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Pohl R, Socha O, Slavíček P, Šála M, Hodgkinson P, Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss 2018; 212:331-344. [PMID: 30234207 DOI: 10.1039/c8fd00070k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.
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Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Petr Slavíček
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
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Shigeta Y, Harada R, Sato R, Kitoh-Nishioka H, Bui TKM, Sato A, Tokiwa T, Kyan A, Ishii Y, Kimatsuka M, Yamasaki S, Kayanuma M, Shoji M. Classical cumulant dynamics for statistical chemical physics. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1315770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ryuma Sato
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | | | - Thi Kieu My Bui
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akimasa Sato
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takaki Tokiwa
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akane Kyan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuki Ishii
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masato Kimatsuka
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sotaro Yamasaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Megumi Kayanuma
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Reyman D, Viñas MH, Tardajos G, Mazario E. The Impact of Dihydrogen Phosphate Anions on the Excited-State Proton Transfer of Harmane. Effect of β-Cyclodextrin on These Photoreactions. J Phys Chem A 2011; 116:207-14. [DOI: 10.1021/jp2074495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dolores Reyman
- Departamentode Química Física Aplicada, Universidad Autónoma de Madrid, E-28049 España
| | - Montserrat H. Viñas
- Departamento de Sistemas Inteligentes Aplicados, Universidad Politécnica de Madrid, E-28031 Madrid, España
| | - Gloria Tardajos
- Departamento Química Física, Universidad Complutense de Madrid, E-28040 Madrid, España
| | - Eva Mazario
- Departamentode Química Física Aplicada, Universidad Autónoma de Madrid, E-28049 España
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Pérez A, Tuckerman ME, Hjalmarson HP, von Lilienfeld OA. Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects. J Am Chem Soc 2010; 132:11510-5. [PMID: 20681591 DOI: 10.1021/ja102004b] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage.
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Affiliation(s)
- Alejandro Pérez
- Department of Chemistry, New York University, New York, New York 10003, USA
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Kamiya K, Boero M, Shiraishi K, Oshiyama A, Shigeta Y. Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate−Histidine Amino Acid Residue Pairs. J Phys Chem B 2010; 114:6567-78. [DOI: 10.1021/jp906148m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katsumasa Kamiya
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Mauro Boero
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Kenji Shiraishi
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Atsushi Oshiyama
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Yasuteru Shigeta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
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