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Chaloupecká E, Kurfiřt M, Červenková Šťastná L, Karban J, Dračínský M. Exploring long-range fluorine-carbon J-coupling for conformational analysis of deoxyfluorinated disaccharides: A combined computational and NMR study. Bioorg Chem 2024; 147:107388. [PMID: 38678775 DOI: 10.1016/j.bioorg.2024.107388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
In this study, we investigated the potential of long-range fluorine-carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine-carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine-carbon coupling. The experimental values for the fluorine-carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine-carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Martin Kurfiřt
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic; University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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2
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Tahmasby M, Darehkordi A, Mohammadi M, Nejadkhorasani F. Pyrido triazin-nucleus synthesis and theoretical studies: 2,3,6-trioxo-8-aryl-1,3,4,6-tetrahydro-]2H[pyrido]1,2-b] [1,2,4[triazin-7,9-dicarbonitryl derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Afonin AV, Rusinska-Roszak D. A molecular tailoring approach – a new guide to quantify the energy of push–pull effects: a case study on (E)-3-(1H-pyrrol-2-yl)prop-2-enones. Phys Chem Chem Phys 2020; 22:22190-22194. [DOI: 10.1039/d0cp04432f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report a new approach to quantify the push–pull effect in molecules with internal charge transfer.
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Affiliation(s)
- Andrei V. Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry
- Siberian Division of Russian Academy of Sciences
- Irkutsk 664033
- Russian Federation
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering
- Poznan University of Technology
- Poznan 60-965
- Poland
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Afonin AV, Pavlov DV, Vashchenko AV. Case study of 2-vinyloxypyridine: Quantitative assessment of the intramolecular C H⋯N hydrogen bond energy and its contribution to the one-bond 13C1H coupling constant. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Dračínský M, Buchta M, Buděšínský M, Vacek-Chocholoušová J, Stará IG, Starý I, Malkina OL. Dihydrogen contacts observed by through-space indirect NMR coupling. Chem Sci 2018; 9:7437-7446. [PMID: 30319744 PMCID: PMC6180313 DOI: 10.1039/c8sc02859a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/11/2018] [Indexed: 11/21/2022] Open
Abstract
"Through-space" indirect spin-spin couplings between hydrogen atoms formally separated by up to 18 covalent bonds have been detected by NMR experiments in model helical molecules. It is demonstrated that this coupling can provide crucial structural information on the molecular conformation in solution. The coupling pathways have been visualised and analysed by computational methods. The conformational dependence of the coupling is explained in terms of orbital interactions.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Michal Buchta
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Jana Vacek-Chocholoušová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Olga L Malkina
- Institute of Inorganic Chemistry , Slovak Academy of Sciences , Dúbravská cesta 9 , SK-84536 Bratislava , Slovakia .
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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Afonin AV, Vashchenko AV. The intramolecular hydrogen bond as a unit of molecular electronics: Molecular switching controlled by overcrowded intramolecular three-centered hydrogen bond. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The equilibrium geometry of the 2,5-bis-[2-(pyridin-2-yl)-vinyl]-1[Formula: see text]-pyrrole calculated at the MP2/6-311[Formula: see text]G([Formula: see text],[Formula: see text]) level of theory evidences the breaking of one of the components in the three-centered intramolecular hydrogen bond due to the steric strain. For this reason, the three-centered intramolecular hydrogen bonding turns out to be asymmetric interaction involving the major and minor components. However, the reversible switching between these components under an external impact is also possible. Two different stable states with unequal geometric and electronic structure are observed in the derivatives of the 2,5-bis-[2-(pyridin-2-yl)-vinyl]-1[Formula: see text]-pyrrole. These molecules represent novel molecular switches operating due to the pendulum-like transition between the nonequivalent two-centered components of the overcrowded three-centered intramolecular hydrogen bond. Implantation of hydrogen bond as a unit of the molecular scale device enhances potential of molecular electronics and could serve as a step towards the construction of artificial biological ensembles.
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Affiliation(s)
- Andrei V. Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Alexander V. Vashchenko
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, 664033 Irkutsk, Russia
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Afonin AV, Sterkhova IV, Vashchenko AV, Sigalov MV. Estimating the energy of intramolecular bifurcated (three-centered) hydrogen bond by X-ray, IR and 1 H NMR spectroscopy, and QTAIM calculations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.106] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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10
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Bártová K, Čechová L, Procházková E, Socha O, Janeba Z, Dračínský M. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines. J Org Chem 2017; 82:10350-10359. [PMID: 28829606 DOI: 10.1021/acs.joc.7b01810] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.
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Affiliation(s)
- Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Faculty of Science, Charles University , 116 36 Prague, Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
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Martínez-Cifuentes M, Weiss-López BE, Santos LS, Araya-Maturana R. Intramolecular hydrogen bond in biologically active o-carbonyl hydroquinones. Molecules 2014; 19:9354-68. [PMID: 24995921 PMCID: PMC6270916 DOI: 10.3390/molecules19079354] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/18/2014] [Accepted: 06/27/2014] [Indexed: 11/16/2022] Open
Abstract
Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LP-->σ* interactions for IHBs, O1…O2-H2 and the delocalization LP-->π* for O2-C2=Cα(β). For the O1…O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2-->π* C2=Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted.
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Affiliation(s)
- Maximiliano Martínez-Cifuentes
- Laboratorio de Síntesis Asimétrica, Instituto de Química de los Recursos Naturales, Universidad de Talca, Talca, Casilla 747, Chile.
| | - Boris E Weiss-López
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Casilla 653, Chile.
| | - Leonardo S Santos
- Laboratorio de Síntesis Asimétrica, Instituto de Química de los Recursos Naturales, Universidad de Talca, Talca, Casilla 747, Chile.
| | - Ramiro Araya-Maturana
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas Y Farmacéuticas, Universidad de Chile, Santiago, Casilla 233, Chile.
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Vashchenko AV, Afonin AV. Intramolecular hydrogen bond C-H⋯N in 1,1′-divinyl-2,2′-diimidazolyl according to the data of ab initio calculations and QTAIM analysis. J STRUCT CHEM+ 2014. [DOI: 10.1134/s002247661306005x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Vashchenko AV, Afonin AV. Features of three-centered hydrogen bonding in di(vinylpyrrolyl)pyridine and di(vinylpyridyl)-pyrrole from the ab initio calculation data and QTAIM analysis. J STRUCT CHEM+ 2013. [DOI: 10.1134/s002247661304001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rusakov YY, Krivdin LB. Modern quantum chemical methods for calculating spin–spin coupling constants: theoretical basis and structural applications in chemistry. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n02abeh004350] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lü R, Qu Z, Yu H, Wang F, Wang S. The electronic and topological properties of interactions between 1-butyl-3-methylimidazolium hexafluorophosphate/tetrafluoroborate and thiophene. J Mol Graph Model 2012; 36:36-41. [DOI: 10.1016/j.jmgm.2012.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/28/2012] [Accepted: 03/17/2012] [Indexed: 11/25/2022]
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Sánchez-Mendoza E, Hernández-Trujillo J. Interpretation of vicinal proton-proton coupling constants of heteroaromatic molecules in terms of topological electron density descriptors. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:866-872. [PMID: 20821374 DOI: 10.1002/mrc.2679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The indirect vicinal proton-proton coupling constants for pyrrole, furan, thiophene and 15 related heteroaromatic compounds were calculated using the Khon-Sham approximation. An analysis of the four Ramsey contributions to the coupling constants was carried out showing that the Fermi contact term is always positive and dominant, although the remaining contributions have a nonnegligible net negative contribution. The trends observed for the proton-proton coupling constants were rationalized in terms of the properties of the electron density. It was found that electron delocalization between the corresponding hydrogen atoms plays a major role on the observed behavior with the charges of the carbon atoms bonded to them and the accompanying geometric variations being also of importance in the coupling mechanism.
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Affiliation(s)
- Ernesto Sánchez-Mendoza
- Departamento de Física y Química Teórica, Facultad de Química, UNAM. México, D. F. 04510, México
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Pence MG, Choi JY, Egli M, Guengerich FP. Structural basis for proficient incorporation of dTTP opposite O6-methylguanine by human DNA polymerase iota. J Biol Chem 2010; 285:40666-72. [PMID: 20961860 DOI: 10.1074/jbc.m110.183665] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
O(6)-methylguanine (O(6)-methylG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, even physiological ones (e.g. S-adenosylmethionine). The efficiency of a truncated, catalytic DNA polymerase ι core enzyme was determined for nucleoside triphosphate incorporation opposite O(6)-methylG, using steady-state kinetic analyses. The results presented here corroborate previous work from this laboratory using full-length pol ι, which showed that dTTP incorporation occurs with high efficiency opposite O(6)-methylG. Misincorporation of dTTP opposite O(6)-methylG occurred with ∼6-fold higher efficiency than incorporation of dCTP. Crystal structures of the truncated form of pol ι with O(6)-methylG as the template base and incoming dCTP or dTTP were solved and showed that O(6)-methylG is rotated into the syn conformation in the pol ι active site and that dTTP misincorporation by pol ι is the result of Hoogsteen base pairing with the adduct. Both dCTP and dTTP base paired with the Hoogsteen edge of O(6)-methylG. A single, short hydrogen bond formed between the N3 atom of dTTP and the N7 atom of O(6)-methylG. Protonation of the N3 atom of dCTP and bifurcation of the N3 hydrogen between the N7 and O(6) atoms of O(6)-methylG allow base pairing of the lesion with dCTP. We conclude that differences in the Hoogsteen hydrogen bonding between nucleotides is the main factor in the preferential selectivity of dTTP opposite O(6)-methylG by human pol ι, in contrast to the mispairing modes observed previously for O(6)-methylG in the structures of the model DNA polymerases Sulfolobus solfataricus Dpo4 and Bacillus stearothermophilus DNA polymerase I.
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Affiliation(s)
- Matthew G Pence
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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