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Kinoshita T, Imai Y, Fukuhara G. Hydrostatic Pressure-Controllable Chiroptical Properties of Chiral Perylene Bisimide Dyes: A Chiral Aggregation Case. J Phys Chem B 2021; 125:5952-5958. [PMID: 34032446 DOI: 10.1021/acs.jpcb.1c02112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hydrostatically pressurized spectroscopic and lifetime decay analyses of optically active perylene bisimides were demonstrated in the pressure range of 0.1-320 MPa to show a π-stacked aggregation. The hydrostatic pressure-induced excitation and circular dichroism spectral changes of the fluorescence perylene dye enabled us to differentiate the slight pressure-sensitive aggregates. This work will lead to a new strategy for creating a pressure-responsive supramolecular polymerization material.
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Affiliation(s)
- Tomokazu Kinoshita
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yoshitane Imai
- Department of Applied Chemistry, Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Kinoshita T, Haketa Y, Maeda H, Fukuhara G. Ground- and excited-state dynamic control of an anion receptor by hydrostatic pressure. Chem Sci 2021; 12:6691-6698. [PMID: 34040743 PMCID: PMC8132960 DOI: 10.1039/d1sc00664a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/31/2021] [Indexed: 12/02/2022] Open
Abstract
Stimulus-responsive supramolecular architectures have become an attractive alternative to conventional ones for many applications in sensing, drug-delivery and switchable memory systems. Herein, we used an anion receptor (H: host) as a hydrostatic-pressure-manipulatable fluorescence foldamer and halide anions as chiral (binaphthylammonium) and achiral (tetrabutylammonium) ion pairs (SS or RR ·X and TBA·X; X = Cl, Br), and then investigated their (chir)optical properties and molecular recognition behavior under hydrostatic pressures. The conformational changes and optical properties of H in various organic solvents were revealed by UV/vis absorption and fluorescence spectra and fluorescence lifetimes upon hydrostatic pressurization. The anion-recognition abilities of H upon interactions with SS or RR·X and TBA·X at different pressure ranges were determined by hydrostatic-pressure spectroscopy to quantitatively afford the binding constant (K anion) and apparent reaction volume changes . The results obtained indicate that hydrostatic pressure as well as solvation plays significant roles in the dynamic control of the present supramolecular system in the ground and excited states. This work will provide a new guideline for further developing hydrostatic-pressure-responsive foldamers and supramolecular materials.
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Affiliation(s)
- Tomokazu Kinoshita
- Department of Chemistry, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
| | - Yohei Haketa
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University Kusatsu 525-8577 Japan
| | - Hiromitsu Maeda
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University Kusatsu 525-8577 Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
- JST, PRESTO 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
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3
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Yao J, Mizuno H, Xiao C, Wu W, Inoue Y, Yang C, Fukuhara G. Pressure-driven, solvation-directed planar chirality switching of cyclophano-pillar[5]arenes (molecular universal joints). Chem Sci 2021; 12:4361-4366. [PMID: 34168749 PMCID: PMC8179620 DOI: 10.1039/d0sc06988d] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 12/27/2022] Open
Abstract
Planar chiral cyclophanopillar[5]arenes with a fused oligo(oxyethylene) or polymethylene subring (MUJs), existing as an equilibrium mixture of subring-included (in) and -excluded (out) conformers, respond to hydrostatic pressure to exhibit dynamic chiroptical property changes, leading to an unprecedented pressure-driven chirality inversion and the largest ever-reported leap of anisotropy (g) factor for the MUJ with a dodecamethylene subring. The pressure susceptivity of MUJs, assessed by the change in g per unit pressure, is a critical function of the size and nature of the subring incorporated and the solvent employed. Mechanistic elucidations reveal that the in-out equilibrium, as the origin of the MUJ's chiroptical property changes, is on a delicate balance of the competitive inclusion of subrings versus solvent molecules as well as the solvation of the excluded subring. The present results further encourage our use of pressure as a unique tool for dynamically manipulating various supramolecular devices/machines.
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Affiliation(s)
- Jiabin Yao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, State Key Laboratory of Biotherapy, Healthy Food Evaluation Research Center, Sichuan University Chengdu 610064 China
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
| | - Chao Xiao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, State Key Laboratory of Biotherapy, Healthy Food Evaluation Research Center, Sichuan University Chengdu 610064 China
| | - Wanhua Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, State Key Laboratory of Biotherapy, Healthy Food Evaluation Research Center, Sichuan University Chengdu 610064 China
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Osaka University Suita 565-0871 Japan
| | - Cheng Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, State Key Laboratory of Biotherapy, Healthy Food Evaluation Research Center, Sichuan University Chengdu 610064 China
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
- JST, PRESTO 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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Fukuchi M, Oyama K, Mizuno H, Miyagawa A, Koumoto K, Fukuhara G. Hydrostatic Pressure-Regulated Cellular Calcium Responses. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:820-826. [PMID: 33410684 DOI: 10.1021/acs.langmuir.0c03141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hydrostatic pressure control has attracted much attention and presents a still challenging objective from mechanobiological viewpoints. Herein, we reveal the calcium entry processes in HeLa cells by means of hydrostatic pressure spectroscopy. The steady-state fluorescence spectral data comprehensively elucidated the factors controlling the outcomes of the hydrostatic pressure-stimulated calcium entry behavior. The present work leads to a new perspective on ion regulations in living cells and an attractive alternative to conventional mechanostimuli.
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Affiliation(s)
- Minami Fukuchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Kotaro Oyama
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanukimachi, Takasaki, Gunma 370-1292, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akihisa Miyagawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Kazuya Koumoto
- Department of Nanobiochemistry, FIRST (Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Miner JC, García AE. Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop. J Chem Phys 2018; 148:222837. [PMID: 29907048 DOI: 10.1063/1.5019939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monovalent salt solutions have strongly coupled interactions with biopolymers, from large polyelectrolytes to small RNA oligomers. High salt concentrations have been known to induce transitions in the structure of RNA, producing non-canonical configurations and even driving RNA to precipitate out of solution. Using all-atom molecular dynamics simulations, we model a monovalent salt species (KCL) at high concentrations (0.1-3m) and calculate the equilibrium distributions of water and ions around a small tetraloop-forming RNA oligomer in a variety of structural arrangements: folded A-RNA (canonical) and Z-RNA (non-canonical) tetraloops and unfolded configurations. From these data, we calculate the ion preferential binding coefficients and Donnan coefficients for the RNA oligomer as a function of concentration and structure. We find that cation accumulation is highest around non-canonical Z-RNA configurations at concentrations below 0.5m, while unfolded configurations accumulate the most co-ions in all concentrations. By contrast, canonical A-RNA structures consistently show the lowest accumulations for all ion species. Water distributions vary markedly with RNA configuration but show little dependency on KCL concentration. Based on Donnan coefficient calculations, the net charge of the solution at the surface of the RNA decreases linearly as a function of salt concentration and becomes net-neutral near 2.5-3m KCL for folded configurations, while unfolded configurations still show a positive solution charge. Our findings show that all-atom molecular dynamics can describe the equilibrium distributions of monovalent salt in the presence of small RNA oligomers at KCL concentrations where ion correlation effects become important. Furthermore, these results provide valuable insights into the distributions of water and ions near the RNA oligomer surface as a function of structural configuration.
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Affiliation(s)
- Jacob Carlson Miner
- Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Angel Enrique García
- Center for Nonlinear Studies, MS B258, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Suginome M, Nagata Y, Yamamoto T. New Chiral Functions Based on the Dynamic Induction of Macromolecular Helical Chirality by Chiral Side Chains. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.
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Arias-Gonzalez JR. Single-molecule portrait of DNA and RNA double helices. Integr Biol (Camb) 2015; 6:904-25. [PMID: 25174412 DOI: 10.1039/c4ib00163j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Calle Faraday no. 9, Cantoblanco, 28049 Madrid, Spain.
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10
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Nagata Y, Takeda R, Suginome M. Pressure-dependent helix inversion of poly(quinoxaline-2,3-diyl)s containing chiral side chains in non-aqueous solvents. Chem Commun (Camb) 2015; 51:11182-5. [DOI: 10.1039/c5cc04255k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(quinoxaline-2,3-diyl)s with chiral (S)-2-butoxymethyl side chains dissolved in 1,2-dichloroethane experience a reversible pressure-dependent helix inversion from P- to M-helical structures between 0.1 MPa and 200 MPa.
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Affiliation(s)
- Yuuya Nagata
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - Ryohei Takeda
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - Michinori Suginome
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
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11
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Pan F, Roland C, Sagui C. Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res 2014; 42:13981-96. [PMID: 25428372 PMCID: PMC4267617 DOI: 10.1093/nar/gku1107] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/30/2022] Open
Abstract
The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5'-CGCGCGCGCGCG-3')2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na(+), K(+) and Mg(2 +), with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6](2+) ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6](2+) to distant phosphates, resulting in acute bending of A-RNA; tight 'ion traps' in Z-RNA between C-O2 and the C-O2' atoms in GpC steps; and others.
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Affiliation(s)
- Feng Pan
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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12
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Paliwoda D, Wawrzyniak P, Katrusiak A. Unwinding Au(+)···Au(+) Bonded Filaments in Ligand-Supported Gold(I) Polymer under Pressure. J Phys Chem Lett 2014; 5:2182-2188. [PMID: 26279531 DOI: 10.1021/jz500778t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ultimately thin single-strand gold filaments, of Au(+)···Au(+) bonded gold(I) diethyldithiocarbamate polymer, AuEt2DTC, can be transformed depending on pressure and solvate contents. When synthesized in the presence of CH2Cl2, it crystallizes into a tetragonal AuEt2DTC·xCH2Cl2 phase α with ligand-supported and unsupported Au(+)···Au(+) bonded filaments modulated into molecular Au8-pitch helices. Low contents of CH2Cl2 favors the β phase of significantly reduced volume and orthorhombic space group Fddd. The α-AuEt2DTC·xCH2Cl2 crystal exhibits a highly unusual negative-area compressibility, due to the spring-like compression of helices. Above 0.05 GPa, the crystal transforms to phase β, where the Au16-pitch helices partly unwind their turns, which relaxes the tension generated by external pressure between neighboring helices of the opposite handedness. This is a unique observation of atomic-scale helical filaments transformation, which otherwise is a universal process analogous to the helix reversal between DNA forms B and Z, and in macroscopic world it is similar to nonperiodic unwind kinks in grapevine tendrils and telephone cords. Pressure also reduces the differences between the ligand-supported and unsupported Au(+)···Au(+) bonds.
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Affiliation(s)
- Damian Paliwoda
- †Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Paulina Wawrzyniak
- †Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Andrzej Katrusiak
- †Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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Takahashi S, Sugimoto N. Effect of pressure on thermal stability of g-quadruplex DNA and double-stranded DNA structures. Molecules 2013; 18:13297-319. [PMID: 24172240 PMCID: PMC6270079 DOI: 10.3390/molecules181113297] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/05/2013] [Accepted: 10/24/2013] [Indexed: 11/16/2022] Open
Abstract
Pressure is a thermodynamic parameter that can induce structural changes in biomolecules due to a volumetric decrease. Although most proteins are denatured by pressure over 100 MPa because they have the large cavities inside their structures, the double-stranded structure of DNA is stabilized or destabilized only marginally depending on the sequence and salt conditions. The thermal stability of the G-quadruplex DNA structure, an important non-canonical structure that likely impacts gene expression in cells, remarkably decreases with increasing pressure. Volumetric analysis revealed that human telomeric DNA changed by more than 50 cm3 mol-1 during the transition from a random coil to a quadruplex form. This value is approximately ten times larger than that for duplex DNA under similar conditions. The volumetric analysis also suggested that the formation of G-quadruplex DNA involves significant hydration changes. The presence of a cosolute such as poly(ethylene glycol) largely repressed the pressure effect on the stability of G-quadruplex due to alteration in stabilities of the interactions with hydrating water. This review discusses the importance of local perturbations of pressure on DNA structures involved in regulation of gene expression and highlights the potential for application of high-pressure chemistry in nucleic acid-based nanotechnology.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; E-Mail:
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; E-Mail:
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-774-98-2580; Fax: +81-774-98-2585
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Giel-Pietraszuk M, Fedoruk-Wyszomirska A, Barciszewski J. Effect of high hydrostatic pressure on hydration and activity of ribozymes. Mol Biol Rep 2010; 37:3713-9. [PMID: 20204525 DOI: 10.1007/s11033-010-0024-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
Abstract
Formation and stabilization of RNA structure in the cell depends on its interaction with solvent and metal ions. High hydrostatic pressure (HHP) is a convenient tool in an analysis of the role of small molecules in the structure stabilization of biological macromolecules. Analysis of HHP effect and various concentrations of ions showed that water induce formation of the active ribozyme structure. So, it is clear that water is the driving force of conformational changes of nucleic acid.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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Fedoruk-Wyszomirska A, Giel-Pietraszuk M, Wyszko E, Szymański M, Ciesiołka J, Barciszewska MZ, Barciszewski J. The mechanism of acidic hydrolysis of esters explains the HDV ribozyme activity. Mol Biol Rep 2008; 36:1647-50. [PMID: 18810653 DOI: 10.1007/s11033-008-9364-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
Abstract
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-esterification reaction. Using high hydrostatic pressure (HHP) technique we showed that HDV ribozyme catalyzes the reaction of RNA cleavage in the absence of magnesium ions according to mechanism of acidic hydrolysis of esters. HHP induces changes of water structure, lowering pH and effect ribozyme catalytic site structure formation without magnesium. HHP, similarly to magnesium ion at ambient pressure stabilizes the higher order RNA structure of HDV, but Mg(2+) is not involved in the catalysis. Our results clearly support the new mechanism of HDV hydrolysis and show advantages of using HHP in analysis of macromolecules interaction.
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Fedoruk-Wyszomirska A, Wyszko E, Giel-Pietraszuk M, Barciszewska MZ, Barciszewski J. High hydrostatic pressure approach proves RNA catalytic activity without magnesium. Int J Biol Macromol 2007; 41:30-5. [PMID: 17222901 DOI: 10.1016/j.ijbiomac.2006.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 12/08/2006] [Indexed: 10/23/2022]
Abstract
High hydrostatic pressure (HHP) technique was used to evaluate a mechanism of RNA hydrolysis with RNA. We showed that hammerhead ribozyme specifically cleaves RNA substrate at HHP in the absence of Mg(2+). A deoxyribozyme "10-23" was active in the same conditions. These results pointed out that the hydrolytic activity of nucleic acid depends on proper tertiary structure of a complex with a substrate. They prove that magnesium ion is not directly involved in catalysis process. On that basis we show the mechanism of RNA hydrolysis catalyzed with nucleic acids at HHP.
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Giel-Pietraszuk M, Barciszewski J. A nature of conformational changes of yeast tRNAPhe. Int J Biol Macromol 2005; 37:109-14. [PMID: 16236354 DOI: 10.1016/j.ijbiomac.2005.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 09/08/2005] [Accepted: 09/08/2005] [Indexed: 10/25/2022]
Abstract
We analysed conformational changes of yeast tRNA(Phe) induced by high hydrostatic pressure (HHP) measured by Fourier-transform infrared (FTIR) and fluorescence spectroscopies. High pressure influences RNA conformation without other cofactors, such as metal ions and salts. FTIR spectra of yeast tRNA(Phe) recorded at high hydrostatic pressure up to 13 kbar with and without magnesium ions showed a shift of the bands towards higher frequencies. That blue shift is due to an increase a higher energy of bonds as a result of shortening of hydrogen bonds followed by dehydration of tRNA. The fluorescence spectra of Y-base tRNA(Phe) at high pressure up to 3 kbar showed a decrease of the intensity band at 430 nm as a consequence of conformational rearrangement of the anticodon loop leading to exposure of Y-base side chain to the solution. We suggest that structural transition of nucleic acids is driven by the changes of water structure from tetrahedral to a cubic-like geometry induced by high pressure and, in consequence, due to economy of hydration.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland.
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Sims GE, Kim SH. Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Res 2003; 31:5607-16. [PMID: 14500824 PMCID: PMC206451 DOI: 10.1093/nar/gkg750] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Revised: 08/04/2003] [Accepted: 08/04/2003] [Indexed: 12/19/2022] Open
Abstract
A global conformational space of 6253 dinucleoside monophosphate (DMP) units consisting of RNA and DNA (free and protein/drug-bound) was 'mapped' using high resolution crystal structures cataloged in the Nucleic Acid Database (NDB). The torsion angles of each DMP were clustered in a reduced three-dimensional space using a classical multi-dimensional scaling method. The mapping of the conformational space reveals nine primary clusters which distinguish among the common A-, B- and Z-forms and their various substates, plus five secondary clusters for kinked or bent structures. Conformational relationships and possible transitional pathways among the substates are also examined using the conformational states of DNA and RNA bound with proteins or drugs as potential pathway intermediates.
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Affiliation(s)
- Gregory E Sims
- Department of Chemistry, University of California at Berkeley and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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21
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Mielcarek M, Barciszewska MZ, Sałanski P, Stobiecki M, Jurczak J, Barciszewski J. Native transfer RNA catalyzes Diels-Alder reaction. Biochem Biophys Res Commun 2002; 294:145-8. [PMID: 12054754 DOI: 10.1016/s0006-291x(02)00452-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this paper we show that transfer ribonucleic acids (tRNAs) catalyze the Diels-Alder cycloaddition reaction. A new DNA oxidative damage product, 6-furfuryladenine (kinetin) or its riboside (diene), was transformed with dimethyl acetylenedicarboxylate or maleic anhydride (dienophile). The reaction proceeds in the presence of tRNA at high pressure but not at ambient condition. If so tRNA in prebiotic conditions (RNA world) had at least two functions: catalytic and a carrier of genetic information. It means that tRNA at high pressure shows catalytic properties and is a true Diels-Alderase.
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Affiliation(s)
- Michal Mielcarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
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Adamiak DA, Rypniewski WR, Milecki J, Adamiak RW. The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. Nucleic Acids Res 2001; 29:4144-53. [PMID: 11600703 PMCID: PMC60216 DOI: 10.1093/nar/29.20.4144] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The crystal and molecular structure of 2'-O-Me(CGCGCG)(2) has been determined at 1.19 A resolution, at 100 K, using synchrotron radiation. The structure in space group P3(2)12 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O(6) and N(7) of guanosine and N(4) of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)(2) structure in the P3(2)12 and P6(1)22 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.
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Affiliation(s)
- D A Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznañ, Poland.
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23
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Barciszewski J, Jurczak J, Porowski S, Specht T, Erdmann VA. The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 260:293-307. [PMID: 10095763 DOI: 10.1046/j.1432-1327.1999.00184.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This review describes and summarizes data on the structure and properties of water under normal conditions, at high salt concentration and under high pressure. We correlate the observed conformational changes in nucleic acids with changes in water structure and activity, and suggest a mechanism of conformational transitions of nucleic acids which accounts for changes in the water structure. From the biophysical, biochemical and crystallographic data we conclude that the Z-DNA form can be induced only at low water activity produced by high salt concentrations or high pressure, and accompanied by the stabilizing conjugative effect of the cytidine O4' electrons of the CG base pairs.
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Affiliation(s)
- J Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego, Poznan, Poland.
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Popenda M, Biala E, Milecki J, Adamiak RW. Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions. Nucleic Acids Res 1997; 25:4589-98. [PMID: 9358170 PMCID: PMC147063 DOI: 10.1093/nar/25.22.4589] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were determined and refined using an iterative relaxation matrix procedure (IRMA) and the restrained MD simulation. Both duplexes form half-turn, right-handed helices with several conformational features which deviate significantly from a canonical A-RNA structure. Duplexes are characterised as having C3'-endo sugar pucker, very low base-pair rise and high helical twist and inclination angles. Helices are overwound with <10 bp per turn. There is limited inter-strand guanine stacking for CG steps. Within CG steps of both duplexes, the planes of the inter-strand cytosines are not parallel while guanines are almost parallel. For the GC steps this pattern is reversed. The 2'-O-methyl groups are spatially close to the 5'-hydrogens of neighbouring residues from the 3'-side and are directed towards the minor groove of 2'-O-Me(CGCGCG)2 forming a hydrophobic layer. Solution structures of both duplexes are similar; the effect of 2'-O-methylation on the parent RNA structure is small. This suggests that intrinsic properties imposed by alternating CG base pairs govern the overall conformation of both duplexes.
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Affiliation(s)
- M Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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25
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Adamiak DA, Milecki J, Popenda M, Adamiak RW, Dauter Z, Rypniewski WR. Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA. Nucleic Acids Res 1997; 25:4599-607. [PMID: 9358171 PMCID: PMC147083 DOI: 10.1093/nar/25.22.4599] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.
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Affiliation(s)
- D A Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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26
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Structure and function of nucleic acids affected by high pressure. ORIGINS LIFE EVOL B 1996. [DOI: 10.1007/bf02459843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Norberg J, Nilsson L. Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2. J Chem Phys 1996. [DOI: 10.1063/1.471341] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Krzyzaniak A, Fürste JP, Erdmann VA, Salanski P, Jurczak J, Barciszewski J. High pressure effects on conformation of homo- and heteroduplexes of nucleic acids. Biochimie 1996; 78:862-7. [PMID: 9116056 DOI: 10.1016/s0300-9084(97)84339-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Four different chemically synthesized single stranded complementary oligonucleotides: DNA I, d(GCGCGCATATAT); RNA I, r(AUAUAUGCGCGC): RNA II, r(GGCCGGUUAAUU); and RNA III, r(AAUUAACCGGCC) were studied in order that the effects of high pressure on heteroduplex and homoduplex structures could be understood. The oligonucleotides were subjected to a high pressure at low and/or high salt buffer and analyzed by circular dichroism spectroscopy. In these conditions, both DNA-RNA and RNA-RNA duplexes with different purine-pyrimidine sequences change their conformation. The heteroduplex DNA I-RNA I with the complementary alternating purine-pyrimidine sequence, does not change its conformation of A type at high salt alone or at high salt and high pressure applied together. The homoduplex RNA II-RNA III with purine-purine-pyrimidine-pyrimidine sequence does not change strongly its. A-RNA conformation either. However, a structure of the homoduplex is affected by high pressure alone or with high salt as concluded from shifting the maximum of the CD spectrum to around 265 nm and inducing higher Cotton effect. These observations clearly suggest some conformational changes of the homoduplex. A single stranded oligonucleotide (RNA I) and oligodeoxynucleotide (DNA I) alone showed up a different conformation. The CD spectrum of RNA I is similar to that of A-RNA structure, out that of DNA I shows a very small Cotton effect and has not an ordered structure.
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Affiliation(s)
- A Krzyzaniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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