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Maciejczyk M, Pyrka M. Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:545-557. [PMID: 37507591 PMCID: PMC10618388 DOI: 10.1007/s00249-023-01672-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.
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Affiliation(s)
- Maciej Maciejczyk
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland.
| | - Maciej Pyrka
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland
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2
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Palafox MA, Pedraza Velasco MLD, Marín JI, Posada-Moreno P. How proton transfer affects the helical parameters in DNA:DNA microhelices. J Biomol Struct Dyn 2022; 40:13759-13777. [PMID: 34806548 DOI: 10.1080/07391102.2021.1994880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton transfer reactions are a widespread phenomenon in many areas of the life sciences and it is one of the origins of the spontaneous point mutations during DNA replication. Because of its importance, many studies have been reported on these reactions. However, the present work is the first one focused on the structural geometrical changes by double proton transfer (DPT). Thus, different Watson-Crick (WC) pairs were optimized first in a simple model with one nucleoside base pair, and in a microhelix form with three nucleoside base pairs. The canonical and few tautomeric forms were considered in DNA:DNA microhelices with A-type and B-type helical forms. The stability of these structures and how the DPT process affects the main geometrical parameters was analyzed, in particular the deformation of the helical parameters. The M06-2X DFT method was used for this purpose. The purine/pyrimidine ring in the keto form appears easier to be deformed than when it is in the enol form. The weaker WC base pair formed with mixed microhelices than with nucleobases alone and the significant deformation of the helical and backbone parameters with the DPT appears to complicate this process in microhelices.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Fisica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid. Ciudad Universitaria s/n, Madrid, Spain
| | | | - Josefa Isasi Marín
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Posada-Moreno
- Departamento de Enfermería, Facultad de Enfermería, Fisioterapia y Podología, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Enfermería, UCM, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
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3
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Turaeva N, Oksengendler BL. Non-poissonian Distribution of Point Mutations in DNA. Front Chem 2020; 8:38. [PMID: 32083056 PMCID: PMC7005246 DOI: 10.3389/fchem.2020.00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/13/2020] [Indexed: 12/01/2022] Open
Abstract
In general, for chemical reactions occurring in systems, where fluctuations are not negligibly small, it is necessary to introduce a master equation for distribution of probability of fluctuations. It has been established that the monomolecular reactions of a type as A ↔ X are described by the master equation, which leads to a Poisson distribution with the variance equal to the average value N 0. However, the consideration of the Löwdin mechanism as autocatalytic non-linear chemical reactions such as A + X ↔ 2X and the corresponding master equation lead to a non-Poissonian probability distribution of fluctuations. In the presented work, first-order autocatalysis has been applied to the Löwdin's mechanism of spontaneous mutations in DNA. Describing double proton transfers between complimentary nucleotide bases along the chain by first-order autocatalytic reactions, the corresponding master equation for protons in tautomeric states becomes non-linear, and at non-equilibrium conditions this leads to the non-Poissonian distribution of spontaneous mutations in DNA. It is also suggested that the accumulation of large fluctuations of successive cooperative concerted protons along the chain may produce higher non-linearities which could have a significant impact on some biochemical processes, occurring in DNA.
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Affiliation(s)
- Nigora Turaeva
- Department of Biological Sciences, Webster University, Saint Louis, MO, United States
| | - Boris L Oksengendler
- Arifov Institute of ion-plasma and Laser Technologies, Tashkent, Uzbekistan
- Ural Federal University, Yekaterinburg, Russia
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4
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Wei SC, Ho JW, Yen HC, Shi HQ, Cheng LH, Weng CN, Chou WK, Chiu CC, Cheng PY. Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents. J Phys Chem A 2018; 122:9412-9425. [PMID: 30452255 DOI: 10.1021/acs.jpca.8b09526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H2O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H2O)1-6, Cy·(MeOH)1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H2O) n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.
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Affiliation(s)
- Shih-Chun Wei
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Jr-Wei Ho
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hung-Chien Yen
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hui-Qi Shi
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Li-Hao Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Nan Weng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Wei-Kuang Chou
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Chung Chiu
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Po-Yuan Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
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5
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Jin L, Lv M, Zhao M, Wang R, Zhao C, Lu J, Wang L, Wang W, Wei Y. Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance. Phys Chem Chem Phys 2018; 19:13515-13523. [PMID: 28497833 DOI: 10.1039/c7cp01008g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H2O, HCOOH, and the HCOOHH2O group to facilitate the tautomerism of the Cyt2t+ to CytN3+ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol-1, respectively, when the reaction is carried out in the absence and presence of H2O, HCOOH, or the HCOOHH2O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t+ to CytN3+ isomer remains unfavorable, and the HCOOH and HCOOHH2O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3+HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t+HCOOH) (τ99.9% = 3.84 × 10-12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3+HCOOH complex (τ = 8.33 × 10-9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3+ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.
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Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Mengdan Lv
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Mengting Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Rui Wang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Ling Wang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Yawen Wei
- Institute of publication Science, Chang'an University, Xi'an 710064, China
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6
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Thermochemistry of the Reaction of Solvated Sodium Ion Clusters with Thymine in the Gas Phase: An Example of the Reaction in Microcosmic Environment. J CLUST SCI 2018. [DOI: 10.1007/s10876-018-1364-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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7
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Jin L, Song X, Cao Z, Luo L, Zhao C, Lu J, Zhang Q. The isomerization of cytosine: Intramolecular hydrogen atom transfer mediated through formic acid. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - Xiaoling Song
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - Zhe Cao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - LiYang Luo
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science; Shaanxi University of Technology; Hanzhong China
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8
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Jin L, Shi S, Zhao Y, Luo L, Zhao C, Lu J, Jiang M. Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Shengnan Shi
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Yang Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Liyang Luo
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Min Jiang
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
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9
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Tolosa S, Sánchez J, Sansón J, Hidalgo A. Steered molecular dynamic simulations of the tautomeric equilibria in solution of DNA bases. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Pyrka M, Maciejczyk M. Theoretical investigations of tautomeric equilibrium of 9-methyl-8-aza-iso-Guanine and its electrostatic properties. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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12
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Ho J, Yen H, Shi H, Cheng L, Weng C, Chou W, Chiu C, Cheng P. Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hung‐Chien Yen
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hui‐Qi Shi
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Li‐Hao Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Nan Weng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Wei‐Kuang Chou
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Chung Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Po‐Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
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13
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Ho J, Yen H, Shi H, Cheng L, Weng C, Chou W, Chiu C, Cheng P. Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence. Angew Chem Int Ed Engl 2015; 54:14772-6. [DOI: 10.1002/anie.201507524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/18/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hung‐Chien Yen
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hui‐Qi Shi
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Li‐Hao Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Nan Weng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Wei‐Kuang Chou
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Chung Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Po‐Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
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14
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Theoretical study of tautomeric equilibria of 2,6-diamino-8-azapurine and 8-aza-iso-Guanine. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Mehr SHM, Fukuyama K, Bishop S, Lelj F, MacLachlan MJ. Deuteration of Aromatic Rings under Very Mild Conditions through Keto-Enamine Tautomeric Amplification. J Org Chem 2015; 80:5144-50. [PMID: 25906051 DOI: 10.1021/acs.joc.5b00539] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have discovered a surprising, mild method for deuteration of select aromatic compounds that is facilitated by a keto-enamine tautomeric intermediate. The mechanism of the reaction has been studied using kinetics experiments and detailed computational analysis. It was found that a chain of water molecules has a substantial role in lowering the activation barrier to the tautomerization-enhanced deuteration reaction. Our results demonstrate that tautomeric forms of aromatic molecules can be exploited to bring about enhanced reactivity.
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Affiliation(s)
- S Hessam M Mehr
- †Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katsuya Fukuyama
- ‡Center for Liberal Arts, Meiji Gakuin University, Yokohama 244-8539, Japan
| | - Stephanie Bishop
- †Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Francesco Lelj
- §Department of Scienze and LaSCaMM of INSTM, Università della Basilicata, 85100 Potenza, Italy
| | - Mark J MacLachlan
- †Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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16
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Salpin JY, Haldys V, Guillaumont S, Tortajada J, Hurtado M, Lamsabhi AM. Gas-Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple-Photon Dissociation Spectroscopy Study. Chemphyschem 2014; 15:2959-71. [DOI: 10.1002/cphc.201402369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 12/07/2022]
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17
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Wincel H. Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1479-87. [PMID: 22821196 PMCID: PMC3414711 DOI: 10.1007/s13361-012-0436-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 06/10/2012] [Accepted: 06/15/2012] [Indexed: 06/01/2023]
Abstract
Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
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18
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Brovarets' OO, Yurenko YP, Dubey IY, Hovorun DM. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. J Biomol Struct Dyn 2012; 29:597-605. [PMID: 22545991 DOI: 10.1080/07391102.2011.672624] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.
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Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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19
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Szalay PG, Watson T, Perera A, Lotrich V, Fogarasi G, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 2. Effect of Biological Environment on the Electronic Excitation Spectrum of Nucleobases. J Phys Chem A 2012; 116:8851-60. [DOI: 10.1021/jp305130q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Géza Fogarasi
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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20
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Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci U S A 2011; 108:17644-8. [PMID: 22006298 DOI: 10.1073/pnas.1114496108] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C • A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.
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Takahashi O, Kobayashi K, Oda A. Modeling the enolization of succinimide derivatives, a key step of racemization of aspartic acid residues: importance of a two-H2O mechanism. Chem Biodivers 2010; 7:1349-56. [PMID: 20564551 DOI: 10.1002/cbdv.200900296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Racemization of aspartic acid residues in peptides and proteins is assumed to proceed via succinimide intermediates. An enolization of the succinimide intermediate is required for the racemization to occur. In this study, we modeled the enolization step by density-functional theory (DFT) calculations (B3LYP/6-31+G**), using two model compounds, N-methylsuccinimide (1) and its formylamino derivative 2. Three mechanisms were investigated for 1, i.e., the direct mechanism without active participation of H(2)O molecules, and one-H(2)O and two-H(2)O mechanisms, in which one or two H(2)O molecules actively participate in the reaction. We found that the two-H(2)O mechanism was the most favorable with an activation barrier of 37 kcal mol(-1). In the two-H(2)O mechanism, a concerted bond reorganization involving a triple H-atom transfer occurred in an eight-membered cyclic structure formed between the imide and two H(2)O molecules. For 2, we investigated only the two-H(2)O mechanism and found that the activation barrier was lowered to 31 kcal mol(-1) due to an H-bond between the CO O-atom of the formylamino group ('the neighboring residue') and one of the H(2)O molecules. Our results suggest that, in proteins, the Asp racemization is severely controlled by the accessibility of H(2)O molecules to the reaction site of the succinimide intermediate.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan.
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Alagona G, Ghio C, Nagy PI. The catalytic effect of water on the keto–enol tautomerism. Pyruvate and acetylacetone: a computational challenge. Phys Chem Chem Phys 2010; 12:10173-88. [DOI: 10.1039/c003999c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kosma K, Schröter C, Samoylova E, Hertel IV, Schultz T. Excited-State Dynamics of Cytosine Tautomers. J Am Chem Soc 2009; 131:16939-43. [DOI: 10.1021/ja907355a] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kyriaki Kosma
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | - Christian Schröter
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | - Elena Samoylova
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | | | - Thomas Schultz
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
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Cerón-Carrasco JP, Requena A, Michaux C, Perpète EA, Jacquemin D. Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair. J Phys Chem A 2009; 113:7892-8. [DOI: 10.1021/jp900782h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - C. Michaux
- Laboratorie de Chimie Biologique Structurale, Facultés Universitaires Notre-Dame de la Paix Rue de Bruxelles, 61. 5000 Namur, Belgium
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