1
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Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
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Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | | | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy,Corresponding author
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2
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Liu L, Scott L, Tariq N, Kume T, Dubins DN, Macgregor RB, Chalikian TV. Volumetric Interplay between the Conformational States Adopted by Guanine-Rich DNA from the c-MYC Promoter. J Phys Chem B 2021; 125:7406-7416. [PMID: 34185535 DOI: 10.1021/acs.jpcb.1c04075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The kinetic and thermodynamic stabilities of G-quadruplex structures have been extensively studied. In contrast, systematic investigations of the volumetric properties of G-quadruplexes determining their pressure stability are still relatively scarce. The G-rich strand from the promoter region of the c-MYC oncogene (G-strand) is known to adopt a range of conformational states including the duplex, G-quadruplex, and coil states depending on the presence of the complementary C-rich strand (C-strand) and solution conditions. In this work, we report changes in volume, ΔV, and adiabatic compressibility, ΔKS, accompanying interconversions of G-strand between the G-quadruplex, duplex, and coil conformations in the presence and absence of C-strand. We rationalize these volumetric characteristics in terms of the hydration and intrinsic properties of the DNA in each of the sampled conformational states. We further use our volumetric results in conjunction with the reported data on changes in expansibility, ΔE, and heat capacity, ΔCP, associated with G-quadruplex-to-coil transitions to construct the pressure-temperature phase diagram describing the stability of the G-quadruplex. The phase diagram is elliptic in shape, resembling the classical elliptic phase diagram of a globular protein, and is distinct from the phase diagram for duplex DNA. The observed similarity of the pressure-temperature phase diagrams of G-quadruplexes and globular proteins stems from their shared structural and hydration features that, in turn, result in the similarity of their volumetric properties. To the best of our knowledge, this is the first pressure-temperature stability diagram reported for a G-quadruplex.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Lily Scott
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Nabeel Tariq
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Takuma Kume
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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3
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Ghosh R, Kishore N. Physicochemical Insights into the Role of Drug Functionality in Fibrillation Inhibition of Bovine Serum Albumin. J Phys Chem B 2020; 124:8989-9008. [DOI: 10.1021/acs.jpcb.0c06167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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4
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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5
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017; 56:5045-5049. [DOI: 10.1002/anie.201701420] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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6
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Bye JW, Freeman CL, Howard JD, Herz G, McGregor J, Falconer RJ. Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation. J SOLUTION CHEM 2017; 46:175-189. [PMID: 28163342 PMCID: PMC5241351 DOI: 10.1007/s10953-016-0554-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/19/2016] [Indexed: 11/15/2022]
Abstract
In this paper we demonstrate the application of pressure perturbation calorimetry (PPC) to the characterization of 2-propanol/water mixtures. PPC of different 2-propanol/water mixtures provides two useful measurements: (i) the change in heat (ΔQ); and (ii) the \documentclass[12pt]{minimal}
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\begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT value. The results demonstrate that the ΔQ values of the mixtures deviate from that expected for a random mixture, with a maximum at ~20–25 mol% 2-propanol. This coincides with the concentration at which molecular dynamics (MD) simulations show a maximum deviation from random distribution, and also the point at which alcohol–alcohol hydrogen bonds become dominant over alcohol–water hydrogen bonds. Furthermore, the \documentclass[12pt]{minimal}
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\begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT value showed transitions at 2.5 mol% 2-propanol and at approximately 14 mol% 2-propanol. Below 2.5 mol% 2-propanol the values of \documentclass[12pt]{minimal}
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\begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT are negative; this is indicative of the presence of isolated 2-propanol molecules surrounded by water molecules. Above 2.5 mol% 2-propanol \documentclass[12pt]{minimal}
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\begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT rises, reaching a maximum at ~14 mol% corresponding to a point where mixed alcohol–water networks are thought to dominate. The values and trends identified by PPC show excellent agreement not only with those obtained from MD simulations but also with results in the literature derived using viscometry, THz spectroscopy, NMR and neutron diffraction.
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Affiliation(s)
- Jordan W Bye
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD England, UK
| | - Colin L Freeman
- Department of Material Science & Engineering, University of Sheffield, Sheffield, S1 3JD England, UK
| | - John D Howard
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD England, UK
| | - Gregor Herz
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD England, UK
| | - James McGregor
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD England, UK
| | - Robert J Falconer
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD England, UK
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7
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Gao M, Arns L, Winter R. Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mimi Gao
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Loana Arns
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology; TU Dortmund; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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8
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Gao M, Arns L, Winter R. Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts. Angew Chem Int Ed Engl 2017; 56:2302-2306. [PMID: 28102930 DOI: 10.1002/anie.201611843] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Indexed: 12/31/2022]
Abstract
Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state. Further, we find a strong interplay between water, salt, and osmolyte in driving the thermodynamics and defining the temperature and pressure stability limit of the RNA. Our results support a universal working mechanism of TMAO and urea to (de)stabilize proteins and the RNA.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Loana Arns
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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9
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Bye JW, Falconer RJ. A study of the relationship between water and anions of the Hofmeister series using pressure perturbation calorimetry. Phys Chem Chem Phys 2015; 17:14130-7. [PMID: 25959090 DOI: 10.1039/c5cp00571j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pressure perturbation calorimetry (PPC) was used to study the relationship between water and sodium salts with a range of different anions. At temperatures around 25 °C the heat on pressurisation (ΔQ) from 1 to 5 bar was negative for all solutions relative to pure water. The raw data showed that as the temperature rose, the gradient was positive relative to pure water and the transition temperature where ΔQ was zero was related to anion surface charge density and was more pronounced for the low-charge density anions. A three component model was developed comprising bulk water, the hydration layer and the solute to calculate the molar expansivity of the hydration layer around the ions in solution. The calculated molar expansivities of water in the hydration layer around the ions were consistently less than pure water. ΔQ at different disodium hydrogen phosphate concentrations showed that the change in molar enthalpy relative to pure water was not linear even as it approached infinite dilution suggesting that while hydration layers can be allocated to the water around ions this does not rule out interactions between water and ions extending beyond the immediate hydration layer.
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Affiliation(s)
- Jordan W Bye
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK.
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10
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Rayan G, Macgregor RB. A look at the effect of sequence complexity on pressure destabilisation of DNA polymers. Biophys Chem 2015; 199:34-8. [DOI: 10.1016/j.bpc.2015.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 11/16/2022]
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11
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Suladze S, Kahse M, Erwin N, Tomazic D, Winter R. Probing volumetric properties of biomolecular systems by pressure perturbation calorimetry (PPC)--the effects of hydration, cosolvents and crowding. Methods 2014; 76:67-77. [PMID: 25168090 DOI: 10.1016/j.ymeth.2014.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 11/16/2022] Open
Abstract
Pressure perturbation calorimetry (PPC) is an efficient technique to study the volumetric properties of biomolecules in solution. In PPC, the coefficient of thermal expansion of the partial volume of the biomolecule is deduced from the heat consumed or produced after small isothermal pressure-jumps. The expansion coefficient strongly depends on the interaction of the biomolecule with the solvent or cosolvent as well as on its packing and internal dynamic properties. This technique, complemented with molecular acoustics and densimetry, provides valuable insights into the basic thermodynamic properties of solvation and volume effects accompanying interactions, reactions and phase transitions of biomolecular systems. After outlining the principles of the technique, we present representative examples on protein folding, including effects of cosolvents and crowding, together with a discussion of the interpretation, and further applications.
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Affiliation(s)
- Saba Suladze
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Marie Kahse
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Nelli Erwin
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Daniel Tomazic
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- TU Dortmund University, Department of Chemistry and Chemical Biology, Physical Chemistry - Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany.
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12
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Gold B, Stone MP, Marky LA. Looking for Waldo: a potential thermodynamic signature to DNA damage. Acc Chem Res 2014; 47:1446-54. [PMID: 24702131 PMCID: PMC3993888 DOI: 10.1021/ar500061p] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
DNA in its
simplest form is an ensemble of nucleic acids, water,
and ions, and the conformation of DNA is dependent on the relative
proportions of all three components. When DNA is covalently damaged
by endogenous or exogenous reactive species, including those produced
by some anticancer drugs, the ensemble undergoes localized changes
that affect nucleic acid structure, thermodynamic stability, and the
qualitative and quantative arrangement of associated cations and water
molecules. Fortunately, the biological effects of low levels of DNA
damage are successfully mitigated by a large number of proteins that
efficiently recognize and repair DNA damage in the midst of a vast
excess of canonical DNA. In this Account, we explore the impact
of DNA modifications on
the high resolution and dynamic structure of DNA, DNA stability, and
the uptake of ions and water and explore how these changes may be
sensed by proteins whose function is to initially locate DNA lesions.
We discuss modifications on the nucleobases that are located in the
major and minor grooves of DNA and include lesions that are observed in vivo, including oxidized bases, as well as some synthetic
nucleobases that allow us to probe how the location and nature of
different substituents affect the thermodynamics and structure of
the DNA ensemble. It is demonstrated that disruption of a cation binding
site in the major groove by modification of the N7-position on the
purines, which is the major site for DNA alkylation, is enthalpically
destabilizing. Accordingly, tethering a cationic charge in the major
groove is enthalpically stabilizing. The combined structural
and thermodynamic studies provide a detailed
picture of how different DNA lesions affect the dynamics of DNA and
how modified bases interact with their environment. Our work supports
the hypothesis that there is a “thermodynamic signature”
to DNA lesions that can be exploited in the initial search that requires
differentiation between canonical DNA and DNA with a lesion. The differentiation
between a lesion and a cognate lesion that is a substrate for a particular
enzyme involves another layer of thermodynamic and kinetic factors.
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Affiliation(s)
- Barry Gold
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Luis A. Marky
- Department
of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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13
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Son I, Shek YL, Dubins DN, Chalikian TV. Hydration Changes Accompanying Helix-to-Coil DNA Transitions. J Am Chem Soc 2014; 136:4040-7. [DOI: 10.1021/ja5004137] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ikbae Son
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Yuen Lai Shek
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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14
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Volumetric characterization of ester- and ether-linked lipid bilayers by pressure perturbation calorimetry and densitometry. Colloids Surf B Biointerfaces 2012; 92:232-9. [DOI: 10.1016/j.colsurfb.2011.11.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/25/2011] [Accepted: 11/28/2011] [Indexed: 11/17/2022]
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15
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Nakamura S, Kidokoro SI. Volumetric Properties of the Molten Globule State of Cytochrome c in the Thermal Three-State Transition Evaluated by Pressure Perturbation Calorimetry. J Phys Chem B 2012; 116:1927-32. [DOI: 10.1021/jp209686e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Shun-ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
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16
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Applications of pressure perturbation calorimetry in biophysical studies. Biophys Chem 2011; 156:13-23. [DOI: 10.1016/j.bpc.2010.12.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 12/29/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
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17
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Singh SK, Szulik MW, Ganguly M, Khutsishvili I, Stone MP, Marky LA, Gold B. Characterization of DNA with an 8-oxoguanine modification. Nucleic Acids Res 2011; 39:6789-801. [PMID: 21572101 PMCID: PMC3159457 DOI: 10.1093/nar/gkr275] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The oxidation of DNA resulting from reactive oxygen species generated during aerobic respiration is a major cause of genetic damage that, if not repaired, can lead to mutations and potentially an increase in the incidence of cancer and aging. A major oxidation product generated in cells is 8-oxoguanine (oxoG), which is removed from the nucleotide pool by the enzymatic hydrolysis of 8-oxo-2′-deoxyguanosine triphosphate and from genomic DNA by 8-oxoguanine-DNA glycosylase. Finding and repairing oxoG in the midst of a large excess of unmodified DNA requires a combination of rapid scanning of the DNA for the lesion followed by specific excision of the damaged base. The repair of oxoG involves flipping the lesion out of the DNA stack and into the active site of the 8-oxoguanine-DNA glycosylase. This would suggest that thermodynamic stability, in terms of the rate for local denaturation, could play a role in lesion recognition. While prior X-ray crystal and NMR structures show that DNA with oxoG lesions appears virtually identical to the corresponding unmodified duplex, thermodynamic studies indicate that oxoG has a destabilizing influence. Our studies show that oxoG destabilizes DNA (ΔΔG of 2–8 kcal mol−1 over a 16–116 mM NaCl range) due to a significant reduction in the enthalpy term. The presence of oxoG has a profound effect on the level and nature of DNA hydration indicating that the environment around an oxoG•C is fundamentally different than that found at G•C. The temperature-dependent imino proton NMR spectrum of oxoG modified DNA confirms the destabilization of the oxoG•C pairing and those base pairs that are 5′ of the lesion. The instability of the oxoG modification is attributed to changes in the hydrophilicity of the base and its impact on major groove cation binding.
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Affiliation(s)
- Sreelekha K Singh
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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18
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Fan HY, Shek YL, Amiri A, Dubins DN, Heerklotz H, Macgregor RB, Chalikian TV. Volumetric characterization of sodium-induced G-quadruplex formation. J Am Chem Soc 2011; 133:4518-26. [PMID: 21370889 DOI: 10.1021/ja110495c] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oligodeoxyribonucleotides (ODN) with repeats of the human telomeric sequence can adopt different tetrahelical conformations that exhibit similar energetic parameters. We studied the volumetric properties of the folded and unfolded states of an ODN with four repeats of the human telomeric sequence, d[A(GGGTTA)(3)GGG], by combining pressure-perturbation calorimetry (PPC), vibrating tube densimetry, ultrasonic velocimetry, and UV melting under high pressure. We carried out our volumetric measurements in aqueous buffers at pH 7 containing 20, 50, and 100 mM NaCl. All of the methods employed yielded volumetric parameters that were in excellent agreement. The molar volume changes, ΔV, of the conformational transition leading to formation of the folded state are large and positive. At 50 mM NaCl, the average transition volume, ΔV(tr), obtained from all the methods is 56.4 ± 3.5 cm(3) mol(-1) at the transition temperature of 47 °C, with ΔV(tr) decreasing with an increase in temperature. We carried out a molecular dynamics simulation of the change in the intrinsic geometric parameters of the ODN accompanying quadruplex formation. On the basis of the experimental and computational results, the folding transition of the ODN is accompanied by a release of 103 ± 44 water molecules from its hydration shell to the bulk. This number corresponds to ~18% of the net hydration of the coil conformation.
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Affiliation(s)
- Helen Y Fan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Fan HY, Nazari M, Chowdhury S, Heerklotz H. Volume and expansivity changes of micelle formation measured by pressure perturbation calorimetry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1693-1699. [PMID: 21226468 DOI: 10.1021/la1042487] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present the application of pressure perturbation calorimetry (PPC) as a new method for the volumetric characterization of the micelle formation of surfactants. The evaluation is realized by a global fit of PPC curves at different surfactant concentration ranging, if possible, from below to far above the CMC. It is based on the knowledge of the temperature dependence of the CMC, which can for example be characterized by isothermal titration calorimetry. We demonstrate the new approach for decyl-β-maltopyranoside (DM). It shows a strong volume increase upon micelle formation of 16 ± 2.5 mL/mol (+4%) at 25 °C, and changes with temperature by -0.1 mL/(mol K). The apparent molar expansivity (E(S)) decreases upon micelle formation from 0.44 to 0.31 mL/(mol K) at 25 °C. Surprisingly, the temperature dependence of the expansivity of DM in solution (as compared with that of maltose) does not agree with the principal behavior described for polar (E(S)(T) decreasing) and hydrophobic (E(S)(T) increasing) solutes or moieties before. The results are discussed in terms of changes in hydration of the molecules and internal packing of the micelles and compared with the volumetric effects of transitions of proteins, DNA, lipids, and polymers.
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Affiliation(s)
- Helen Y Fan
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON M5S 3M2, Canada
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Niskanen J, Karesoja M, Rossi T, Tenhu H. Temperature and pH responsive hybrid nanoclay grafted with PDMAEMA. Polym Chem 2011. [DOI: 10.1039/c1py00143d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cameron DL, Jakus J, Pauleta SR, Pettigrew GW, Cooper A. Pressure Perturbation Calorimetry and the Thermodynamics of Noncovalent Interactions in Water: Comparison of Protein−Protein, Protein−Ligand, and Cyclodextrin−Adamantane Complexes. J Phys Chem B 2010; 114:16228-35. [DOI: 10.1021/jp107110t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diane L. Cameron
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Joanna Jakus
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Sofia R. Pauleta
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Graham W. Pettigrew
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Alan Cooper
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
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Tsamaloukas AD, Pyzocha NK, Makhatadze GI. Pressure Perturbation Calorimetry of Unfolded Proteins. J Phys Chem B 2010; 114:16166-70. [DOI: 10.1021/jp106294p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alekos D. Tsamaloukas
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Neena K. Pyzocha
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - George I. Makhatadze
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
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Pressure-induced helix–coil transition of DNA copolymers is linked to water activity. Biophys Chem 2009; 144:62-6. [DOI: 10.1016/j.bpc.2009.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 06/17/2009] [Accepted: 06/17/2009] [Indexed: 11/18/2022]
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