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Díaz-Muñoz M, Hernández-Muñoz R, Butanda-Ochoa A. Structure-activity features of purines and their receptors: implications in cell physiopathology. MOLECULAR BIOMEDICINE 2022; 3:5. [PMID: 35079944 PMCID: PMC8789959 DOI: 10.1186/s43556-022-00068-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
The purine molecular structure consists of fused pyrimidine and imidazole rings. Purines are main pieces that conform the structure of nucleic acids which rule the inheritance processes. Purines also work as metabolic intermediates in different cell functions and as messengers in the signaling pathways throughout cellular communication. Purines, mainly ATP and adenosine (ADO), perform their functional and pharmacological properties because of their structural/chemical characteristics that make them either targets of mutagenesis, mother frameworks for designing molecules with controlled effects (e.g. anti-cancer), or chemical donors (e.g., of methyl groups, which represent a potential chemoprotective action against cancer). Purines functions also come from their effect on specific receptors, channel-linked and G-protein coupled for ATP, and exclusively G-coupled receptors for ADO (also known as ADORAs), which are involved in cell signaling pathways, there, purines work as chemical messengers with autocrine, paracrine, and endocrine actions that regulate cell metabolism and immune response in tumor progression which depends on the receptor types involved in these signals. Purines also have antioxidant and anti-inflammatory properties and participate in the cell energy homeostasis. Therefore, purine physiology is important for a variety of functions relevant to cellular health; thus, when these molecules present a homeostatic imbalance, the stability and survival of the cellular systems become compromised.
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Affiliation(s)
- Mauricio Díaz-Muñoz
- Departamento de Neurobiología Celular Y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, UNAM, Boulevard Juriquilla 3001, C.P. 76230, Juriquilla, Querétaro, México
| | - Rolando Hernández-Muñoz
- Departamento de Biología Celular Y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria/Circuito Exterior, C.P. 04510, Ciudad de México, México
| | - Armando Butanda-Ochoa
- Departamento de Biología Celular Y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria/Circuito Exterior, C.P. 04510, Ciudad de México, México.
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2
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Gheorghiu A, Coveney PV, Arabi AA. The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface Focus 2020; 10:20190120. [PMID: 33178413 PMCID: PMC7653342 DOI: 10.1098/rsfs.2019.0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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3
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Arabi AA, Matta CF. Effects of Intense Electric Fields on the Double Proton Transfer in the Watson–Crick Guanine–Cytosine Base Pair. J Phys Chem B 2018; 122:8631-8641. [DOI: 10.1021/acs.jpcb.8b05053] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alya A. Arabi
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, P.O. Box 144534, United Arab Emirates
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada
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4
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Gatti C, Macetti G, Boyd RJ, Matta CF. An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States †. J Comput Chem 2018; 39:1112-1128. [PMID: 29681131 DOI: 10.1002/jcc.25222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 01/29/2023]
Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, 20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, Via Brera 28, Milano, 20121, Italy
| | - Giovanni Macetti
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, Milano, 20133, Italy
| | - Russell J Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3
| | - Chérif F Matta
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3.,Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada, B3H 3C3.,Dép. de chimie, Université Laval, Québec, Québec, Canada, G1V 0A6
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5
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Gharat PM, Maity DK, Pal H, Dutta Choudhury S. Inhibition of the prototropic tautomerism in chrysazine by p-sulfonatocalixarene hosts. Org Biomol Chem 2018; 16:5178-5187. [DOI: 10.1039/c8ob00978c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This study reveals the unusual inhibition of excited-state prototropic tautomerism of Chrysazine by p-sulfonatocalix[4,6]arene hosts.
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Affiliation(s)
- Poojan Milan Gharat
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - Dilip Kumar Maity
- Homi Bhabha National Institute
- Training School Complex
- Mumbai 400094
- India
| | - Haridas Pal
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
- Homi Bhabha National Institute
| | - Sharmistha Dutta Choudhury
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
- Homi Bhabha National Institute
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6
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Structure, stability, energy barrier and ionization energies of chemically modified DNA-bases: Quantum chemical calculations on 37 favored and rare tautomeric forms of tetraphosphoadenine. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Grebneva HA. Mechanisms of targeted frameshift mutations: Insertions arising during error-prone or SOS synthesis of DNA containing cis-syn cyclobutane thymine dimers. Mol Biol 2014. [DOI: 10.1134/s0026893314030066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Gardner N, Magers D, Hill G. Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives. J Mol Model 2013; 19:3543-9. [PMID: 23722555 DOI: 10.1007/s00894-013-1833-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/20/2013] [Indexed: 10/26/2022]
Abstract
The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of adenine and thymine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre-translational effects and post translational effects of adenine and thymine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory (DFT) B3LYP functional accompanied with 6-311G(d,p), 6-311+G(d,p) and 6-311++G(df,pd) basis sets. Our results reveal that the thymine tautomer has a higher EA and IP than the adenine tautomers. The higher EA suggests that an electron that attaches to the AT base pair would predominately attach to the thymine instead of adenine. The higher IP would suggest that an electron that is removed from the AT base pair would be predominately removed from the adenine within the base pair. Understanding how tautomerization, ionization and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.
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Affiliation(s)
- Noel Gardner
- Jackson State University, 1400 J. R. Lynch, Jackson, MS 39217, USA
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9
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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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10
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11
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Arabi AA, Matta CF. Effects of external electric fields on double proton transfer kinetics in the formic acid dimer. Phys Chem Chem Phys 2011; 13:13738-48. [DOI: 10.1039/c1cp20175a] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Electron density analysis of tautomeric mechanisms of adenine, thymine and guanine and the pairs of thymine with adenine or guanine. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Nam K, Gao J, York DM. Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. J Am Chem Soc 2008; 130:4680-91. [PMID: 18345664 DOI: 10.1021/ja0759141] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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14
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Kosenkov D, Gorb L, Shishkin OV, Sponer J, Leszczynski J. Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+. J Phys Chem B 2007; 112:150-7. [PMID: 18069814 DOI: 10.1021/jp075888t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O-->Mg and Mg<--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.
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Affiliation(s)
- Dmytro Kosenkov
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, USA
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15
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Fonseca Guerra C, Bickelhaupt FM, Saha S, Wang F. Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine. J Phys Chem A 2007; 110:4012-20. [PMID: 16539424 DOI: 10.1021/jp057275r] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86. We have also explored the correlations between the Kohn-Sham orbitals of the different tautomers at the BP86/QZ4P and SAOP/QZ4P levels. Finally, we discuss implications of the existence of the tautomeric forms of adenine for the DNA replication.
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Affiliation(s)
- C Fonseca Guerra
- Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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16
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Delchev VB, Shterev IG, Mikosch H, Kochev NT. Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study. J Mol Model 2007; 13:1001-8. [PMID: 17629753 DOI: 10.1007/s00894-007-0226-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 06/13/2007] [Indexed: 11/24/2022]
Abstract
Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744-2750, 1999).
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Affiliation(s)
- Vassil B Delchev
- Computer Chemistry group, University of Plovdiv, Plovdiv, Bulgaria.
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17
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Rincón E, Yáñez M, Toro-Labbé A, Mó O. Effect of Ni(ii), Cu(ii) and Zn(ii) association on the keto-enol tautomerism of thymine in the gas phase. Phys Chem Chem Phys 2007; 9:2531-7. [PMID: 17508085 DOI: 10.1039/b618050g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of Ni(II), Cu(II) and Zn(II) association on the diketo/keto-enol tautomerism of thymine has been investigated through the use of B3LYP density functional theory calculations. Final energies were obtained at the B3LYP/6-311+G(2df,2p)//B3LYP/6-311+G(d,p) level of theory. Ni(II) and Cu(II) lead to an oxidation of thymine which for Zn(ii) is only partial and catalyze the tautomerization process, this catalytic effect being much larger for Ni(2+) and Zn(2+) than for Cu(2+). One of the most significant consequences of the oxidation of the base is that the calculated BDE's are primarily dictated by the value of the second ionization potential of the metal, and therefore follow the sequence Cu(2+) > Ni(2+) > Zn(2+). Also importantly, metal dication association leads to a stabilization of the keto-enol tautomer, which becomes the most stable form upon interaction with Ni(2+) and Zn(2+). This stabilization enhancement is the consequence of three concomitant factors, namely, (i) a stronger interaction of the metal cation with the carbonyl oxygen, (ii) the interaction of the metal with the dehydrogenated ring nitrogen, (iii) an aromatization of the six-membered ring.
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Affiliation(s)
- Elizabeth Rincón
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile, Santiago, Chile
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18
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Grebneva HA. A model for targeted substitution mutagenesis during SOS replication of double-stranded DNA containing cis-syn cyclobutane thymine dimers. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2006; 47:733-45. [PMID: 17111422 DOI: 10.1002/em.20256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A model for ultraviolet mutagenesis is described that is based on the formation of rare tautomeric bases in pyrimidine dimers. It is shown that during SOS synthesis the modified DNA-polymerase inserts canonical bases opposite the dimers; the inserted bases are capable of forming hydrogen bonds with bases in the template DNA. SOS-replication of double-stranded DNA having thymine dimers, with one or both bases in a rare tautomeric conformation, results in targeted transitions, transversions, or one-nucleotide gaps. Structural analysis indicates that one type of dimer containing a single tautomeric base (TT*(1), with the "*" indicating a rare tautomeric base and the subscript referring to the particular conformation) can cause A:T --> G:C transition or homologous A:T --> T:A transversion, while another dimer (TT*(2)) can cause a one-nucleotide gap. The dimers containing T*(4) result in A:T --> C:G transversion, while TT*(5) dimers can cause A:T --> C:G transversion or homologous A:T --> T:A transversion. If both bases in the dimer are in a rare tautomeric form, then tandem mutations or double-nucleotide gaps can be formed. The dimers containing the rare tautomeric forms T*'(1) , T*'(2), T*'(3), T*'(4), and T*'(5) may not result in mutations. The question of whether dimers containing T*'(4) and T*'(5) result in mutations requires further investigation.
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Affiliation(s)
- Helen A Grebneva
- Donetsk Physical and Technical Institute, National Academy of Science of Ukraine, Donetsk, Ukraine.
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19
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Gorb L, Kaczmarek A, Gorb A, Sadlej AJ, Leszczynski J. Thermodynamics and Kinetics of Intramolecular Proton Transfer in Guanine. Post Hartree−Fock Study. J Phys Chem B 2005; 109:13770-6. [PMID: 16852725 DOI: 10.1021/jp050394m] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The most stable tautomers and rotamers of guanine are characterized by post Hartree-Fock ab initio calculations at the MP2 and CCSD(T) levels employing extended basis sets. Four of the lowest-energy structures (7H-oxo-amino- < 9H-oxo-amino- < 9H-syn-hydroxo-amino- < 9H-anti-hydroxo-amino-guanine) are found to lie within ca. 1 kcal/mol. The next form of guanine is established to lie more than 3 kcal/mol higher than the global minimum tautomer. The transition states of the following reversible reactions: 9H-oxo-amino-guanine right harpoon over left harpoon 9H-syn-hydroxo-amino-guanine right harpoon over left harpoon 9H-anti-hydroxo-amino-guanine have been studied. The calculated energy data were used to obtain thermodynamic parameters and to estimate the composition of the equilibrium mixture of conformers at 0 K and room temperature. The rate constants for the tautomerization of 9H-oxo-amino-guanine were determined by using the instanton approach. Their predicted values characterize an extremely slow chemical process, which is expected to reach the equilibrium in ca. 2500 h. Despite being so slow, we have shown that such a rate of the tautomerization describes a process that is much faster than the one characterized by the observed frequency of spontaneous point mutations. Therefore, additional stabilization factors, e.g., hydrations and interactions with enzymes are necessary to secure the known fidelity of DNA synthesis.
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Affiliation(s)
- Leonid Gorb
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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20
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Probing ab initio MP2 approach towards the prediction of vibrational infrared spectra of DNA base pairs. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Gorb L, Shishkin O, Leszczynski J. Charges of phosphate groups. A role in stabilization of 2'-deoxyribonucleotides. A DFT investigation. J Biomol Struct Dyn 2005; 22:441-54. [PMID: 15588107 DOI: 10.1080/07391102.2005.10507015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have analyzed the relative stabilities and Gibbs tautomeric free energy for tautomeric transitions of neutral 2'-deoxyribonucleotides and its mono- and di-protonated forms. Geometry optimizations of these nucleic acid constituents have been performed at the DFT/B3LYP level using the standard 6-31G(d) basis set. The prediction of relative stabilities, Gibbs tautomeric free energy has been made at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level of theory. For each nucleoside four major conformers, i.e., north/anti, north/syn, south/anti, and south/syn have been taken into consideration. We have found the substantial effect of the uncompensated charge on the relative stability of 2'-deoxyribonucleotides. In particular, when the charge of 2'-deoxyribonucleotide anions is completely compensated by protons, the syn conformations have been found to be the global minima due to stabilization provided by intramolecular hydrogen bonds. However, the negative charge that appears due to the successive removal of the protons from the phosphate group destabilizes these syn conformations and stabilizes preferably the south/anti conformations (except of 2'-deoxyguanosine phosphate). Only 2'-deoxyribonucleotides, possessing south/anti and north/anti orientations, containing guanine and cytosine can contribute significantly to the rate of spontaneous point mutations due to the formation of biologically relevant amounts of 'rare' tautomers. However, we found strong influence of uncompensated negative charge for 2'-deoxyribonucleotides which possess syn conformations. Finally we have found that the proton transfer could result in the spontaneous change of 2'-deoxyribonucleotides conformations. We conclude that this phenomenon could be considered as a new way for the stabilization of 'rare' isomers for such DNA bases as cytosine and thymine.
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Affiliation(s)
- Leonid Gorb
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, MS 39217, USA.
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22
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Li P, Bu Y. Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase. J Comput Chem 2005; 26:552-60. [PMID: 15726572 DOI: 10.1002/jcc.20191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.
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Affiliation(s)
- Ping Li
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Repubic of China
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23
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Markova N, Enchev V, Timtcheva I. Oxo−Hydroxy Tautomerism of 5-Fluorouracil: Water-Assisted Proton Transfer. J Phys Chem A 2005; 109:1981-8. [PMID: 16833532 DOI: 10.1021/jp046132m] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Post-Hartree-Fock ab initio quantum chemical calculations were performed for 5-fluorouracil in the gas phase and in a three-water cluster. Full geometry optimizations of the 5-fluorouracil-water complexes were carried out at the MP2/6-31+G(d,p) level of theory. MP4/6-31+G(d,p)//MP2/6-31+G(d,p) and MP4/6-31++G(d,p)//MP2/6-31+G(d,p) single-point calculations were performed to obtain more accurate energies. In water solution, 5-fluorouracil exists mainly in the 2,4-dioxo form (A). We propose that the populations of the 2-hydroxy-4-oxo (B) and 4-hydroxy-2-oxo (D) tautomers are 1 x 10(-4)% and 3.9 x 10(-8)%, respectively, on the basis of the relative stabilities of the tautomers calculated at the MP4/6-31++G(d,p)//MP2/6-31+G(d,p) level of theory. A profound difference between isolated and hydrated 5-fluorouracil is noted for the height of the tautomerization barrier. In the absence of water, the process of proton transfer is very slow. The addition of water molecules decreases the barrier by 2.3 times, making the process much faster. The minimum energy path (MP2/6-31+G(d,p)) for water-assisted proton transfer in trihydrated 5-fluorouracil was followed. CNDO/S-CI calculations predict singlet pi-pi(*) electron transitions at 312 nm for B and at 318 nm for D. The fluorescence spectrum of 5-fluorouracil in water confirms the presence of the hydroxy tautomer.
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Affiliation(s)
- Nadezhda Markova
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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24
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Li P, Bu Y. Multiwater-Assisted Proton Transfer Study in Glycinamide Using Density Functional Theory. J Phys Chem B 2004. [DOI: 10.1021/jp048919i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ping Li
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China and Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China and Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China
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25
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Li P, Bu Y. Investigations of Double Proton Transfer Behavior between Glycinamide and Formamide Using Density Functional Theory. J Phys Chem A 2004. [DOI: 10.1021/jp048527b] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ping Li
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China
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26
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Li P, Bu Y, Ai H, Yan S, Han K. Double Proton Transfer and One-Electron Oxidation Behaviors in Double H-Bonded Glycinamide−Formamidine Complex and Comparison with Biological Base Pair. J Phys Chem B 2004. [DOI: 10.1021/jp047567c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ping Li
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China, Department of Chemistry, Qufu Normal University, Qufu 273165, People's Republic of China, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Science Academy of China, Dalian, 116023, People's Republic of China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China, Department of Chemistry, Qufu Normal University, Qufu 273165, People's Republic of China, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Science Academy of China, Dalian, 116023, People's Republic of China
| | - Hongqi Ai
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China, Department of Chemistry, Qufu Normal University, Qufu 273165, People's Republic of China, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Science Academy of China, Dalian, 116023, People's Republic of China
| | - Shihai Yan
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China, Department of Chemistry, Qufu Normal University, Qufu 273165, People's Republic of China, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Science Academy of China, Dalian, 116023, People's Republic of China
| | - Keli Han
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China, Department of Chemistry, Qufu Normal University, Qufu 273165, People's Republic of China, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Science Academy of China, Dalian, 116023, People's Republic of China
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27
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Ab Initio Study of the Prototropic Tautomerism of Cytosine and Guanine and Their Contribution to Spontaneous Point Mutations. Int J Mol Sci 2003. [DOI: 10.3390/i4070410] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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28
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Florián J, Goodman MF, Warshel A. Computer simulation studies of the fidelity of DNA polymerases. Biopolymers 2003; 68:286-99. [PMID: 12601790 DOI: 10.1002/bip.10244] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), and the empirical valence bond (EVB) methods, we examined the stability of several mismatched base pairs in DNA duplex in aqueous solution, the contribution of binding energy to the fidelity of DNA polymerases beta and T7, and the mechanism and energetics of the polymerization reaction catalyzed by T7 DNA polymerase.
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Affiliation(s)
- Jan Florián
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA
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Podolyan Y, Gorb L, Leszczynski J. Double-Proton Transfer in the Formamidine−Formamide Dimer. Post-Hartree−Fock Gas-Phase and Aqueous Solution Study. J Phys Chem A 2002. [DOI: 10.1021/jp021666d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yevgeniy Podolyan
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217-0510
| | - Leonid Gorb
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217-0510
| | - Jerzy Leszczynski
- The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217-0510
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