crowded environment.
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Affiliation(s)
- J Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - M Adányi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - L Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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38
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Trajkovski M, Endoh T, Tateishi-Karimata H, Ohyama T, Tanaka S, Plavec J, Sugimoto N. Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations. Nucleic Acids Res 2019; 46:4301-4315. [PMID: 29648656 PMCID: PMC5934638 DOI: 10.1093/nar/gky250] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/28/2018] [Indexed: 01/18/2023] Open
Abstract
Molecular crowding conditions provided by high concentration of cosolutes are utilized for characterization of biomolecules in cell-mimicking environment and development of drug-delivery systems. In this context, (poly)ethylene glycols are often used for studying non-canonical DNA structures termed G-quadruplexes, which came into focus by emerging structural biology findings and new therapeutic drug design approaches. Recently, several reports were made arguing against using (poly)ethylene glycols in role of molecular crowding agents due to their direct impact on DNA G-quadruplex stability and topology. However, the available data on structural details underlying DNA interaction is very scarce and thus limits in-depth comprehension. Herein, structural and thermodynamic analyses were strategically combined to assess G-quadruplex-cosolute interactions and address previously reported variances regarding the driving forces of G-rich DNA structural transformations under molecular crowding conditions. With the use of complementary (CD, NMR and UV) spectroscopic methods and model approach we characterized DNA G-quadruplex in the presence of the smallest and one of the largest typically used (poly)ethylene glycols. Dehydration effect is the key contributor to ethylene-glycol-induced increased stability of the G-quadruplex, which is in the case of the large cosolute mainly guided by the subtle direct interactions between PEG 8000 and the outer G-quartet regions.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1000, Slovenia
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1000, Slovenia.,EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, p. p. 537, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
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39
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Kurseev SA, Solovjev AM, Neumann MM, Medvedko AV, Sakharov IY. Chemiluminescent and Colorimetric Aptamer-Based Assays of Human α-Thrombin. ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1640718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sergei A. Kurseev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton M. Solovjev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina M. Neumann
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Ivan Yu. Sakharov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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40
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Arns L, Knop JM, Patra S, Anders C, Winter R. Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes. Biophys Chem 2019; 251:106190. [PMID: 31146215 DOI: 10.1016/j.bpc.2019.106190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
In this review we discuss results from temperature and pressure dependent single-molecule Förster resonance energy transfer (smFRET) studies on nucleic acids in the presence of macromolecular crowders and organic osmolytes. As representative examples, we have chosen fragments of both DNAs and RNAs, i.e., a synthetic DNA hairpin, a human telomeric G-quadruplex and the microROSE RNA hairpin. To mimic the effects of intracellular components, our studies include the macromolecular crowding agent Ficoll, a copolymer of sucrose and epichlorohydrin, and the organic osmolytes trimethylamine N-oxide, urea and glycine as well as natural occurring osmolyte mixtures from deep sea organisms. Furthermore, the impact of mutations in an RNA sequence on the conformational dynamics is examined. Different from proteins, the effects of the osmolytes and crowding agents seem to strongly dependent on the structure and chemical make-up of the nucleic acid.
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Affiliation(s)
- Loana Arns
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Jim-Marcel Knop
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Satyajit Patra
- Aix Marseille Université, CNRS, Centralle Marseille, Institut Fresnel, F-13013 Marseille, France
| | - Christian Anders
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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41
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Bielskutė S, Plavec J, Podbevšek P. Impact of Oxidative Lesions on the Human Telomeric G-Quadruplex. J Am Chem Soc 2019; 141:2594-2603. [PMID: 30657306 PMCID: PMC6727377 DOI: 10.1021/jacs.8b12748] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Telomere
attrition is closely associated with cell aging and exposure
to reactive oxygen species (ROS). While oxidation products of nucleotides
have been studied extensively in the past, the underlying secondary/tertiary
structural changes in DNA remain poorly understood. In this work,
we systematically probed guanine positions in the human telomeric
oligonucleotide sequence (hTel) by substitutions with the major product
of ROS, 8-oxo-7,8-dihydroguanine (oxoG), and evaluated
the G-quadruplex forming ability of such oligonucleotides. Due to
reduced hydrogen-bonding capability caused by oxoG, a loss
of G-quadruplex structure was observed for most oligonucleotides containing
oxidative lesions. However, some positions in the hTel sequence were
found to tolerate substitutions with oxoG. Due to oxoG’s preference for the syn conformation, distinct responses were observed when replacing guanines
with different glycosidic conformations. Accommodation of oxoG at sites originally in syn or anti in nonsubstituted hTel G-quadruplex requires a minor structural
rearrangement or a major conformational shift, respectively. The system
responds by retaining or switching to a fold where oxoG
is in syn conformation. Most importantly, these G-quadruplex
structures are still stable at physiological temperatures and should
be considered detrimental in higher-order telomere structures.
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Affiliation(s)
- Stasė Bielskutė
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Janez Plavec
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia
| | - Peter Podbevšek
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia
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42
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Sharawy M, Consta S. Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K ions. J Chem Phys 2019; 149:225102. [PMID: 30553268 DOI: 10.1063/1.5050534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Guanine quadruplex (G-quadruplex) structures play a vital role in stabilizing the DNA genome and in protecting healthy cells from transforming into cancer cells. The structural stability of G-quadruplexes is greatly enhanced by the binding of monovalent cations such as Na+ or K+ into the interior axial channel. We computationally study the free energy of binding of Na+ and K+ ions to two intramolecular G-quadruplexes that differ considerably in their degree of rigidity and the presence or absence of terminal nucleotides. The goal of our study is two-fold. On the one hand, we study the free energy of binding every ion, which complements the experimental findings that report the average free energy for replacing Na+ with K+ ions. On the other hand, we examine the role of the G-quadruplex structure in the binding free energy. In the study, we employ all-atom molecular dynamics simulations and the alchemical transformation method for the computation of the free energies. To compare the cation-dependent contribution to the structural stability of G-quadruplexes, we use a two-step approach to calculate the individual free energy difference ΔG of binding two Na+ and two K+ to two G-quadruplexes: the unimolecular DNA d[T2GT2(G3T)3] (Protein Data Bank ID 2M4P) and the human telomeric DNA d[AGGG(TTAGGG)3] (PDB ID 1KF1). In contrast to the experimental studies that estimate the average free energy of binding, we find a varying difference of approximately 2-9 kcal/mol between the free energy contribution of binding the first and second cation, Na+ or K+. Furthermore, we found that the free energy of binding K+ is not affected by the chemical nature of the two quadruplexes. By contrast, Na+ showed dependency on the G-quadruplex structure; the relatively small size allows Na+ to explore larger configurational space than K+. Numerical results presented here may offer reference values for future design of cationic drug-like ligands that replace the metal ions in G-quadruplexes.
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Affiliation(s)
- Mahmoud Sharawy
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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43
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Zhou B, Chen YT, Yang XY, Wang YS, Hu XJ, Suo QL. An Ultrasensitive Colorimetric Strategy for Detection of Cadmium Based on the Peroxidase-like Activity of G-Quadruplex-Cd(II) Specific Aptamer. ANAL SCI 2018; 35:277-282. [PMID: 30393236 DOI: 10.2116/analsci.18p248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We rationally designed an ultrasensitive and label-free sensing platform for determination of cadmium (Cd). The sensing platform contains G-quadruplex-Cd(II) specific aptamer (GCDSA) constructed by incorporating G-rich sequence at the end of 5' and the critical domain of the Cd-4 aptamer. GCDSA designed act as both a special recognition sequence for Cd2+ and a signal DNAzyme. In absence of Cd2+, GCDSA may mainly exist in a random coil sequence. Upon addition of Cd2+, GCDSA could probably be induced to fold into a G-quadruplex structure. The generation of plentiful active G-quadruplex interacts with hemin to form a peroxidase-like DNAzyme, leading to increased absorbance signal of the sensing system. ΔA was directly proportional to the two segments of concentrations for Cd2+, with the detection of limit of 0.15 nM. The proposed method avoids the labeled oligonucleotides and allows directly quantitative analysis of the samples by cheap instruments, with an excellent dynamic range.
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Affiliation(s)
- Bin Zhou
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology
| | - Ya-Ting Chen
- College of Public Health, University of South China
| | - Xin-Yi Yang
- College of Public Health, University of South China
| | | | - Xi-Jiang Hu
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology
| | - Qing-Li Suo
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology
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44
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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45
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Villani G. Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere. ACS OMEGA 2018; 3:9934-9944. [PMID: 31459122 PMCID: PMC6644616 DOI: 10.1021/acsomega.8b01678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 05/17/2023]
Abstract
The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM—CNR
(UOS Pisa), Area della Ricerca di Pisa, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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46
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Takahashi S, Kim KT, Podbevšek P, Plavec J, Kim BH, Sugimoto N. Recovery of the Formation and Function of Oxidized G-Quadruplexes by a Pyrene-Modified Guanine Tract. J Am Chem Soc 2018; 140:5774-5783. [PMID: 29608858 DOI: 10.1021/jacs.8b01577] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor ( VEGF) gene differed topologically from unoxidized G4. The oxidized VEGF G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guanine tract that replaces the oxidized guanine tract and forms stable intermolecular G4s with the other intact guanine tracts. When this oligonucleotide was used, the oxidized G4 stalled replication and was stabilized by nucleolin as with the unmodified G4. This strategy generally enables recovery of the function of any oxidized G4s and therefore has potential for cancer therapy.
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Affiliation(s)
| | - Ki Tae Kim
- Department of Chemistry, Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Republic of Korea
| | - Peter Podbevšek
- Slovenian NMR Center , National Institute of Chemistry , SI-1000 Ljubljana , Slovenia
| | - Janez Plavec
- Slovenian NMR Center , National Institute of Chemistry , SI-1000 Ljubljana , Slovenia
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Republic of Korea
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47
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Paul S, Samanta A. Ground- and Excited-State Interactions of a Psoralen Derivative with Human Telomeric G-Quadruplex DNA. J Phys Chem B 2018; 122:2277-2286. [PMID: 29376354 DOI: 10.1021/acs.jpcb.7b12475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
G-quadruplex DNA has been a recent target for anticancer agents, and its binding interactions with small molecules, often used as anticancer drugs, have become an important area of research. Considering that psoralens have long been studied in the context of duplex DNA but that very little is known about their potential as G-quadruplex binders and their excited-state interaction with the latter has not been explored, we have studied herein the binding of a planar water-soluble psoralen derivative, 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), with the 22-mer human telomeric G-quadruplex-forming sequence, AGGG(TTAGGG)3, labeled here as (hTel22), and investigated the consequences of photoexcitation of AMT by calorimetric and spectroscopic techniques. The results show an enthalpy-driven 1:1 binding of AMT with hTel22 via end-stacking mode. Fluorescence quenching experiments on 6-fluorescein amidite-labeled oligomers indicate that the binding site is nearer to the 3' end of hTel22 in the diagonal loop region. Femtosecond time-resolved transient absorption measurements indicate electron transfer from the guanine moiety of hTel22 to photoexcited AMT, leading to the formation of a radical pair species (AMT•-G•+), which survives for 30 ps and is favored by a parallel/quasi-parallel orientation between the two. The findings reveal psoralens as a prospective class of compounds for the development of anticancer therapeutics by targeting the G-quadruplex DNA.
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Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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48
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Lee J, Im H, Chong SH, Ham S. Role of electrostatic interactions in determining the G-quadruplex structures. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.11.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Greco ML, Kotar A, Rigo R, Cristofari C, Plavec J, Sissi C. Coexistence of two main folded G-quadruplexes within a single G-rich domain in the EGFR promoter. Nucleic Acids Res 2017; 45:10132-10142. [PMID: 28973461 PMCID: PMC5737278 DOI: 10.1093/nar/gkx678] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/22/2017] [Indexed: 12/15/2022] Open
Abstract
EGFR is an oncogene which codifies for a tyrosine kinase receptor that represents an important target for anticancer therapy. Indeed, several human cancers showed an upregulation of the activity of this protein. The promoter of this gene contains some G-rich domains, thus representing a yet unexplored point of intervention to potentially silence this gene. Here, we explore the conformational equilibria of a 30-nt long sequence located at position −272 (EGFR-272). By merging spectroscopic and electrophoretic analysis performed on the wild-type sequence as well as on a wide panel of related mutants, we were able to prove that in potassium ion containing solution this sequence folds into two main G-quadruplex structures, one parallel and one hybrid. They show comparable thermal stabilities and affinities for the metal ion and, indeed, they are always co-present in solution. The folding process is driven by a hairpin occurring in the domain corresponding to the terminal loop which works as an important stabilizing element for both the identified G-quadruplex arrangements.
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Affiliation(s)
- Maria L Greco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Camilla Cristofari
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
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50
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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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