1
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Lacen A, Symasek A, Gunter A, Lee HT. Slow G-Quadruplex Conformation Rearrangement and Accessibility Change Induced by Potassium in Human Telomeric Single-Stranded DNA. J Phys Chem B 2024; 128:5950-5965. [PMID: 38875355 PMCID: PMC11216195 DOI: 10.1021/acs.jpcb.4c00719] [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: 02/01/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The guanine-rich telomeric repeats can form G-quadruplexes (G4s) that alter the accessibility of the single-stranded telomeric overhang. In this study, we investigated the effects of Na+ and K+ on G4 folding and accessibility through cation introduction and exchange. We combined differential scanning calorimetry (DSC), circular dichroism (CD), and single molecule Förster resonance energy transfer (smFRET) to monitor the stability, conformational dynamics, and complementary strand binding accessibility of G4 formed by single-stranded telomeric DNA. Our data showed that G4 formed through heating and slow cooling in K+ solution exhibited fewer conformational dynamics than G4 formed in Na+ solution, which is consistent with the higher thermal stability of G4 in K+. Monitoring cation exchange with real time smFRET at room temperature shows that Na+ and K+ can replace each other in G4. When encountering high K+ at room or body temperature, G4 undergoes a slow conformational rearrangement process which is mostly complete by 2 h. The slow conformational rearrangement ends with a stable G4 that is unable to be unfolded by a complementary strand. This study provides new insights into the accessibility of G4 forming sequences at different time points after introduction to a high K+ environment in cells, which may affect how the nascent telomeric overhang interacts with proteins and telomerase.
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Affiliation(s)
- Arianna
N. Lacen
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Andrew Symasek
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Alan Gunter
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Hui-Ting Lee
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
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2
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Umesh, Chandran VC, Saha P, Nath D, Bera S, Bhattacharya S, Pal A. A hydrogel based on Fe(II)-GMP demonstrates tunable emission, self-healing mechanical strength and Fenton chemistry-mediated notable antibacterial properties. NANOSCALE 2024. [PMID: 38899974 DOI: 10.1039/d4nr01011f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Supramolecular hydrogels serve as an excellent platform to enable in situ reactive oxygen species (ROS) generation while maintaining controlled localized conditions, thereby mitigating cytotoxicity. Herein, we demonstrate hydrogel formation using guanosine-5'-monophosphate (GMP) with tetra(4-carboxylphenyl) ethylene (1) to exhibit aggregation-induced emission (AIE) and tunable mechanical strength in the presence of divalent metal ions such as Ca2+, Mg2+, and Fe2+. The addition of divalent metal ions leads to structural transformation in the metallogels (M-1GMP). Furthermore, the incorporation of Fe2+ ions into the hydrogel (Fe-1GMP) promotes the Fenton reaction that could be upregulated upon adding ascorbic acid (AA), demonstrating antibacterial efficacy via ROS generation. In vitro studies on AA-loaded Fe-1GMP demonstrate excellent bacterial killing efficacy against E. coli, S. aureus and vancomycin-resistant enterococci (VRE) strains. Finally, in vivo studies involving topical administration of Fe-1GMP to Balb/c mice with skin infections further suggest the potential antibacterial efficacy of the hydrogel. Taken together, the hydrogel with its unique combination of mechanical tunability, ROS generation capability and antibacterial efficacy can be used for biomedical applications, particularly in wound healing and infection control.
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Affiliation(s)
- Umesh
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Vysakh C Chandran
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Pranay Saha
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
| | - Debasish Nath
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
| | - Sayan Bera
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Yerpedu Mandal, Tirupati District, Andhra Pradesh, 517619, India
| | - Asish Pal
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab 140306, India.
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3
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Szymczyk A, Popiołek M, Baran D, Olszewski M, Ziółkowski R, Malinowska E. Aptamer and Electrochemical Aptasensor towards Selenate Ions (SeO 42-). Int J Mol Sci 2024; 25:6660. [PMID: 38928366 PMCID: PMC11203472 DOI: 10.3390/ijms25126660] [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: 05/25/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Selenium is an essential inorganic compound in human and animal nutrition, involved in the proper functioning of the body. As a micronutrient, it actively contributes to the regulation of various metabolic activities, i.e., thyroid hormone, and protection against oxidative stress. However, Se exhibits a narrow concentration window between having a positive effect and exerting a toxic effect. In higher doses, it negatively affects living organisms and causes DNA damage through the formation of free radicals. Increased reactivity of Se anions can also disrupt the integrity and function of DNA-repairing proteins. As the permissible concentration of Se in drinking water is 10 µg/L, it is vital to develop sensitive and robust methods of Se detection in aqueous samples. In this study, for the first time, we proposed a selective aptamer for selenate ion detection, chosen following the SELEX process, and its application in the construction of an electrochemical aptasensor towards SeO42- ions. Measurement conditions such as the used redox marker and pH value of the measurement solution were chosen. The proposed aptasensor is characterized by good selectivity and an LOD of 1 nM. Conditions for biosensor regeneration and storage were also investigated in this research.
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Affiliation(s)
- Anna Szymczyk
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
- Doctoral School, Warsaw University of Technology, Plac Politechniki 1, 00-661 Warsaw, Poland
| | - Martyna Popiołek
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Dominika Baran
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-664 Warsaw, Poland;
| | - Robert Ziółkowski
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Elżbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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4
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Piteša T, Polonius S, González L, Mai S. Excitonic Configuration Interaction: Going Beyond the Frenkel Exciton Model. J Chem Theory Comput 2024. [PMID: 38885637 DOI: 10.1021/acs.jctc.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We present the excitonic configuration interaction (ECI) method─a fragment-based analogue of the CI method for electronic structure calculations of multichromophoric systems. It can also be viewed as a generalization of the exciton approach, with the following properties: (i) It constructs the effective Hamiltonian exclusively from monomer calculations. (ii) It employs the strong orthogonality assumption and is exact within McWeeny's group function theory, thus requiring only one-electron density matrices of the monomer states. (iii) It is agnostic of the monomer electronic structure method, allowing us to use/combine different methods. (iv) It includes an embedding point charge scheme (called excitonic Hartree-Fock, EHF) to improve the accuracy of the monomer states, but such that the effective full-system Hamiltonian is not explicitly dependent on the embedding. (v) It is systematically improvable, by expanding the set of monomer states and by including configurations where two or more monomers are excited (defining the ECIS, ECISD, etc., methods). The performance of ECI is assessed by computing the absorption spectrum of two exemplary multichromophoric systems, using CIS as the monomer electronic structure method. The accuracy of ECI significantly depends on the chosen embedding charges and the ECI expansion. The most accurate assessed combinations─ECIS or ECISD with EHF embedding─yield spectra that agree qualitatively and quantitatively with full-system direct calculations, with deviations of the excitation energies below 0.1 eV. We also show that ECISD based on CIS monomer calculations can predict states where two monomers are excited simultaneously (e.g., triplet-triplet double-local excitations) that are inaccessible in a full-system CIS calculation.
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Affiliation(s)
- Tomislav Piteša
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Severin Polonius
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna 1090, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna Research Platform Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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5
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Troisi R, Sica F. Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins. Curr Opin Struct Biol 2024; 87:102846. [PMID: 38848656 DOI: 10.1016/j.sbi.2024.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024]
Abstract
Since the discovery of G-quadruplex (G4) participation in vital cellular processes, the regulation of the interaction of naturally occurring G4s with the relative target proteins has emerged as a promising approach for therapeutic development. Additionally, a synthetic strategy has produced several oligonucleotide aptamers, embodying a G4 module, which exhibit relevant biological activity by binding selectively to a target protein. In this context, the G4-protein structures available in the Protein Data Bank represent a valuable molecular view of the different G4 topologies involved in protein interaction. Interestingly, recent results have showed the co-existence of G4s with other structural domains such as duplexes. Overall, these findings allow a better understanding of the mechanisms that regulate intricate biological functions and suggest new design for innovative medical treatments.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy; Institute of Biostructures and Bioimaging, CNR, via Pietro Castellino 111, 80131 Naples, Italy. https://twitter.com/TroRom
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy.
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6
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Choudhury SD, Kumar P, Choudhury D. Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3585-3616. [PMID: 38019298 DOI: 10.1007/s00210-023-02857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth-promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena.
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Affiliation(s)
- Satabdi Datta Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, 175005, India
| | - Diptiman Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
- Centre for Excellence in Emerging Materials, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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7
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Gorb L, Voiteshenko I, Hurmach V, Zarudnaya M, Nyporko A, Shyryna T, Platonov M, Roszak S, Rasulev B. From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA. NAR Genom Bioinform 2024; 6:lqae062. [PMID: 38835951 PMCID: PMC11148665 DOI: 10.1093/nargab/lqae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.
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Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Ivan Voiteshenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Vasyl Hurmach
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Margarita Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Tetiana Shyryna
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Maksym Platonov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Szczepan Roszak
- Faculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA
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8
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Mehrdad SA, Cucchiarini A, Mergny JL, Noureini SK. Heavy metal ions interactions with G-quadruplex-prone DNA sequences. Biochimie 2024:S0300-9084(24)00123-8. [PMID: 38821199 DOI: 10.1016/j.biochi.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The industrial world exposes living organisms to a variety of metal pollutants. Here we investigated whether such elements affect G-rich sequences susceptible to fold into G-quadruplex (GQ) structures. Thermal stability and conformation of these oligoncleotides was studied at various molar ratios of a variety of heavy metal salts using thermal FRET, transition-FRET (t-FRET) and circular dichroism. Metal ions affected the thermal stability of the GQs to different extents; some metals had no effect on Tm while other metals caused small to moderate changes in Tm at 1:1 or 1:10 molar ratio. While most of the metals had no major effect, Al3+, Cd2+, Pb2+, Hg2+ and Zn2+ altered the thermal stability and structural features of the GQs. Some metals such as Pb2+ and Hg2+ exhibit differential interactions with telomere, c-myc and c-kit GQs. Overall, toxic heavy metals affect G-quadruplex stability in a sequence and topology dependent manner. This study provides new insight into how heavy metal exposure may affect gene expression and cellular responses.
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Affiliation(s)
- Seyyed-Ali Mehrdad
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Sakineh Kazemi Noureini
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran.
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9
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Chakraborty G, Balinin K, Villar-Guerra RD, Emondts M, Portale G, Loznik M, Niels Klement WJ, Zheng L, Weil T, Chaires JB, Herrmann A. Supramolecular DNA-based catalysis in organic solvents. iScience 2024; 27:109689. [PMID: 38706840 PMCID: PMC11067378 DOI: 10.1016/j.isci.2024.109689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/04/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
The distinct folding accompanied by its polymorphic character renders DNA G-quadruplexes promising biomolecular building blocks to construct novel DNA-based and supramolecular assemblies. However, the highly polar nature of DNA limits the use of G-quadruplexes to water as a solvent. In addition, the archetypical G-quadruplex fold needs to be stabilized by metal-cations, which is usually a potassium ion. Here, we show that a noncovalent PEGylation process enabled by electrostatic interactions allows the first metal-free G-quadruplexes in organic solvents. Strikingly, incorporation of an iron-containing porphyrin renders the self-assembled metal-free G-quadruplex catalytically active in organic solvents. Hence, these "supraG4zymes" enable DNA-based catalysis in organic media. The results will allow the broad utilization of DNA G-quadruplexes in nonaqueous environments.
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Affiliation(s)
- Gurudas Chakraborty
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Konstantin Balinin
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Rafael del Villar-Guerra
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Meike Emondts
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Giuseppe Portale
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Mark Loznik
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Wiebe Jacob Niels Klement
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Lifei Zheng
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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10
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Cui Y, Liu H, Ming Y, Zhang Z, Liu L, Liu R. Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data. Brief Funct Genomics 2024; 23:265-275. [PMID: 37357985 DOI: 10.1093/bfgp/elad024] [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: 03/17/2023] [Revised: 05/20/2023] [Accepted: 06/01/2023] [Indexed: 06/27/2023] Open
Abstract
G-quadruplex (G4), a non-classical deoxyribonucleic acid structure, is widely distributed in the genome and involved in various biological processes. In vivo, high-throughput sequencing has indicated that G4s are significantly enriched at functional regions in a cell-type-specific manner. Therefore, the prediction of G4s based on computational methods is necessary instead of the time-consuming and laborious experimental methods. Recently, G4 CUT&Tag has been developed to generate higher-resolution sequencing data than ChIP-seq, which provides more accurate training samples for model construction. In this paper, we present a new dataset construction method based on G4 CUT&Tag sequencing data and an XGBoost prediction model based on the machine learning boost method. The results show that our model performs well within and across cell types. Furthermore, sequence analysis indicates that the formation of G4 structure is greatly affected by the flanking sequences, and the GC content of the G4 flanking sequences is higher than non-G4. Moreover, we also identified G4 motifs in the high-resolution dataset, among which we found several motifs for known transcription factors (TFs), such as SP2 and BPC. These TFs may directly or indirectly affect the formation of the G4 structure.
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Affiliation(s)
- Yizhi Cui
- School of Computer Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324003, Zhejiang, China
| | - Hongzhi Liu
- School of Computer Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Yutong Ming
- School of Computer Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Zheng Zhang
- Department of Computer Science and Software Engineering, Auburn University, Auburn, 36830, Alabama, USA
| | - Li Liu
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324003, Zhejiang, China
| | - Ruijun Liu
- School of Computer Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
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11
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Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [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: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
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Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
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12
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Hisey JA, Radchenko EA, Mandel NH, McGinty R, Matos-Rodrigues G, Rastokina A, Masnovo C, Ceschi S, Hernandez A, Nussenzweig A, Mirkin S. Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures. Nucleic Acids Res 2024; 52:4361-4374. [PMID: 38381906 PMCID: PMC11077069 DOI: 10.1093/nar/gkae124] [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: 07/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | | | - Ryan J McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115, USA
| | | | | | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD20892, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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13
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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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14
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Song K, Li B, Li H, Zhang R, Zhang X, Luan R, Liu Y, Yang L. The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress. Int J Mol Sci 2024; 25:4331. [PMID: 38673916 PMCID: PMC11050182 DOI: 10.3390/ijms25084331] [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: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants.
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Affiliation(s)
- Kangkang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Bin Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Haozhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Rui Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohua Zhang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Ruiwei Luan
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
- College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Ying Liu
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China; (K.S.); (B.L.)
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15
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Tanabe K, Miyazaki K, Umeno H, Takemoto M, Nakano S. Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes. Biochimie 2024; 219:110-117. [PMID: 37972915 DOI: 10.1016/j.biochi.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Affiliation(s)
- Kazuya Tanabe
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouichi Miyazaki
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hikari Umeno
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Marina Takemoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - S Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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16
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Bisoi A, Sarkar S, Singh PC. Loop nucleobases-dependent folding of G-quadruplex in normal and cancer cell-mimicking KCl microenvironments. Int J Biol Macromol 2024; 265:131050. [PMID: 38522708 DOI: 10.1016/j.ijbiomac.2024.131050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
In this study, the folding of G-quadruplex (G4) from the telomeric DNA sequences having loop nucleobases of different chemical natures, numbers, and arrangements in 10 mM and 100 mM KCl salt conditions mimicking the cancerous and normal KCl salt microenvironments have been investigated. The data suggest that the structure and stability of the G4 are highly dependent on the KCl salt concentration. In general, the conformational flexibility of the folded G4 is higher in KCl salt relevant to cancer than in the normal case for any loop arrangements with the same number of nucleobases. The stability of the G4 decreases with the increase in the number of loop nucleobases for both salt conditions. However, the decrease in the stability of G4 having adenine in the loop region is significantly higher than the case of thymine, particularly more prominent in the KCl salt relevant to the cancer. The topology of the folded G4 and its stability also depend delicately on the permutation of the nucleobases in the loop and the salt concentrations for a particular sequence. The findings indicate that the structure and stability of G4 are noticeably different in KCl salt relevant to physiological and cancer conditions.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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17
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Dobrovodsky D, Danhel A, Renciuk D, Mergny JL, Fojta M. N-methyl mesoporphyrin IX (NMM) as electrochemical probe for detection of guanine quadruplexes. Bioelectrochemistry 2024; 156:108611. [PMID: 37995502 DOI: 10.1016/j.bioelechem.2023.108611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
G-quadruplexes (G4) are stable alternative secondary structures of nucleic acids. With increasing understanding of their roles in biological processes and their application in bio- and nanotechnology, the exploration of novel methods for the analysis of these structures is becoming important. In this work, N-methyl mesoporphyrin IX (NMM) was used as a voltammetric probe for an easy electrochemical detection of G4s. Cyclic voltammetry on a hanging mercury drop electrode (HMDE) was used to detect NMM with a limit of detection (LOD) of 40 nM. Characteristic reduction signal of NMM was found to be substantially higher in the presence of G4 oligodeoxynucleotides (ODNs) than in the presence of single- or double-stranded ODNs and even ODNs susceptible to form G4s but in their unfolded, single-stranded forms. Gradual transition from unstructured single strand to G4, induced by increasing concentrations of the G4 stabilizing K+ ions, was detected by an electrochemical method for the first time. All obtained results were supported by circular dichroism spectroscopy. This work expands on the concept of electrochemical probes utilization in DNA secondary structure recognition and offers a proof of principle that can be potentially employed in the development of novel electroanalytical methods for nucleic acid structure studies.
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Affiliation(s)
- Daniel Dobrovodsky
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Ales Danhel
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic.
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18
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Luige J, Armaos A, Tartaglia GG, Ørom UAV. Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation. Nat Commun 2024; 15:2585. [PMID: 38519458 PMCID: PMC10959947 DOI: 10.1038/s41467-024-46731-9] [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: 04/06/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
RNA-binding proteins are central for many biological processes and their characterization has demonstrated a broad range of functions as well as a wide spectrum of target structures. RNA G-quadruplexes are important regulatory elements occurring in both coding and non-coding transcripts, yet our knowledge of their structure-based interactions is at present limited. Here, using theoretical predictions and experimental approaches, we show that many chromatin-binding proteins bind to RNA G-quadruplexes, and we classify them based on their RNA G-quadruplex-binding potential. Combining experimental identification of nuclear RNA G-quadruplex-binding proteins with computational approaches, we build a prediction tool that assigns probability score for a nuclear protein to bind RNA G-quadruplexes. We show that predicted G-quadruplex RNA-binding proteins exhibit a high degree of protein disorder and hydrophilicity and suggest involvement in both transcription and phase-separation into membrane-less organelles. Finally, we present the G4-Folded/UNfolded Nuclear Interaction Explorer System (G4-FUNNIES) for estimating RNA G4-binding propensities at http://service.tartaglialab.com/new_submission/G4FUNNIES .
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Affiliation(s)
- Johanna Luige
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Catalan Institution for Research and Advanced Studies ICREA Passeig Lluis Companys, 23 08010, Barcelona, Spain.
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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19
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Figueiredo J, Mergny JL, Cruz C. G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives. Life Sci 2024; 340:122481. [PMID: 38301873 DOI: 10.1016/j.lfs.2024.122481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti-cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau cedex, France; Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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20
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Minero GA, Møllebjerg A, Thiesen C, Johansen M, Jørgensen N, Birkedal V, Otzen DE, Meyer R. Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity. Nucleic Acids Res 2024; 52:1575-1590. [PMID: 38296834 PMCID: PMC10939358 DOI: 10.1093/nar/gkae034] [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: 06/30/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Many bacteria form biofilms to protect themselves from predators or stressful environmental conditions. In the biofilm, bacteria are embedded in a protective extracellular matrix composed of polysaccharides, proteins and extracellular DNA (eDNA). eDNA most often is released from lysed bacteria or host mammalian cells, and it is the only matrix component most biofilms appear to have in common. However, little is known about the form DNA takes in the extracellular space, and how different non-canonical DNA structures such as Z-DNA or G-quadruplexes might contribute to its function in the biofilm. The aim of this study was to determine if non-canonical DNA structures form in eDNA-rich staphylococcal biofilms, and if these structures protect the biofilm from degradation by nucleases. We grew Staphylococcus epidermidis biofilms in laboratory media supplemented with hemin and NaCl to stabilize secondary DNA structures and visualized their location by immunolabelling and fluorescence microscopy. We furthermore visualized the macroscopic biofilm structure by optical coherence tomography. We developed assays to quantify degradation of Z-DNA and G-quadruplex DNA oligos by different nucleases, and subsequently investigated how these enzymes affected eDNA in the biofilms. Z-DNA and G-quadruplex DNA were abundant in the biofilm matrix, and were often present in a web-like structures. In vitro, the structures did not form in the absence of NaCl or mechanical shaking during biofilm growth, or in bacterial strains deficient in eDNA or exopolysaccharide production. We thus infer that eDNA and polysaccharides interact, leading to non-canonical DNA structures under mechanical stress when stabilized by salt. We also confirmed that G-quadruplex DNA and Z-DNA was present in biofilms from infected implants in a murine implant-associated osteomyelitis model. Mammalian DNase I lacked activity against Z-DNA and G-quadruplex DNA, while Micrococcal nuclease could degrade G-quadruplex DNA and S1 Aspergillus nuclease could degrade Z-DNA. Micrococcal nuclease, which originates from Staphylococcus aureus, may thus be key for dispersal of biofilm in staphylococci. In addition to its structural role, we show for the first time that the eDNA in biofilms forms a DNAzyme with peroxidase-like activity in the presence of hemin. While peroxidases are part of host defenses against pathogens, we now show that biofilms can possess intrinsic peroxidase activity in the extracellular matrix.
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Affiliation(s)
| | - Andreas Møllebjerg
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Celine Thiesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Mikkel Illemann Johansen
- Department Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens bvld 99, 8200 Aarhus N, Denmark
| | - Nis Pedersen Jørgensen
- Department Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens bvld 99, 8200 Aarhus N, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus, Denmark
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21
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Johnson S, Paul T, Sanford S, Schnable BL, Detwiler A, Thosar S, Van Houten B, Myong S, Opresko P. BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions. Nucleic Acids Res 2024; 52:1763-1778. [PMID: 38153143 PMCID: PMC10939409 DOI: 10.1093/nar/gkad1209] [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: 06/16/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
BG4 is a single-chain variable fragment antibody shown to bind various G-quadruplex (GQ) topologies with high affinity and specificity, and to detect GQ in cells, including GQ structures formed within telomeric TTAGGG repeats. Here, we used ELISA and single-molecule pull-down (SiMPull) detection to test how various lengths and GQ destabilizing base modifications in telomeric DNA constructs alter BG4 binding. We observed high-affinity BG4 binding to telomeric GQ independent of telomere length, although three telomeric repeat constructs that cannot form stable intramolecular GQ showed reduced affinity. A single guanine substitution with 8-aza-7-deaza-G, T, A, or C reduced affinity to varying degrees depending on the location and base type, whereas two G substitutions in the telomeric construct dramatically reduced or abolished binding. Substitution with damaged bases 8-oxoguanine and O6-methylguanine failed to prevent BG4 binding although affinity was reduced depending on lesion location. SiMPull combined with FRET revealed that BG4 binding promotes folding of telomeric GQ harboring a G to T substitution or 8-oxoguanine. Atomic force microscopy revealed that BG4 binds telomeric GQ with a 1:1 stoichiometry. Collectively, our data suggest that BG4 can recognize partially folded telomeric GQ structures and promote telomeric GQ stability.
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Affiliation(s)
- Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Brittani L Schnable
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15213, USA
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22
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Cervenak M, Molnár OR, Horváth P, Smeller L. Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3. Int J Mol Sci 2024; 25:2482. [PMID: 38473730 DOI: 10.3390/ijms25052482] [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: 12/19/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The G-quadruplex is one of the non-canonical structures formed by nucleic acids, which can be formed by guanine-rich sequences. They became the focus of much research when they were found in several oncogene promoter regions and also in the telomeres. Later on, they were discovered in viruses as well. Various ligands have been developed in order to stabilize DNA G-quadruplexes, which were believed to have an anti-cancer or antiviral effect. We investigated three of these ligands, and whether they can also affect the stability of the G-quadruplex-forming sequences of the RNA genome of SARS-CoV-2. All three investigated oligonucleotides showed the G-quadruplex form. We characterized their stability and measured their thermodynamic parameters using the Förster resonance energy transfer method. The addition of the ligands caused an increase in the unfolding temperature, but this effect was smaller compared to that found earlier in the case of G-quadruplexes of the hepatitis B virus, which has a DNA genome.
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Affiliation(s)
- Miklós Cervenak
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
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23
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Jarczewska M, Sokal M, Olszewski M, Malinowska E. Studies on the Aptasensor Miniaturization for Electrochemical Detection of Lead Ions. BIOSENSORS 2024; 14:110. [PMID: 38392029 PMCID: PMC10886534 DOI: 10.3390/bios14020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Lead poses severe effects on living organisms, and since Pb2+ ions tend to accumulate in different organs, it is crucial to monitor Pb2+ concentration in samples such as water and soil. One of the approaches is the utilization of biosensors combined with aptamer-based layers for the electrochemical detection of lead ions. Herein, we present the studies of applying miniaturized screen-printed transducers as solid surfaces to fabricate aptamer layers. As the research is the direct continuation of our previous studies regarding the use of gold disk electrodes, the working parameters of elaborated aptasensors were defined, including the range of linear response (10-100 nM), selectivity as well as stability, regeneration, and feasibility of application for the analysis of real samples. This was achieved using voltammetric techniques including cyclic and square-wave voltammetry in the presence of methylene blue redox indicator.
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Affiliation(s)
- Marta Jarczewska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marta Sokal
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-664 Warsaw, Poland;
| | - Elzbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Center for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, 19 Poleczki, 02-822 Warsaw, Poland
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24
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Gu L, Ding Y, Zhou Y, Zhang Y, Wang D, Liu J. Selective Hemin Binding by a Non-G-quadruplex Aptamer with Higher Affinity and Better Peroxidase-like Activity. Angew Chem Int Ed Engl 2024; 63:e202314450. [PMID: 38150561 DOI: 10.1002/anie.202314450] [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: 09/26/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 12/29/2023]
Abstract
Previous aptamers for porphyrins and metalloporphyrins were all guanine-rich sequences that can fold in G-quadruplex structures. Due to stacking-based binding, these aptamers can hardly tell different porphyrins apart, and they can also bind other planar molecules, hindering their practical applications. In this work, we used the capture selection method to obtain aptamers for hemin and protoporphyrin IX (PPIX). The hemin aptamer (Hem1) features two highly conserved repeating binding loops, and it cannot form a G-quadruplex, which was supported by its Mg2+ -dependent but K+ -independent hemin binding and CD spectroscopy. Isothermal titration calorimetry revealed much higher enthalpy change for the new aptamer, and the best aptamer showed a Kd of 43 nM hemin. Hem1 can also enhance the peroxidase-like activity of hemin. This work demonstrates that aptamers have alternative ways to bind porphyrins allowing selective recognition of different porphyrins.
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Affiliation(s)
- Lide Gu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Yang Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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25
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Gemmill DL, Nelson CR, Badmalia MD, Pereira HS, Kerr L, Wolfinger MT, Patel TR. The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17. Biochem Cell Biol 2024; 102:96-105. [PMID: 37774422 DOI: 10.1139/bcb-2023-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023] Open
Abstract
Zika virus (ZIKV) infection remains a worldwide concern, and currently no effective treatments or vaccines are available. Novel therapeutics are an avenue of interest that could probe viral RNA-human protein communication to stop viral replication. One specific RNA structure, G-quadruplexes (G4s), possess various roles in viruses and all domains of life, including transcription and translation regulation and genome stability, and serves as nucleation points for RNA liquid-liquid phase separation. Previous G4 studies on ZIKV using a quadruplex forming G-rich sequences Mapper located a potential G-quadruplex sequence in the 3' terminal region (TR) and was validated structurally using a 25-mer oligo. It is currently unknown if this structure is conserved and maintained in a large ZIKV RNA transcript and its specific roles in viral replication. Using bioinformatic analysis and biochemical assays, we demonstrate that the ZIKV 3' TR G4 is conserved across all ZIKV isolates and maintains its structure in a 3' TR full-length transcript. We further established the G4 formation using pyridostatin and the BG4 G4-recognizing antibody binding assays. Our study also demonstrates that the human DEAD-box helicases, DDX3X132-607 and DDX17135-555, bind to the 3' TR and that DDX17135-555 unfolds the G4 present in the 3' TR. These findings provide a path forward in potential therapeutic targeting of DDX3X or DDX17's binding to the 3' TR G4 region for novel treatments against ZIKV.
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Affiliation(s)
- Dannielle L Gemmill
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Corey R Nelson
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Higor S Pereira
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Liam Kerr
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- RNA Forecast e.U., 1140 Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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26
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Bethur E, Guha R, Zhao Z, Katz BB, Ashby PD, Zeng H, Copp SM. Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution. ACS NANO 2024; 18:3002-3010. [PMID: 38227309 PMCID: PMC10832345 DOI: 10.1021/acsnano.3c08008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Silver cations can mediate base pairing of guanine (G) DNA oligomers, yielding linear parallel G-Ag+-G duplexes with enhanced stabilities compared to those of canonical DNA duplexes. To enable their use in programmable DNA nanotechnologies, it is critical to understand solution-state formation and the nanomechanical stiffness of G-Ag+-G duplexes. Using temperature-controlled circular dichroism (CD) spectroscopy, we find that heating mixtures of G oligomers and silver salt above 50 °C fully destabilizes G-quadruplex structures and converts oligomers to G-Ag+-G duplexes. Electrospray ionization mass spectrometry supports that G-Ag+-G duplexes form at stoichiometries of 1 Ag+ per base pair, and CD spectroscopy suggests that as the Ag+/base stoichiometry increases further, G-Ag+-G duplexes undergo additional morphological changes. Using liquid-phase atomic force microscopy, we find that this excess Ag+ enables assembly of long fiberlike structures with ∼2.5 nm heights equivalent to a single DNA duplex but with lengths that far exceed a single duplex. Finally, using the conditions established to form single G-Ag+-G duplexes, we use a surface forces apparatus (SFA) to compare the solution-phase stiffness of single G-Ag+-G duplexes with dG-dC Watson-Crick-Franklin duplexes. SFA shows that G-Ag+-G duplexes are 1.3 times stiffer than dG-dC duplexes, confirming gas-phase ion mobility spectrometry measurements and computational predictions. These findings may guide the development of structural DNA nanotechnologies that rely on silver-mediated base pairing.
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Affiliation(s)
- Eshana Bethur
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Rweetuparna Guha
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Ziqian Zhao
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Paul D. Ashby
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongbo Zeng
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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27
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Majumder P, Shukla C, Arya A, Sharma S, Datta B. G-quadruplexes in MTOR and induction of autophagy. Sci Rep 2024; 14:2525. [PMID: 38291093 PMCID: PMC10827794 DOI: 10.1038/s41598-024-52561-y] [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: 11/02/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024] Open
Abstract
G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy, a crucial homeostatic mechanism of the cell, is often dysregulated in neurodegenerative diseases and cancers. We used QGRS mapper to identify 470 G4 sequences in MTOR, a key negative regulator of autophagy. We sought to identify a functional context by leveraging the effect of G4-targeting ligands on MTOR G4 sequences. The effect of Bis-4,3, a G4 selective dimeric carbocyanine dye, was compared with the known G4-stabilizing activity of the porphyrin, TMPyP4 in HeLa and SHSY-5Y cells. Our results show that treatment with G4-selective ligands downregulates MTOR RNA and mTOR protein expression levels. This is the first report describing G4 motifs in MTOR. This study indicates a possible role of G4 stabilizing ligands in induction of autophagy by downregulation of mTOR levels, albeit not precluding MTOR independent pathways.
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Affiliation(s)
- Piyali Majumder
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Arjun Arya
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Shubham Sharma
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India.
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India.
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28
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Valle-Orero J, Rieu M, Allemand JF, Bujaa D, Joubert A, Tran PLT, Croquette V, Boulé JB. Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers. Methods Enzymol 2024; 695:119-158. [PMID: 38521583 DOI: 10.1016/bs.mie.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplexes (G4s) are nucleic acids secondary structures that may form in guanine-rich sequences, either intra or inter-molecularly. Ability of a primary sequence to form a G4 can be predicted computationally with an improving accuracy as well as tested in bulk using biophysical measurements. As a result, G4 density maps have been devised for a large number of genomes from all life kingdoms. Experimental validation of the formation of G4s in vivo however remains indirect and relies on their stabilization with small molecules, antibodies or proteins, or mutational studies, in order to measure downstream effects on gene expression or genome stability for example. Although numerous techniques exist to observe spontaneous formation of G4s in single-stranded DNA, observing G4 formation in double-stranded DNA (dsDNA) is more challenging. However, it is particularly relevant to understand if a given G4 sequence forms stably in a dsDNA context, if it is stable enough to dock proteins or pose a challenge to molecular motors such as helicases or polymerases. In essence, G4s can be a threat to genomic stability but carry as well as the potential to be elements of a structural language in the non-replicating genome. To study quantitatively the formation dynamics and stability of single intramolecular G4s embedded in dsDNA, we have adapted techniques of DNA manipulation under magnetic tweezers. This technique also allows to study encounters of molecular motors with G4 at a single molecule resolution, in order to gain insight into the specificity of G4 resolution by molecular motors, and its efficiency. The procedures described here include the design of the G4 substrate, the study of G4 formation probability and lifetime in dsDNA, as well as procedures to characterize the encounter between the Pif1 helicase and a G4 until G4 resolution. The procedures that we described here can easily be extended to the study of other G4s or molecular motors.
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Affiliation(s)
- Jessica Valle-Orero
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Computer Science, Mathematics and Environmental Sciences, The American University of Paris, Paris, France.
| | - Martin Rieu
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Jean-François Allemand
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Dulamkhuu Bujaa
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France
| | - Phong Lan Thao Tran
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France; Depixus SAS, 3-5 impasse Reille, Paris, France
| | - Vincent Croquette
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; ESPCI Paris, PSL University, Paris, France.
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France.
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29
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Zheng YY, Dartawan R, Wu Y, Wu C, Zhang H, Lu J, Hu A, Vangaveti S, Sheng J. Structural effects of inosine substitution in telomeric DNA quadruplex. Front Chem 2024; 12:1330378. [PMID: 38312345 PMCID: PMC10834636 DOI: 10.3389/fchem.2024.1330378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
The telomeric DNA, a distal region of eukaryotic chromosome containing guanine-rich repetitive sequence of (TTAGGG)n, has been shown to adopt higher-order structures, specifically G-quadruplexes (G4s). Previous studies have demonstrated the implication of G4 in tumor inhibition through chromosome maintenance and manipulation of oncogene expression featuring their G-rich promoter regions. Besides higher order structures, several regulatory roles are attributed to DNA epigenetic markers. In this work, we investigated how the structural dynamics of a G-quadruplex, formed by the telomeric sequence, is affected by inosine, a prevalent modified nucleotide. We used the standard (TTAGGG)n telomere repeats with guanosine mutated to inosine at each G position. Sequences (GGG)4, (IGG)4, (GIG)4, (GGI)4, (IGI)4, (IIG)4, (GII)4, and (III)4, bridged by TTA linker, are studied using biophysical experiments and molecular modeling. The effects of metal cations in quadruplex folding were explored in both Na+ and K+ containing buffers using CD and UV-melting studies. Our results show that antiparallel quadruplex topology forms with the native sequence (GGG)4 and the terminal modified DNAs (IGG)4 and (GGI)4 in both Na+ and K+ containing buffers. Specifically, quadruplex hybrid was observed for (GGG)4 in K+ buffer. Among the other modified sequences, (GIG)4, (IGI)4 and (GII)4 show parallel features, while (IIG)4 and (III)4 show no detectable conformation in the presence of either Na+ or K+. Our studies indicate that terminal lesions (IGG)4 and (GGI)4 may induce certain unknown conformations. The folding dynamics become undetectable in the presence of more than one inosine substitution except (IGI)4 in both buffer ions. In addition, both UV melting and CD melting studies implied that in most cases the K+ cation confers more thermodynamic stability compared to Na+. Collectively, our conformational studies revealed the diverse structural polymorphisms of G4 with position dependent G-to-I mutations in different ion conditions.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ricky Dartawan
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Yuhan Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Chengze Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Hope Zhang
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jeanne Lu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ashley Hu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jia Sheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
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30
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Ugrina M, Burkhart I, Müller D, Schwalbe H, Schwierz N. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Res 2024; 52:87-100. [PMID: 37986217 PMCID: PMC10783511 DOI: 10.1093/nar/gkad1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
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Affiliation(s)
- Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
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31
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Robinson J, Stenspil SG, Maleckaite K, Bartlett M, Di Antonio M, Vilar R, Kuimova MK. Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy. J Am Chem Soc 2024; 146:1009-1018. [PMID: 38151240 PMCID: PMC10786036 DOI: 10.1021/jacs.3c11908] [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: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.
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Affiliation(s)
- Jenna Robinson
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Stine G. Stenspil
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Karolina Maleckaite
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Molly Bartlett
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Marco Di Antonio
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Ramon Vilar
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
| | - Marina K. Kuimova
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
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32
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [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: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [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: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
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Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
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34
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Satapathy SN, Nial PS, Tulsiyan KD, Subudhi U. Light rare earth elements stabilize G-quadruplex structure in variants of human telomeric sequences. Int J Biol Macromol 2024; 254:127703. [PMID: 37918592 DOI: 10.1016/j.ijbiomac.2023.127703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Recently, light rare earth elements (LREEs) are gaining importance in modern-day technologies. Thus, the entry of LREEs into biochemical pathways cannot be ignored, which might affect the conformation of biomacromolecules. Herein, for the first time, we discover the G-quadruplex formation in the human telomeric variants in presence of micromolar concentrations of LREEs. Thermal melting show that the LREE-induced unimolecular G-quadruplex structure. Isothermal titration calorimetry, UV-vis, and CD spectroscopy results suggest the binding stoichiometry of lanthanide ions to telomeric variants is 2:1. The data confirms that the LREE ions coordinate between adjacent G-quartets. The excess LREE ions are most likely binding to quadruplex loops. The CD spectra revealed that the LREE-induced quadruplex in human telomere and its variant have antiparallel orientation. The binding equilibria of LREEs have been studied both in the presence and absence of competing metal cations. Addition of LREEs to the Na+ or K+-induced G-quadruplexes led to conformational change, which may be ascribed to the displacement of K+ or Na+ ions by LREE ions and formation of a more compact LREE-induced G-quadruplex structure in human telomeric variant. Moreover, the thymine in the central loop of the human telomeric sequence stabilizes LREE induced G-quadruplex.
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Affiliation(s)
- Sampat N Satapathy
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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35
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Lopina OD, Sidorenko SV, Fedorov DA, Klimanova EA. G-Quadruplexes as Sensors of Intracellular Na+/K + Ratio: Potential Role in Regulation of Transcription and Translation. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S262-S277. [PMID: 38621755 DOI: 10.1134/s0006297924140153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 04/17/2024]
Abstract
Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.
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Affiliation(s)
- Olga D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | | - Dmitry A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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36
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Khatri S, Pandey P, Mejia G, Ghimire G, Leng F, He J. Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes. J Am Chem Soc 2023; 145:28075-28084. [PMID: 37996390 PMCID: PMC11036617 DOI: 10.1021/jacs.3c09311] [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] [Indexed: 11/25/2023]
Abstract
Glass nanopipettes have gained widespread use as a versatile single-entity detector in chemical and biological sensing, analysis, and imaging. Its advantages include low cost, easy accessibility, simplicity of use, and high versatility. However, conventional nanopipettes based on the volume exclusion mechanism have limitations in detecting small biomolecules due to their small volume and high mobility in aqueous solution. To overcome this challenge, we have employed a novel approach by capitalizing on the strong nanoconfinement effect of nanopipettes. This is achieved by utilizing both the hard confinement provided by the long taper nanopipette tip at the cis side and the soft confinement offered by the hydrogel at the trans side. Through this approach, we have effectively slowed down the exit motion of small molecules, allowing us to enrich and jam them at the nanopipette tip. Consequently, we have achieved high throughput detection of small biomolecules with sizes as small as 1 nm, including nucleoside triphosphates, short peptides, and small proteins with excellent signal-to-noise ratios. Furthermore, molecular complex formation through specific intermolecular interactions, such as hydrogen bonding between closely spaced nucleotides in the jam-packed nanopipette tip, has been detected based on the unique ionic current changes.
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Affiliation(s)
- Santosh Khatri
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - German Mejia
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Govinda Ghimire
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Fenfei Leng
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
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37
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Kharel P, Ivanov P. Identification of bona fide RNA G-quadruplex binding proteins. Methods Enzymol 2023; 695:255-274. [PMID: 38521588 DOI: 10.1016/bs.mie.2023.12.001] [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] [Indexed: 03/25/2024]
Abstract
RNAs often accomplish their diverse functions through direct interactions with RNA-binding proteins (RBPs) in a sequence- and/or structure-dependent manner. RNA G-quadruplexes (rG4s) are unique secondary structures formed by guanine-rich RNA sequences which impact RNA function independently and in combination with RBPs. Efforts from several labs have identified dozens of rG4 specific RBPs (rG4BPs), although the research is still in the growing phase. Here we present methods for the systematic identification of rG4BPs using a pull-down approach that takes advantage of the chemical modification of guanine bases. This allows abolishing the rG4 structures while still maintaining the base composition intact, and hence helps in recognizing true rG4BPS (in contrast to G-rich motif binders). In combination with other biochemical assays, such an approach can be efficiently used for the identification and characterization of bona fide rG4BPs.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; HMS Initiative for RNA Medicine, Boston, MA, United States.
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38
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Smith DK. Supramolecular gels - a panorama of low-molecular-weight gelators from ancient origins to next-generation technologies. SOFT MATTER 2023; 20:10-70. [PMID: 38073497 DOI: 10.1039/d3sm01301d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Supramolecular gels, self-assembled from low-molecular-weight gelators (LMWGs), have a long history and a bright future. This review provides an overview of these materials, from their use in lubrication and personal care in the ancient world, through to next-generation technologies. In academic terms, colloid scientists in the 19th and early 20th centuries first understood such gels as being physically assembled as a result of weak interactions, combining a solid-like network having a degree of crystalline order with a highly mobile liquid-like phase. During the 20th century, industrial scientists began using these materials in new applications in the polymer, oil and food industries. The advent of supramolecular chemistry in the late 20th century, with its focus on non-covalent interactions and controlled self-assembly, saw the horizons for these materials shifted significantly beyond their historic rheological applications, expanding their potential. The ability to tune the LMWG chemical structure, manipulate hierarchical assembly, develop multi-component systems, and introduce new types of responsive and interactive behaviour, has been transformative. Furthermore, the dynamics of these materials are increasingly understood, creating metastable gels and transiently-fueled systems. New approaches to shaping and patterning gels are providing a unique opportunity for more sophisticated uses. These supramolecular advances are increasingly underpinning and informing next-generation applications - from drug delivery and regenerative medicine to environmental remediation and sustainable energy. In summary, this article presents a panorama over the field of supramolecular gels, emphasising how both academic and industrial scientists are building on the past, and engaging new fundamental insights and innovative concepts to open up exciting horizons for their future use.
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Affiliation(s)
- David K Smith
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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Bhowmik S, Ghosh T, Sanghvi YS, Das AK. Synthesis and Structural Studies of Nucleobase Functionalized Hydrogels for Controlled Release of Vitamins. ACS APPLIED BIO MATERIALS 2023; 6:5301-5309. [PMID: 37971725 DOI: 10.1021/acsabm.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The development of biomolecule-derived biocompatible scaffolds for drug delivery applications is an emerging research area. Herein, we have synthesized a series of nucleobase guanine (G) functionalized amino acid conjugates having different chain lengths to study their molecular self-assembly in the hydrogel state. The gelation properties have been induced by the correct choice of chain lengths of fatty acids present in nucleobase functionalized molecules. The effect of alkali metal cations, pH, and the concentration of nucleobase functionalized amino acid conjugates in the molecular self-assembly process has been explored. The presence of Hoogsteen hydrogen bonding interaction drives the formation of a G-quadruplex functionalized hydrogel. The DOSY nuclear magnetic resonance is also performed to evaluate the self-assembling behavior of the newly formed nucleobase functionalized hydrogel. The nanofibrillar morphology is responsible for the formation of a hydrogel, which has been confirmed by various microscopic experiments. The mechanical behaviors of the hydrogel were evaluated by rheological experiments. The in vitro biostability of the synthesized nucleobase amino acid conjugate is also investigated in the presence of hydrolytic enzymes proteinase K and chymotrypsin. Finally, the nucleobase functionalized hydrogel has been used as a drug delivery platform for the control and sustained pH-responsive release of vitamins B2 and B12. This synthesized nucleobase functionalized hydrogel also exhibits noncytotoxic behavior, which has been evaluated by their in vitro cell viability experiment using HEK 293 and MCF-7 cell lines.
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Affiliation(s)
- Sourav Bhowmik
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
| | - Tapas Ghosh
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Apurba K Das
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India
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40
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Zareie AR, Verma SC. Nucleolin Regulates the Expression of Kaposi's Sarcoma-Associated Herpesvirus' Latency-Associated Nuclear Antigen through G-Quadruplexes in the mRNA. Viruses 2023; 15:2438. [PMID: 38140679 PMCID: PMC10747643 DOI: 10.3390/v15122438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) establishes life-long latent infection and is linked to several human malignancies. Latency-associated nuclear antigen (LANA) is highly expressed during latency, and is responsible for the replication and maintenance of the viral genome. The expression of LANA is regulated at transcriptional/translational levels through multiple mechanisms, including the secondary structures in the mRNA sequence. LANA mRNA has multiple G-quadruplexes (G4s) that are bound by multiple proteins to stabilize/destabilize these secondary structures for regulating LANA. In this manuscript, we demonstrate the role of Nucleolin (NCL) in regulating LANA expression through its interaction with G-quadruplexes of LANA mRNA. This interaction reduced LANA's protein expression through the sequestration of mRNA into the nucleus, demonstrated by the colocalization of G4-carrying mRNA with NCL. Furthermore, the downregulation of NCL, by way of a short hairpin, showed an increase in LANA translation following an alteration in the levels of LANA mRNA in the cytoplasm. Overall, the data presented in this manuscript showed that G-quadruplexes-mediated translational control could be regulated by NCL, which can be exploited for controlling KSHV latency.
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Affiliation(s)
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA;
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Zhang X, Ren K, Xiao C, Chen X. Guanosine-driven hyaluronic acid-based supramolecular hydrogels with peroxidase-like activity for chronic diabetic wound treatment. Acta Biomater 2023; 172:206-217. [PMID: 37839631 DOI: 10.1016/j.actbio.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Guanosine is often used to construct supramolecular hydrogels due to its self-assembly properties, however, the high temperature and strong alkaline construction methods greatly limit its application in biomedical fields. In this work, a guanosine-driven hyaluronic acid-based supramolecular hydrogel was developed under mild condition by employing phenylboronic acid-functionalized hyaluronic acid (HA-PBA) backbone and guanosine molecules. Guanosines self-assembled into G-quartet planes under potassium ion conditions, and formed boronic ester bonds with HA-PBA, which induced rapid formation of dynamically cross-linked hydrogels. Hemin was then binding to the G-quartet plane via π-π interactions in the hydrogels, which exhibited peroxidase activity and were highly effective in killing bacteria by generating hydroxyl radicals in the presence of H2O2. Furthermore, glucose oxidase (GOx) was incorporated into the hydrogels and the HP/G@hemin@GOx hydrogels showed good antibacterial properties, modulation of wound glucose and ROS level, and good therapeutic efficacy for diabetic chronic wounds. Overall, the self-assembly of guanosine has been shown for the first time to be a feasible method for constructing natural polymer-based supramolecular hydrogels. This guanosine-driven HA-based supramolecular hydrogel can act as a potential wound dressing for chronic diabetic wound treatment. STATEMENT OF SIGNIFICANCE: Chronic wound repair remains an unsolved clinical challenge. Herein, we propose to utilize phenylboronic acid-modified hyaluronic acid and guanosine to construct supramolecular gels with peroxidase activity for chronic wound treatment. The self-assembly behavior of guanosine drives the natural macromolecular backbone to form the hydrogel, and the proposed method simplifies the gelation conditions and improves its biosafety. The G-quartets formed by the self-assembly of guanosine can act as the loading site for hemin. G-quartet/hemin complex imported peroxidase activity to the hydrogels, endowing them with the ability to kill bacteria and regulate ROS levels of cells in the wound site. This guanosine-driven supramolecular hydrogel significantly increased the rate of wound healing in diabetic mice, promising a new strategy for chronic wound treatment.
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Affiliation(s)
- Xiaonong Zhang
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
| | - Kaixuan Ren
- Department of Polymer Materials, School of Materials Science and Engineering, Shanghai University, Shanghai, 200444, PR China.
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China.
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
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42
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Tran VT, Turek-Herman J, Ferreira M, Martin KN, Beseiso D, Williams BR, Rosu F, Gabelica V, Burgmayer SJN, Yatsunyk LA. Interactions of ruthenium(II) polypyridyl complexes with human telomeric DNA. J Inorg Biochem 2023; 249:112388. [PMID: 37837940 PMCID: PMC10668861 DOI: 10.1016/j.jinorgbio.2023.112388] [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: 05/12/2023] [Revised: 09/12/2023] [Accepted: 09/24/2023] [Indexed: 10/16/2023]
Abstract
Eight [Ru(bpy)2L]2+ and three [Ru(phen)2L]2+complexes (where bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline are ancillary ligands, and L = a polypyridyl experimental ligand) were investigated for their G-quadruplex binding abilities. Fluorescence resonance energy transfer melting assays were used to screen these complexes for their ability to selectively stabilize human telomeric DNA variant, Tel22. The best G-quadruplex stabilizers were further characterized for their binding properties (binding constant and stoichiometry) using UV-vis, fluorescence spectroscopy, and mass spectrometry. The ligands' ability to alter the structure of Tel22 was determined via circular dichroism and PAGE studies. We identified me2allox as the experimental ligand capable of conferring excellent stabilizing ability and good selectivity to polypyridyl Ru(II) complexes. Replacing bpy by phen did not significantly impact interactions with Tel22, suggesting that binding involves mostly the experimental ligand. However, using a particular ancillary ligand can help fine-tune G-quadruplex-binding properties of Ru(II) complexes. Finally, the fluorescence "light switch" behavior of all Ru(II) complexes in the presence of Tel22 G-quadruplex was explored. All Ru(II) complexes displayed "light switch" properties, especially [Ru(bpy)2(diamino)]2+, [Ru(bpy)2(dppz)]2+, and [Ru(bpy)2(aap)]2+. Current work sheds light on how Ru(II) polypyridyl complexes interact with human telomeric DNA with possible application in cancer therapy or G-quadruplex sensing.
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Affiliation(s)
- Vienna T Tran
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Joshua Turek-Herman
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Michelle Ferreira
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | - Dana Beseiso
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
| | | | - Frederic Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600 Pessac, France.
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600 Pessac, France; Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Pessac, France.
| | | | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA, USA.
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43
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Riccardi C, Pérez de Carvasal K, Platella C, Meyer A, Smietana M, Morvan F, Montesarchio D. Probing naphthalene diimide and 3-hydroxypropylphosphate as end-conjugating moieties for improved thrombin binding aptamers: Structural and biological effects. Bioorg Chem 2023; 141:106917. [PMID: 37865055 DOI: 10.1016/j.bioorg.2023.106917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
The limitations associated with the in vivo use of the thrombin binding aptamer (TBA or TBA15) have dramatically stimulated the search of suitable chemically modified analogues in order to discover effective and reversible inhibitors of thrombin activity. In this context, we previously proposed cyclic and pseudo-cyclic TBA analogues with improved stability that proved to be more active than the parent aptamer. Herein, we have investigated a novel library of TBA derivatives carrying naphthalene diimide (NDI) moieties at the 3'- or 5'-end. In a subset of the investigated oligonucleotides, additional 3-hydroxypropylphosphate (HPP) groups were introduced at one or both ends of the TBA sequence. Evaluation of the G-quadruplex thermal stability, serum nuclease resistance and in vitro anticoagulant activity of the new TBA analogues allowed rationalizing the effect of these appendages on the activity of the aptamer on the basis of their relative position. Notably, most of the different TBA analogues tested were more potent thrombin inhibitors than unmodified TBA. Particularly, the analogue carrying an NDI group at the 5'-end and an HPP group at the 3'-end, named N-TBA-p, exhibited enhanced G-quadruplex thermal stability (ΔTm + 14° C) and ca. 10-fold improved nuclease resistance in serum compared to the native aptamer. N-TBA-p also induced prolonged and dose-dependent clotting times, showing a ca. 11-fold higher anticoagulant activity compared to unmodified TBA, as determined by spectroscopic methods. Overall, N-TBA-p proved to be in vitro a more efficient thrombin inhibitor than all the best ones previously investigated in our group. Its interesting features, associated with its easy preparation, make it a very promising candidate for future in vivo studies.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Kévan Pérez de Carvasal
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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44
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Liu Y, Wang X, Campolo G, Teng X, Ying L, Edel JB, Ivanov AP. Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores. ACS NANO 2023; 17:22999-23009. [PMID: 37947369 PMCID: PMC10690843 DOI: 10.1021/acsnano.3c08456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation in the brain has been significantly implicated in Parkinson's disease (PD). Beyond the brain, oligomers of α-Synuclein are also found in cerebrospinal fluid (CSF) and blood, where the analysis of these aggregates may provide diagnostic routes and enable a better understanding of disease mechanisms. However, detecting α-Syn in CSF and blood is challenging due to its heterogeneous protein size and shape, and low abundance in clinical samples. Nanopore technology offers a promising route for the detection of single proteins in solution; however, the method often lacks the necessary selectivity in complex biofluids, where multiple background biomolecules are present. We address these limitations by developing a strategy that combines nanopore-based sensing with molecular carriers that can specifically capture α-Syn oligomers with sizes of less than 20 nm. We demonstrate that α-Synuclein oligomers can be detected directly in clinical samples, with minimal sample processing, by their ion current characteristics and successfully utilize this technology to differentiate cohorts of PD patients from healthy controls. The measurements indicate that detecting α-Syn oligomers present in CSF may potentially provide valuable insights into the progression and monitoring of Parkinson's disease.
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Affiliation(s)
- Yaxian Liu
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Giulia Campolo
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiangyu Teng
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Liming Ying
- National
Heart and Lung Institute, Imperial College
London, Molecular Sciences Research Hub, London W12 0BZ, United Kingdom
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
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45
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Dodaro A, Pavan M, Menin S, Salmaso V, Sturlese M, Moro S. Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes. Front Mol Biosci 2023; 10:1294543. [PMID: 38028536 PMCID: PMC10679717 DOI: 10.3389/fmolb.2023.1294543] [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: 09/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases.
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Affiliation(s)
| | | | | | | | | | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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46
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [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: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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47
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Khan S, Singh A, Nain N, Kukreti S. Alkali cation-mediated topology displayed by an exonic G-rich sequence of TRPA1 gene. J Biomol Struct Dyn 2023; 41:9997-10008. [PMID: 36458452 DOI: 10.1080/07391102.2022.2150686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
G-rich sequences are intrinsic parts of the genome, widespread in promoters, telomeres, or other regulatory regions. The in vivo existence and biological significance have established the functional aspect of G-quadruplex structures and thus have developed immense interest in exploring their therapeutic aspects. Herein, using biophysical methods, we examined the structural status and comprehensive cation-dependence of a 17-bp G-rich genomic sequence (SKGT17) located in the coding region of the human TRPA1 gene, known to be associated with various neurovascular, cardiovascular, and respiratory conditions. TRPA1 is primarily seen as a therapeutic target for the development of novel analgesics. Bioinformatics analysis has suggested that 17-bp quadruplex motif is a binding site for transcription factor 'Sp1'. The formation and recognition of SKGT17 G-quadruplex might impact its regulatory functioning. Biophysical studies confirmed that the presence of alkali metal ions facilitated the formation of G-quadruplex in parallel topology. Native gel further substantiated the formation of a biomolecular species. Circular dichroism (CD), UV-thermal melting (Tm), and CD melting confirmed the formation of parallel G-quadruplex with metal ion-dependent stability. The stability of the G-quadruplex formed is found to be significantly high in the presence of K+ ions than that of other ions. Intriguingly, we have also established that this segment of the TRAP1 gene favors G-quadruplex formation over its participation in the corresponding duplex formation under K+ ions conditions. This study attempts to explain the rationale for the stabilization of G-quadruplex in the presence of alkali metal ions and may add to a better understanding and insights into DNA-metal ions interactions.
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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48
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Szeltner Z, Ferenc G, Juhász T, Kupihár Z, Váradi Z, Szüts D, Kovács L. Probing telomeric-like G4 structures with full or partial 2'-deoxy-5-hydroxyuridine substitutions. Biochimie 2023; 214:33-44. [PMID: 36707016 DOI: 10.1016/j.biochi.2023.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 01/14/2023] [Indexed: 01/26/2023]
Abstract
Guanine quadruplexes (G4s) are stable four-stranded secondary DNA structures held together by noncanonical G-G base tetrads. We synthesised the nucleoside analogue 2'-deoxy-5-hydroxyuridine (H) and inserted its phosphoramidite into telomeric repeat-type model oligonucleotides. Full and partial substitutions were made, replacing all guanines in all the three tetrads of a three-tier G4 structure, or only in the putative upper, central, or lower tetrads. We characterised these modified structures using CD, UV absorbance spectroscopy, native gel studies, and a capture oligo-based G4 disruption kinetic assay. The strand separation activity of BLM helicase on these substituted structures was also investigated. Two of the partially H-substituted constructs adopted G4-like structures, but displayed lower thermal stabilities compared to unsubstituted G4. The construct modified in its central tetrad remained mostly denatured, but the possibility of a special structure for the fully replaced variant remained open. H substitutions did not interfere with the G4-resolving activity of BLM helicase, but its efficiency was highly influenced by construct topology and even more by the G4 ligand PhenDC3. Our results suggest that the H modification can be incorporated into G quadruplexes, but only at certain positions to maintain G4 stability. The destabilizing effect observed for 2'-deoxy-5-hydroxyuridine indicates that the cytosine deamination product 5-hydroxyuracil and its nucleoside counterpart in RNA (5-hydroxyuridine), might also be destabilizing in cellular DNA and RNA quadruplexes. The kinetic assay employed in this study can be generally employed for a fast comparison of the stabilities of various G4s either in their free or ligand-bound states.
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Affiliation(s)
- Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, Eötvös Loránd Research Network, Temesvári Krt. 62, H-6726, Szeged, Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary
| | - Zoltán Kupihár
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary
| | - Zoltán Váradi
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117, Budapest, Hungary.
| | - Lajos Kovács
- Department of Medicinal Chemistry, University of Szeged, Dom Tér 8, H-6720, Szeged, Hungary.
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49
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Sardana D, Alam P, Yadav K, Clovis NS, Kumar P, Sen S. Unusual similarity of DNA solvation dynamics in high-salinity crowding with divalent cations of varying concentrations. Phys Chem Chem Phys 2023; 25:27744-27755. [PMID: 37814577 DOI: 10.1039/d3cp02606j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Double-stranded DNA bears the highest linear negative charge density (2e- per base-pair) among all biopolymers, leading to strong interactions with cations and dipolar water, resulting in the formation of a dense 'condensation layer' around DNA. Interactions involving proteins and ligands binding to DNA are primarily governed by strong electrostatic forces. Increased salt concentrations impede such electrostatic interactions - a situation that prevails in oceanic species due to their cytoplasm being enriched with salts. Nevertheless, how these interactions' dynamics are affected in crowded hypersaline environments remains largely unexplored. Here, we employ steady-state and time-resolved fluorescence Stokes shifts (TRFSS) of a DNA-bound ligand (DAPI) to investigate the static and dynamic solvation properties of DNA in the presence of two divalent cations, magnesium (Mg2+), and calcium (Ca2+) at varying high to very-high concentrations of 0.15 M, 1 M and 2 M. We compare the results to those obtained in physiological concentrations (0.15 M) of monovalent Na+ ions. Combining data from fluorescence femtosecond optical gating (FOG) and time-correlated single photon counting (TCSPC) techniques, dynamic fluorescence Stokes shifts in DNA are analysed over a broad range of time-scales, from 100 fs to 10 ns. We find that while divalent cation crowding strongly influences the DNA stability and ligand binding affinity to DNA, the dynamics of DNA solvation remain remarkably similar across a broad range of five decades in time, even in a high-salinity crowded environment with divalent cations, as compared to the physiological concentration of the Na+ ion. Steady-state and time-resolved data of the DNA-groove-bound ligand are seemingly unaffected by ion-crowding in hypersaline solution, possibly due to ions being mostly displaced by the DNA-bound ligand. Furthermore, the dynamic coupling of cations with nearby water may possibly contribute to a net-neutral effect on the overall collective solvation dynamics in DNA, owing to the strong anti-correlation of their electrostatic interaction energy fluctuations. Such dynamic scenarios may persist within the cellular environment of marine life and other biological cells that experience hypersaline conditions.
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Affiliation(s)
- Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Kavita Yadav
- 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.
| | - Pramod Kumar
- 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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50
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Kaur S, Kundu N, Sharma T, Shankaraswamy J, Saxena S. Identification of G4 motifs of various stem cell markers and their biophysical and biochemical characterization. J Biomol Struct Dyn 2023:1-10. [PMID: 37837414 DOI: 10.1080/07391102.2023.2259478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 10/16/2023]
Abstract
Regulatory regions in the human genome, enriched in guanine-rich DNA sequences have a remarkable enrichment of G-rich sequences having a tendency to fold into G-quadruplex structures. To identify the G-quadruplex forming motifs in regulatory regions of stem cell markers, gene sequences of various stem cell markers were downloaded and analyzed to see the abundance of G-rich sequences. We observed the enrichment of G-rich sequences in stem cell markers (CD13, CD19, CD24 and CD38) which could possibly play a critical role in its regulation. We used Circular Dichroism (CD), UV-Thermal denaturation (UV-Tm) and polyacrylamide gel electrophoresis (PAGE) to demonstrate the formation of a G-quadruplex by G-rich sequences present in these stem cell markers. We observed that these G-rich sequences containing minimum consecutive G3 stretch separated by loop length ranging from one to three bases long adopt G-quadruplexes with different molecularity involving two-strands, three-strand and four-strand with parallel and antiparallel conformation. Interestingly, we proposed the formation of three-stranded G-quadruplex by CD13 in 100 mM Na+, CD19 in 100 mM K+, 100 mM K+ with 40 wt% PEG 200, and CD38 in 100 mM K+ + 40 wt% PEG 200. The formation of such diverse G-quadruplex structures in the regulatory regions leaves the fair possibility of recognition by regulatory factors to modulate the gene expression. First time, this study may give insight into the structural polymorphism of G4 forming motifs in different stem cell markers to design the best suitable ligand and to target them for therapeutic development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Sri Konda Laxman Telangana State Horticultural University, Mojerla, Telangana, India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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