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Lah J, Hadži S. Thermodynamic Origin of the Linear Pressure Dependence of DNA Thermal Stability. J Phys Chem Lett 2024; 15:9064-9069. [PMID: 39194396 PMCID: PMC11382263 DOI: 10.1021/acs.jpclett.4c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
High pressure affects the structure and function of DNA and is a key parameter for studying the origin and physical limits of life. Different types of DNA structures systematically show a linear pressure dependence of thermal stability (up to ∼200 MPa), which is maintained even when the solution composition is changed. The reasons behind the linear pressure dependence are not understood. We have performed a thermodynamic analysis of the pressure-, temperature- and composition-dependent (un)folding of various polynucleotide duplexes and G-quadruplexes. We demonstrate that the reason for the observed linearity is the link between compressibility and expansibility, both of which largely depend on DNA hydration. We predicted the temperature and pressure dependence of compressibility and expansibility of (un)folding and explain how they affect the corresponding volume change and thermodynamic stability parameters. These predictions indicate the existence of a convergence temperature at which compressibility and volume of (un)folding simultaneously become equal to zero.
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Affiliation(s)
- Jurij Lah
- Faculty of Chemistry and Chemical technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - San Hadži
- Faculty of Chemistry and Chemical technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
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2
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Smeller L. Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures. Int J Mol Sci 2023; 24:ijms24021803. [PMID: 36675317 PMCID: PMC9866529 DOI: 10.3390/ijms24021803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Four-stranded folded structures, such as G-quadruplexes and i-motifs in the genome, have attracted a growing interest nowadays since they have been discovered in the telomere and in several oncogene promoter regions. Their biological relevance is undeniable since their existence in living cells has been observed. In vivo they take part in the regulation of gene expression, in vitro they are used in the analytical biochemistry. They are attractive and promising targets for cancer therapy. Pressure studies can reveal specific aspects of the molecular processes. Pressure tuning experiments allow the determination of the volumetric parameters of the folded structures and of the folding-unfolding processes. Here, we review the thermodynamic parameters with a special focus on the volumetric ones, which were determined using pressure tuning spectroscopic experiments on the G-quadruplex and i-motif nucleic acid forms.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
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Knop JM, Mukherjee S, Jaworek MW, Kriegler S, Manisegaran M, Fetahaj Z, Ostermeier L, Oliva R, Gault S, Cockell CS, Winter R. Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View. Chem Rev 2023; 123:73-104. [PMID: 36260784 DOI: 10.1021/acs.chemrev.2c00491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.
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Affiliation(s)
- Jim-Marcel Knop
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Sanjib Mukherjee
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Simon Kriegler
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Magiliny Manisegaran
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Zamira Fetahaj
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
| | - Rosario Oliva
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, EH9 3FDEdinburgh, United Kingdom
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, D-44221Dortmund, Germany
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Oliva R, Winter R. Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems. J Phys Chem Lett 2022; 13:12099-12115. [PMID: 36546666 DOI: 10.1021/acs.jpclett.2c03186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.
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Affiliation(s)
- Rosario Oliva
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry I, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 6, Dortmund44227, Germany
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Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex. Int J Mol Sci 2022; 23:ijms23105690. [PMID: 35628500 PMCID: PMC9145931 DOI: 10.3390/ijms23105690] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Previous studies suggest that berberine, an isoquinoline alkaloid, has antiviral potential and is a possible therapeutic candidate against SARS-CoV-2. The molecular underpinnings of its action are still unknown. Potential targets include quadruplexes (G4Q) in the viral genome as they play a key role in modulating the biological activity of viruses. While several DNA-G4Q structures and their binding properties have been elucidated, RNA-G4Qs such as RG-1 of the N-gene of SARS-CoV-2 are less explored. Using biophysical techniques, the berberine binding thermodynamics and the associated conformational and hydration changes of RG-1 could be characterized and compared with human telomeric DNA-G4Q 22AG. Berberine can interact with both quadruplexes. Substantial changes were observed in the interaction of berberine with 22AG and RG-1, which adopt different topologies that can also change upon ligand binding. The strength of interaction and the thermodynamic signatures were found to dependent not only on the initial conformation of the quadruplex, but also on the type of salt present in solution. Since berberine has shown promise as a G-quadruplex stabilizer that can modulate viral gene expression, this study may also contribute to the development of optimized ligands that can discriminate between binding to DNA and RNA G-quadruplexes.
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Sugimoto W, Kinoshita N, Nakata M, Ohyama T, Tateishi-Karimata H, Nishikata T, Sugimoto N, Miyoshi D, Kawauchi K. Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene. Chem Commun (Camb) 2021; 58:48-51. [PMID: 34811561 DOI: 10.1039/d1cc05523b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We identified cytosine-rich regions adjacent to guanine-rich regions in protease genes. A typical GC-rich sequence derived from the TMPRSS2 gene showed structural competition between a G-quadruplex and a hairpin loop, and this competition significantly affected transcription efficiency. These results suggest an impact of neighboring sequences on the gene expression of guanine-rich sequences.
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Affiliation(s)
- Wataru Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Natsuki Kinoshita
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Minori Nakata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nishikata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan. .,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
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Chalikian TV, Macgregor RB. Volumetric Properties of Four-Stranded DNA Structures. BIOLOGY 2021; 10:813. [PMID: 34440045 PMCID: PMC8389613 DOI: 10.3390/biology10080813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022]
Abstract
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute-solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.
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Affiliation(s)
- Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada;
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