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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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2
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Lucia-Tamudo J, Cárdenas G, Anguita-Ortiz N, Díaz-Tendero S, Nogueira JJ. Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches. J Chem Inf Model 2022; 62:3365-3380. [PMID: 35771991 PMCID: PMC9326891 DOI: 10.1021/acs.jcim.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The determination
of the redox properties of nucleobases is of
paramount importance to get insight into the charge-transfer processes
in which they are involved, such as those occurring in DNA-inspired
biosensors. Although many theoretical and experimental studies have
been conducted, the value of the one-electron oxidation potentials
of nucleobases is not well-defined. Moreover, the most appropriate
theoretical protocol to model the redox properties has not been established
yet. In this work, we have implemented and evaluated different static
and dynamic approaches to compute the one-electron oxidation potentials
of solvated nucleobases. In the static framework, two thermodynamic
cycles have been tested to assess their accuracy against the direct
determination of oxidation potentials from the adiabatic ionization
energies. Then, the introduction of vibrational sampling, the effect
of implicit and explicit solvation models, and the application of
the Marcus theory have been analyzed through dynamic methods. The
results revealed that the static direct determination provides more
accurate results than thermodynamic cycles. Moreover, the effect of
sampling has not shown to be relevant, and the results are improved
within the dynamic framework when the Marcus theory is applied, especially
in explicit solvent, with respect to the direct approach. Finally,
the presence of different tautomers in water does not affect significantly
the one-electron oxidation potentials.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Gustavo Cárdenas
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Nuria Anguita-Ortiz
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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3
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Gorini F, Scala G, Cooke MS, Majello B, Amente S. Towards a comprehensive view of 8-oxo-7,8-dihydro-2'-deoxyguanosine: Highlighting the intertwined roles of DNA damage and epigenetics in genomic instability. DNA Repair (Amst) 2021; 97:103027. [PMID: 33285475 PMCID: PMC7926032 DOI: 10.1016/j.dnarep.2020.103027] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of DNA oxidation, is a pre-mutagenic lesion which is prone to mispair, if left unrepaired, with 2'-deoxyadenosine during DNA replication. While unrepaired or incompletely repaired 8-oxodG has classically been associated with genome instability and cancer, it has recently been reported to have a role in the epigenetic regulation of gene expression. Despite the growing collection of genome-wide 8-oxodG mapping studies that have been used to provide new insight on the functional nature of 8-oxodG within the genome, a comprehensive view that brings together the epigenetic and the mutagenic nature of the 8-oxodG is still lacking. To help address this gap, this review aims to provide (i) a description of the state-of-the-art knowledge on both the mutagenic and epigenetic roles of 8-oxodG; (ii) putative molecular models through which the 8-oxodG can cause genome instability; (iii) a possible molecular model on how 8-oxodG, acting as an epigenetic signal, could cause the translocations and deletions which are associated with cancer.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Barbara Majello
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy.
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4
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Mukherjee M, Tripathi D, Brehm M, Riplinger C, Dutta AK. Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study. J Chem Theory Comput 2020; 17:105-116. [DOI: 10.1021/acs.jctc.0c00655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Divya Tripathi
- Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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5
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Giorgio M, Dellino GI, Gambino V, Roda N, Pelicci PG. On the epigenetic role of guanosine oxidation. Redox Biol 2020; 29:101398. [PMID: 31926624 PMCID: PMC6926346 DOI: 10.1016/j.redox.2019.101398] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 01/14/2023] Open
Abstract
Chemical modifications of DNA and RNA regulate genome functions or trigger mutagenesis resulting in aging or cancer. Oxidations of macromolecules, including DNA, are common reactions in biological systems and often part of regulatory circuits rather than accidental events. DNA alterations are particularly relevant since the unique role of nuclear and mitochondrial genome is coding enduring and inheritable information. Therefore, an alteration in DNA may represent a relevant problem given its transmission to daughter cells. At the same time, the regulation of gene expression allows cells to continuously adapt to the environmental changes that occur throughout the life of the organism to ultimately maintain cellular homeostasis. Here we review the multiple ways that lead to DNA oxidation and the regulation of mechanisms activated by cells to repair this damage. Moreover, we present the recent evidence suggesting that DNA damage caused by physiological metabolism acts as epigenetic signal for regulation of gene expression. In particular, the predisposition of guanine to oxidation might reflect an adaptation to improve the genome plasticity to redox changes.
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Affiliation(s)
- Marco Giorgio
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Gambino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Niccolo' Roda
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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6
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Reibnegger G. A DFT Study on the One-Electron Reduction/Oxidation of Biologically Relevant Pteridine Derivatives. ChemistrySelect 2018. [DOI: 10.1002/slct.201802368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gilbert Reibnegger
- Physiological Chemistry; Otto-Loewi Research Center; Medical University of Graz; Neue Stiftingtalstr. 6 Graz A-8010 Austria
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7
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Fuchi Y, Fukuda T, Sasaki S. Luminescent europium sensors for specific detection of 8-oxo-dGTP by time-gated fluorescence. Bioorg Med Chem 2018; 26:3254-3260. [PMID: 29731311 DOI: 10.1016/j.bmc.2018.04.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023]
Abstract
The 9-hydroxy-1,3-diazaphenoxazine-2-one unit was conjugated with the Eu3+-cyclen complex through a linker. This diazaphenoxazine group was expected as an antenna unit for the excitation of europium ion, and a selective recognition site for 8-oxo-dGTP base. Among the synthesized three derivatives, the highest fluorescence emission was obtained by the complex constructed of an ethylene linker and the cyclen unit with three N,N-dimethylacetamide groups. The Eu3+-cyclen complex exhibited a selective response to the 8-oxo-dGTP in aqueous media by a time-resolved fluorescence assay.
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Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Fukuda
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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9
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Engineering Redox Potential of Lithium Clusters for Electrode Material in Lithium-Ion Batteries. J CLUST SCI 2017. [DOI: 10.1007/s10876-017-1260-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Lu N, Bu Y. Computational design of three Cu-induced triangular pyrimidines based DNA motifs with improved conductivity. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Novel DNA triangular pyrimidine derivatives are designed by metal decoration through replacement of H by Cu in the Watson–Crick hydrogen bond region. The DFT method is used to examine the coordination of triangle-arranged Cu with three pyrimidines in nonplanar three-bladed turbine geometries. The Cu···Cu cuprophilic bonds are ascribed to the partially occupied d orbitals without direct molecular orbital (MO) interactions. Four-center bonds depend on Cu–N/O bonds, which are contributed by p orbitals of N/O atoms along or perpendicular to the bond axis. The activity of frontier MOs is modulated, leading to the decrease of gaps, ionization potentials (IPs), and electron affinities (EAs) desired for the improvement of conductivity. The hole trapping ability is assured by virtue of the spin density distributed on Cu. On average, the single electron density is located on π orbitals of three aromatic base rings. There is paramagnetic electron delocalization on the inner d orbitals of triangle region. The analysis of electron localization function ELF-π and electrostatic potential maps reveals that the outer strong π–π stacking interaction together with the inner d orbital channel enable effective transduction of electrical signals along the Cu–DNA nanowires. The 3Cu-induced triangular pyrimidines have important potential applications as structural motifs of molecular electronic devices.
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Affiliation(s)
- Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian, P. R. China, 271018
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, P. R. China, 250100
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11
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Close DM, Wardman P. Calculations of the Energetics of Oxidation of Aqueous Nucleosides and the Effects of Prototropic Equilibria. J Phys Chem A 2016; 120:4043-8. [PMID: 27219530 DOI: 10.1021/acs.jpca.6b02653] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently the calculated standard reduction potentials of the radical-cations of N-methyl substituted DNA bases have been reported that agree fairly well with the experimental results. However, there are issues reflecting the fact that the experimental results usually relate to the couple E(o)(Nuc(•),H(+)/NucH(+)), whereas the calculated results are for the E(o)(Nuc(•+)/Nuc) couple. To calculate the midpoint reduction potential at pH 7 (Em7), it is important to have accurate acid dissociation constants (pKs) for both ground-state bases and their radicals, and the effects of uncertainty in some of these values (e.g., that of the adenosine radical) must be considered. Calculations of the pKs of the radicals of the nucleic acid bases (as nucleosides) have been performed to explore the effects the various pKs have on calculating the values of Em7 and to see what improvements can be made with the accuracy of the calculations.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University , Johnson City, Tennessee 37614, United States
| | - Peter Wardman
- Gray Cancer Institute, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Oxford OX3 7DQ, United Kingdom
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12
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13
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Palafox MA, Rastogi V. 6-Aminouracil: Geometries and spectra in the isolated state and in the solid state simulation. A comparison with 5-aminouracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Mechanism and enantioselectivity in α-alkylation of carbonyl compounds via photoredox organocatalysis: A DFT study. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Lu N, Bu Y, Wang H. Intensified effects of multi-Cu modification on the electronic properties of the modified base pairs containing hetero-ring-expanded pyrimidine bases. Phys Chem Chem Phys 2016; 18:2913-23. [PMID: 26733396 DOI: 10.1039/c5cp06133d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel DNA base pair derivatives (A2CunU, A2CunC, G3CunU, and G3CunC) are designed by aromatic expansion of pyrimidine bases with four kinds of hetero-rings (denoted by nC and nU, n = 1, 2, 3, and 4) and metal-decoration through Cu replacement of hydrogens in the Watson-Crick hydrogen bond region. Their structures and properties are calculated for examining the cooperative effects of the two modification ways. The calculated results reveal that multiple Cu decoration makes up the deficiencies of size-expansion, and exhibits not only increase of structural stability and reduction of ionization potentials, but also ideal shrink of the HOMO-LUMO gaps, notable enhancement of interbase coupling as well as remarkable redshifts of π → π* transitions for all M-x modified base pairs. The decrease extents of the gaps and ionization potentials follow the same order G3CunU > G3CunC > A2CunU > A2CunC, and in each series (denoted by different n), the gaps, ionization potentials and first π → π* transition energies have an order of 4 < 1 < 2 < 3. The Cu d orbitals function as bridges for π electron delocalization on the conjugated aromatic rings of two bases, leading to an enhancement of transverse electronic communication, as verified by spin density delocalization, orbital composition changes, redshift of the π → π* transition and also advocated by the electron-sharing indexes such as delocalization index, Mayer bond orders and multicenter bonding. Electron localization function ELF-π isosurfaces above the molecular plane further suggested that effective longitudinal conduction is closely relevant with the bicyclic domain involving good electron delocalization and strong π-π stacking between layers. This work presents theoretical evidence for the cooperative effects of metal decoration and ring-expansion modifications on the electronic properties of the modified base pairs and also proves that the base pairs designed here could be competent building blocks for the DNA-based nanowires with improved electron activity and excellent conductivity.
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Affiliation(s)
- Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China and School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Huatian Wang
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China
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16
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Adhikary A, Kumar A, Bishop CT, Wiegand TJ, Hindi RM, Adhikary A, Sevilla MD. π-Radical to σ-Radical Tautomerization in One-Electron-Oxidized 1-Methylcytosine and Its Analogs. J Phys Chem B 2015; 119:11496-505. [PMID: 26237072 DOI: 10.1021/acs.jpcb.5b05162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, iminyl σ-radical formation in several one-electron-oxidized cytosine analogs, including 1-MeC, cidofovir, 2'-deoxycytidine (dCyd), and 2'-deoxycytidine 5'-monophosphate (5'-dCMP), were investigated in homogeneous, aqueous (D2O or H2O) glassy solutions at low temperatures by employing electron spin resonance (ESR) spectroscopy. Upon employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones, thus confirming its assignment. ESR and DFT studies show that the cytosine iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical [cytosine π-aminyl radical, C(N4-H)(•)]. Employing 1-MeC samples at various pHs ranging from ca. 8 to 11, ESR studies show that the tautomeric equilibrium between C(N4-H)(•) and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that, in the iminyl σ-radical, the unpaired spin is localized on the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form, as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG = -32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in double-stranded DNA by a radiation-induced ionization-deprotonation process that is only 10 kcal/mol above the lowest energy path.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Casandra T Bishop
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Tyler J Wiegand
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ragda M Hindi
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ananya Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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17
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Thapa B, Schlegel HB. Calculations of pKa's and redox potentials of nucleobases with explicit waters and polarizable continuum solvation. J Phys Chem A 2014; 119:5134-44. [PMID: 25291241 DOI: 10.1021/jp5088866] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SMD implicit solvation model augmented with one and four explicit water molecules was used to calculate pKa's and redox potentials of N-methyl-substituted nucleic acid bases guanine, adenine, cytosine, thymine, and uracil. Calculations were carried out with the B3LYP/6-31+G(d,p) level of theory. The same numbers of water molecules were hydrogen bonded to the neutral, protonated, and deprotonated nucleobases in their unoxidized and oxidized forms. The improvement in pKa1 involving neutrals and cations was modest. By contrast, the improvement in pKa2 involving neutrals and anions was quite significant, reducing the mean absolute error from 4.6 pKa units with no waters, to 2.6 with one water and 1.7 with four waters. For the oxidation of nucleobases, adding explicit waters did little to improve E(X(•),H(+)/XH), possibly because both species in the redox couple are neutral molecules at pH 7.
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Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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18
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Wang WY, Ma NN, Sun SL, Qiu YQ. Impact of Redox Stimuli on Ferrocene–Buckybowl Complexes: Switchable Optoelectronic and Nonlinear Optical Properties. Organometallics 2014. [DOI: 10.1021/om500224g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wen-Yong Wang
- Institute of Functional Material
Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, Jilin, People’s Republic of China
| | - Na-Na Ma
- Institute of Functional Material
Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, Jilin, People’s Republic of China
| | - Shi-Ling Sun
- Institute of Functional Material
Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, Jilin, People’s Republic of China
| | - Yong-Qing Qiu
- Institute of Functional Material
Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, Jilin, People’s Republic of China
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19
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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20
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Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces. MINERALS 2014. [DOI: 10.3390/min4020345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Kumar A, Sevilla MD. π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 2013; 117:11623-32. [PMID: 24000793 DOI: 10.1021/jp407897n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(•), and uracil, U(N3-H)(•), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(•+), C(N4-H)(•), adenine, A(•+), A(N6-H)(•), and guanine, G(•+), G(N2-H)(•), G(N1-H)(•), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(•) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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22
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Psciuk BT, Schlegel HB. Computational Prediction of One-Electron Reduction Potentials and Acid Dissociation Constants for Guanine Oxidation Intermediates and Products. J Phys Chem B 2013; 117:9518-31. [DOI: 10.1021/jp4062412] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian T. Psciuk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United
States
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Suzuki A, Kimura K, Ishioroshi S, Saito I, Nemoto N, Saito Y. Synthesis of solvatofluorochromic 7-arylethynylated 7-deaza-2′-deoxyadenosine derivatives: application to the design of environmentally sensitive fluorescent probes forming stable DNA duplexes. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.02.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Affiliation(s)
- David M. Close
- Department
of Physics, Box
70652, East Tennessee State University,
Johnson City, Tennessee 37614, United States
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Psciuk BT, Lord RL, Munk BH, Schlegel HB. Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases. J Chem Theory Comput 2012; 8:5107-23. [PMID: 26593200 DOI: 10.1021/ct300550x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14-0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH(+•)/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X(•),H(+)/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1-0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between guanine and 8-oxoguanine is in good agreement with the measured values.
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Affiliation(s)
- Brian T Psciuk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Richard L Lord
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara H Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Polavarapu A, Stillabower JA, Stubblefield SGW, Taylor WM, Baik MH. The mechanism of guanine alkylation by nitrogen mustards: a computational study. J Org Chem 2012; 77:5914-21. [PMID: 22681226 DOI: 10.1021/jo300351g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermodynamics and kinetics for the monofunctional binding of nitrogen mustard class of anticancer drugs to purine bases of DNA were studied computationally using guanine and adenine as model substrates. Mechlorethamine and melphalan are used as model systems in order to better understand the difference in antitumor activity of aliphatic and aromatic mustards, respectively. In good agreement with experiments that suggested the accumulation of a reactive intermediate in the case of mechlorethamine, our model predicts a significant preference for the formation of corresponding aziridinium ion for mechlorethamine, while the formation of the aziridinium ion is not computed to be preferred when melphalan is used. Two effects are found that contribute to this difference. First, the ground state of the drug shows a highly delocalized lone pair on the amine nitrogen of the melphalan, which makes the subsequent cyclization more difficult. Second, because of the aromatic substituent connected to the amine nitrogen of melphalan, a large energy penalty has to be paid for solvation. A detailed study of energy profiles for the two-step mechanism for alkylation of guanine and adenine was performed. Alkylation of guanine is ∼6 kcal mol(-1) preferred over adenine, and the factors contributing to this preference were explained in our previous study of cisplatin binding to purine bases. A detailed analysis of energy profiles of mechlorethamine and melphalan binding to guanine and adenine are presented to provide an insight into rate limiting step and the difference in reactivity and stability of the intermediate in both nitrogen mustards, respectively.
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Affiliation(s)
- Abhigna Polavarapu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
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27
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Quantum Chemical Calculation of Donor–Acceptor Coupling for Charge Transfer in DNA. Top Curr Chem (Cham) 2012. [DOI: 10.1007/b94472] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Saito Y, Suzuki A, Ishioroshi S, Saito I. Synthesis and photophysical properties of novel push–pull-type solvatochromic 7-deaza-2′-deoxypurine nucleosides. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.06.089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Thazhathveetil AK, Trifonov A, Wasielewski MR, Lewis FD. Increasing the speed limit for hole transport in DNA. J Am Chem Soc 2011; 133:11485-7. [PMID: 21728369 DOI: 10.1021/ja204815d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transport of positive charge or holes in DNA occurs via a thermally activated multi-step hopping mechanism. The fastest hopping rates reported to date are those for repeating poly(purine) sequences in which hopping occurs via a random walk mechanism with rate constants of k(hop) = 4.3 × 10(9) s(-1) for poly(dG) and 1.2 × 10(9) s(-1) for poly(dA). We report here the dynamics of charge separation in DNA conjugates possessing repeating 7-deazaadenine (dzA) sequences. These data provide an estimated value of k(hop) = 4.2 × 10(10) s(-1) for poly(dzA), an order of magnitude faster than for poly(dG).
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Affiliation(s)
- Arun K Thazhathveetil
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60206-3113, USA
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30
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Zhang FQ, Guan W, Yan LK, Zhang YT, Xu MT, Hayfron-Benjamin E, Su ZM. On the Origin of the Relative Stability of Wells–Dawson Isomers: A DFT Study of α-, β-, γ-, α*-, β*-, and γ*-[(PO4)2W18O54]6– Anions. Inorg Chem 2011; 50:4967-77. [DOI: 10.1021/ic200203s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Fu-Qiang Zhang
- Department of Chemistry, Shangqiu Normal University, Shangqiu 476000, People's Republic of China
| | - Wei Guan
- Institute of Functional Material Chemistry, Department of Chemistry, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Li-Kan Yan
- Institute of Functional Material Chemistry, Department of Chemistry, Northeast Normal University, Changchun 130024, People's Republic of China
| | - Yin-Tang Zhang
- Department of Chemistry, Shangqiu Normal University, Shangqiu 476000, People's Republic of China
| | - Mao-Tian Xu
- Department of Chemistry, Shangqiu Normal University, Shangqiu 476000, People's Republic of China
| | | | - Zhong-Min Su
- Institute of Functional Material Chemistry, Department of Chemistry, Northeast Normal University, Changchun 130024, People's Republic of China
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31
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Han L, Bu Y. Computational design of ring-expanded pyrimidine-based DNA motifs with improved conductivity. Phys Chem Chem Phys 2011; 13:5906-14. [DOI: 10.1039/c0cp02297g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Xu LC, Li QS, Zhang ZQ, Miao TF, Zheng KC, Ji LN. A theoretical study on the substituent effect of DNA-photocleavage by [Ru(phen)2(6-R-dppz)]2+ (R=H, OH, and NO2). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Theoretical study on redox potentials of organic radicals in different solvents. RESEARCH ON CHEMICAL INTERMEDIATES 2010. [DOI: 10.1007/s11164-010-0212-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Kobayashi K. Evidence of formation of adenine dimer cation radical in DNA: the importance of adenine base stacking. J Phys Chem B 2010; 114:5600-4. [PMID: 20369809 DOI: 10.1021/jp100589w] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deprotonation of the adenine (A) base in both mononucleotide and oligonucleotide (ODN) was measured by nanosecond pulse radiolysis. The cation radical (A(+*)) of deoxyadenosine (dA), produced by oxidation with SO(4)(-*), rapidly deprotonated to form the neutral A radical (A(- H)(*)) with a rate constant of 2.0 x 10(7) s(-1) and a pK(a) value of 4.2, as determined by transient spectroscopy. A similar process was observed in experiments performed on a variety of double-stranded ODNs containing adenine x thymine (A x T) base pairs. The transient spectrum of A(+)(*) in an ODN composed of alternating A x T pairs was essentially identical to that of free dA and differed from the spectra of ODNs containing AA and AAA. In contrast, the spectra of A(- H)(*) were not affected by the sequence. These results suggest that the positive charge on A(+)(*) in ODNs is delocalized as the dimer is stabilized by pi-orbital stacking between adjacent A's. The rate constants for deprotonation of A(+)(*) in ODNs containing AA and AAA (0.9-1.1 x 10(7) s(-1)) were a factor of 2 smaller than the rate constants for deprotonation of A(+)(*) in ODNs containing alternating A x T and dA (2.0 x 10(7) s(-1)). This suggests that the formation of a charge resonance stabilized dimer AA(+)(*) in DNA produced a significant barrier to deprotonation.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan.
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35
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Steenken S, Reynisson J. DFT calculations on the deprotonation site of the one-electron oxidised guanine-cytosine base pair. Phys Chem Chem Phys 2010; 12:9088-93. [PMID: 20532316 DOI: 10.1039/c002528c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As calculated by the density functional theory (DFT), the acidity of cytosine's exocyclic amine group (C-N(4)H2) in the base pair G-C is considerably increased upon its one-electron oxidation. The proton affinity (PA) of the amine moiety is lowered by ionisation of G-C (which yields G(*+)-C) from -348.1 to -269.1 kcal mol(-1). The PA is further decreased by 7.6 kcal mol(-1) as a result of the ensuing proton transfer from G(*+) to C to yield the spin-charge separated base pair G(-H)(*)-C(+H)(+). Under these conditions and taking the hydration energy of H(+) into account, the overall proton transfer from the C-N(4)H2 group to the aqueous phase in the major groove is exothermic by -2.4 kcal mol(-1). This proton transfer to water from the initially present DNA radical cation constitutes separation of charge from spin and thus reduces positive charge transfer in double stranded DNA.
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Affiliation(s)
- Steen Steenken
- Department of Chemistry & Auckland Bioengineering Institute, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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36
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Henry JB, Mount AR. Calculation of the Redox Properties of Aromatics and Prediction of Their Coupling Mechanism and Oligomer Redox Properties. J Phys Chem A 2009; 113:13023-8. [PMID: 19799452 DOI: 10.1021/jp907792b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- John B. Henry
- School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Andrew R. Mount
- School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
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37
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Kumar A, Sevilla MD. Influence of hydration on proton transfer in the guanine-cytosine radical cation (G*+-C) base pair: a density functional theory study. J Phys Chem B 2009; 113:11359-61. [PMID: 19485319 PMCID: PMC2740929 DOI: 10.1021/jp903403d] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Upon one-electron oxidation, all molecules including DNA bases become more acidic in nature. For the GC base pair, experiments suggest that a facile proton transfer takes place in the G(*+)-C base pair from N(1) of G(*+) to N(3) of cytosine. This intrabase pair proton-transfer reaction has been extensively considered using theoretical methods for the gas phase, and it is predicted that the proton transfer is slightly unfavorable, in disagreement with experiment. In the present study, we consider the effect of the first hydration layer on the proton-transfer reaction in G(*+)-C by the use of density functional theory (DFT) using B3LYP/6-31+G** calculations of the G(*+)-C base pair in the presence of 6 and 11 water molecules. Under the influence of hydration of 11 waters, a facile proton transfer from N(1) of G(*+) to N(3) of C is predicted. The zero-point energy (ZPE)-corrected forward and backward energy barriers, for the proton transfer from N(1) of G(*+) to N(3) of C, was found to be 1.4 and 2.6 kcal/mol, respectively. The proton-transferred G(*)-(H(+))C + 11H(2)O was found to be 1.2 kcal/mol more stable than G(*+)-C + 11H(2)O, in agreement with experiment. The present calculation demonstrates that the inclusion of the first hydration shell around the G(*+)-C base pair has an important effect on the internal proton-transfer energetics.
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38
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Han L, Li H, Cukier RI, Bu Y. Hetero-Ring-Expansion Design for Adenine-Based DNA Motifs: Evidence from DFT Calculations and Molecular Dynamics Simulations. J Phys Chem B 2009; 113:4407-12. [DOI: 10.1021/jp8088726] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li Han
- The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China, and Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
| | - Huifang Li
- The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China, and Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
| | - Robert I. Cukier
- The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China, and Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
| | - Yuxiang Bu
- The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China, and Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
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39
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Benniston AC, Allen BD, Harriman A, Llarena I, Rostron JP, Stewart B. Accessing molecular memoryvia a disulfide switch. NEW J CHEM 2009. [DOI: 10.1039/b814676d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Lin JC, Singh RRP, Cox DL. Theoretical study of DNA damage recognition via electron transfer from the [4Fe-4S] complex of MutY. Biophys J 2008; 95:3259-68. [PMID: 18599627 PMCID: PMC2547449 DOI: 10.1529/biophysj.108.132183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 06/11/2008] [Indexed: 11/18/2022] Open
Abstract
The mechanism of site-specific recognition of DNA by proteins has been a long-standing issue. The DNA glycosylase MutY, for instance, must find the rare 8-oxoguanine-adenine mismatches among the large number of basepairs in the DNA. This protein has a [4Fe-4S] cluster, which is highly conserved in species as diverse as Escherichia Coli and Homo sapiens. The mixed-valent nature of this cluster suggests that charge transfer may play a role in MutY's function. We have studied the energetics of the charge transfer in Bacillus stearothermophilus MutY-DNA complex using multiscale calculation including density functional theory and molecular dynamics. The [4Fe-4S] cluster in MutY is found to undergo 2+ to 3+ oxidation when coupling to DNA through hole transfer, especially when MutY is near an oxoguanine modified base (oxoG). Employing the Marcus theory for electron transfer, we find near optimal Frank-Condon factors for electron transfer from MutY to oxoguanine modified base. MutY has modest selectivity for oxoguanine over guanine due to the difference in oxidation potential. The tunneling matrix element is significantly reduced with the mutation R149W, whereas the mutation L154F reduces the tunneling matrix element as well as the Frank-Condon factor. Both L154F and R149W mutations are known to dramatically reduce or eliminate repair efficiency. We suggest a scenario where the charge transfer leads to a stabilization of the specific binding conformation, which is likely the recognition mode, thus enabling it to find the damaged site efficiently.
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Affiliation(s)
- Jong-Chin Lin
- Department of Physics, University of California, Davis, California 95616, USA
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41
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Guan W, Yang G, Liu C, Song P, Fang L, Yan L, Su Z. Reversible Redox-Switchable Second-Order Optical Nonlinearity in Polyoxometalate: A Quantum Chemical Study of [PW11O39(ReN)]n− (n = 3−7). Inorg Chem 2008; 47:5245-52. [DOI: 10.1021/ic8001527] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Wei Guan
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Guochun Yang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Chunguang Liu
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Ping Song
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Liang Fang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Likai Yan
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Zhongmin Su
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
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42
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Zhao P, Xu LC, Huang JW, Zheng KC, Liu J, Yu HC, Ji LN. DNA binding and photocleavage properties of a novel cationic porphyrin-anthraquinone hybrid. Biophys Chem 2008; 134:72-83. [DOI: 10.1016/j.bpc.2008.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 01/19/2008] [Accepted: 01/19/2008] [Indexed: 10/22/2022]
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43
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Xu LC, Shi S, Li J, Liao SY, Zheng KC, Ji LN. A combined computational and experimental study on DNA-photocleavage of Ru(ii) polypyridyl complexes [Ru(bpy)2(L)]2+ (L = pip, o-mopip and p-mopip). Dalton Trans 2008:291-301. [DOI: 10.1039/b710546k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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44
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45
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Alcolea Palafox M, Tardajos G, Guerrero-Martínez A, Rastogi V, Mishra D, Ojha S, Kiefer W. FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.07.032] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Moens J, Geerlings P, Roos G. A Conceptual DFT Approach for the Evaluation and Interpretation of Redox Potentials. Chemistry 2007; 13:8174-84. [PMID: 17506046 DOI: 10.1002/chem.200601896] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Conceptual DFT aims at describing the properties of molecules in interactions by using chemical reactivity descriptors. Herein, the redox behaviour of a given species, as quantified by the redox potential, is linked to DFT-based descriptors. We made use of a hierarchical decomposition of the corresponding half-reactions into one-electron reduction, protonation, dissociation and water-forming or dissociation reactions. Most of these reactions can be readily described through reactivity descriptors, such as the electrophilicity, nucleofugality and electrofugality, as defined in conceptual DFT. The final expression linking the corresponding free energy changes to the redox potential seems to give correct predictions for the redox potentials of bromo, chloro and nitro oxo acids in the gas phase, as in a polarised continuum model.
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Affiliation(s)
- Jan Moens
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
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47
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48
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Fu Y, Liu L, Wang YM, Li JN, Yu TQ, Guo QX. Quantum-chemical predictions of redox potentials of organic anions in dimethyl sulfoxide and reevaluation of bond dissociation enthalpies measured by the electrochemical methods. J Phys Chem A 2007; 110:5874-86. [PMID: 16640384 DOI: 10.1021/jp055682x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A first-principle theoretical protocol was developed that could predict the absolute pK(a) values of over 250 structurally unrelated compounds in DMSO with a precision of 1.4 pK(a) units. On this basis we developed the first theoretical protocol that could predict the standard redox potentials of over 250 structurally unrelated organic anions in DMSO with a precision of 0.11 V. Using the two new protocols we systematically reevaluated the bond dissociation enthalpies (BDEs) measured previously by the electrochemical methods. It was confirmed that for most compounds the empirical equation (BDE = 1.37 pK(HA) + 23.1E(o) + constant) was valid. The constant in this equation was determined to be 74.0 kcal/mol, compared to 73.3 kcal/mol previously reported. Nevertheless, for a few compounds the empirical equation could not be used because the solvation energy changed dramatically during the bond cleavage, which resulted from the extraordinary change of dipole moment during the reaction. In addition, we found 40 compounds (mostly oximes and amides) for which the experimental values were questionable by over 5 kcal/mol. Further analyses revealed that all these questionable BDEs could be explained by one of the three following reasons: (1) the experimental pK(a) value is questionable; (2) the experimental redox potential is questionable; (3) the solvent effect cannot be neglected. Thus, by developing practical theoretical methods and utilizing them to solve realistic problems, we hope to demonstrate that ab initio theoretical methods can now be developed to make not only reliable, but also useful, predictions for solution-phase organic chemistry.
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Affiliation(s)
- Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei.
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von Sonntag C. Free-Radical-Induced DNA Damage as Approached by Quantum-Mechanical and Monte Carlo Calculations: An Overview from the Standpoint of an Experimentalist. ADVANCES IN QUANTUM CHEMISTRY 2007. [DOI: 10.1016/s0065-3276(06)52002-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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