1
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Paz MM, Champeil E. Insight Into Factors Governing Formation, Synthesis and Stereochemical Configuration of DNA Adducts Formed by Mitomycins. CHEM REC 2023; 23:e202200193. [PMID: 36251922 DOI: 10.1002/tcr.202200193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/19/2022] [Indexed: 01/24/2023]
Abstract
Mitomycin C, (MC), an antitumor drug used in the clinics, is a DNA alkylating agent. Inert in its native form, MC is reduced to reactive mitosenes in cellulo which undergo nucleophilic attack by DNA bases to form monoadducts as well as interstrand crosslinks (ICLs). These properties constitute the molecular basis for the cytotoxic effects of the drug. The mechanism of DNA alkylation by mitomycins has been studied for the past 30 years and, until recently, the consensus was that drugs of the mitomycins family mainly target CpG sequences in DNA. However, that paradigm was recently challenged. Here, we relate the latest research on both MC and dicarbamoylmitomycin C (DMC), a synthetic derivative of MC which has been used to investigate the regioselectivity of mitomycins DNA alkylation as well as the relationship between mitomycins reductive activation pathways and DNA adducts stereochemical configuration. We also review the different synthetic routes to access mitomycins nucleoside adducts and oligonucleotides containing MC/DMC DNA adducts located at a single position. Finally, we briefly describe the DNA structural modifications induced by MC and DMC adducts and how site specifically modified oligonucleotides have been used to elucidate the role each adduct plays in the drugs cytotoxicity.
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Affiliation(s)
- Manuel M Paz
- Instituto de Materiais (iMATUS), Departamento de Química Orgánica, Facultad de Química, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
| | - Elise Champeil
- Department of sciences, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
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2
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Zacarias O, Petrovic AG, Abzalimov R, Pradhan P, Champeil E. Synthesis of Oligonucleotides Containing Trans Mitomycin C DNA Adducts at N 6 of Adenine and N 2 of Guanine. Chemistry 2021; 27:14263-14272. [PMID: 34319608 PMCID: PMC8516704 DOI: 10.1002/chem.202102338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 11/09/2022]
Abstract
Mitomycin C, (MC), an antitumor drug, is a DNA alkylating agent currently used in the clinics. Inert in its native form, MC is reduced to reactive mitosenes, which undergo nucleophilic attack by guanine or adenine bases in DNA to form monoadducts as well as interstrand crosslinks (ICLs). Although ICLs are considered the most cytotoxic lesions, the role of each individual adduct in the drug's cytotoxicity is still not fully understood. Synthetic routes have been developed to access modified oligonucleotides containing dG MC-monoadducts and dG-MC-dG ICL at a single position of their base sequences to investigate the biological effects of these adducts. However, until now, oligonucleotides containing monoadducts formed by MC at the adenine base had not been available, thus preventing the examination of the role played by these lesions in the toxicity of MC. Here, we present a route to access these substrates. Structural proof of the adducted oligonucleotides were provided by enzymatic digestion to nucleosides and high-resolution mass spectral analysis. Additionally, parent oligonucleotides containing a dG monoadduct and a dG-MC-dG ICL were also produced. The stability and physical properties of all substrates were compared via CD spectroscopy and UV melting temperature studies. Finally, virtual models were created to explore the conformational space and structural features of these MC-DNA complexes.
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Affiliation(s)
- Owen Zacarias
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Ana G Petrovic
- New York Institute of Technology, 1855 Broadway, EGGC 405 A, New York, NY, 10023, USA
| | - Rinat Abzalimov
- City University of New York, Advanced Research Center, 85 St Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Padmanava Pradhan
- The City College, 138th Street at Convent Avenue, New York, New York, 10031, USA
| | - Elise Champeil
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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3
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Qiu ZM, Zhang XP. THE RELATIVE STABILITY OF PROTONATED
BASE PAIRS BETWEEN XANTHINE AND DNA BASES. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Aguilar W, Zacarias O, Romaine M, Proni G, Petrovic AG, Abzalimov R, Paz MM, Champeil E. Synthesis of Oligonucleotides containing the cis-Interstrand Crosslink Produced by Mitomycins in their Reaction with DNA. Chemistry 2020; 26:12570-12578. [PMID: 32574396 PMCID: PMC7681910 DOI: 10.1002/chem.202002452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 01/25/2023]
Abstract
Mitomycin C (MC) an antitumor drug and decarbamoylmitomycin C (DMC), a derivative of MC lacking the carbamoyl moiety, are DNA alkylating agents which can form DNA interstrand crosslinks (ICLs) between deoxyguanosine residues located on opposing DNA strands. MC forms primarily deoxyguanosine adducts with a 1"-R stereochemistry at the guanine-mitosene bond (1"-α, trans) whereas DMC forms mainly adducts with a 1"-S stereochemistry (1"-β, cis). The crosslinking reaction is diastereospecific: trans-crosslinks are formed exclusively at CpG sequences, while cis-crosslinks are formed only at GpC sequences. Until now, oligonucleotides containing 1"-β-deoxyguanosine adducts or ICL at a specific site could not be synthesized, thus limiting the investigation of the role played by the stereochemical configuration at C1'' in the toxicity of these compounds. Here, a novel biomimetic synthesis to access these substrates is presented. Structural proof of the adducted oligonucleotides and ICL were provided by enzymatic digestion to nucleosides, high resolution mass spectral analysis, CD spectroscopy and UV melting temperature studies. Finally, a virtual model of the 25-mer 1"-β ICL synthesized was created to explore the conformational space and structural features of the crosslinked duplex.
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Affiliation(s)
- William Aguilar
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Owen Zacarias
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Marian Romaine
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Gloria Proni
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
| | - Ana G Petrovic
- New York Institute of Technology, 1855 Broadway, EGGC 405A, New York, NY, 10023, USA
| | - Rinat Abzalimov
- City University of New York, Advanced Research Center, 85 St Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Manuel M Paz
- Departamento de Química Orgánica, Facultad de Química, Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, 15782, Spain
| | - Elise Champeil
- Science Department, John Jay College of Criminal Justice, 524 West 59th street, New York, NY, 10019, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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5
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Niknam E, Moaddeli A, Khalafi-Nezhad A. Palladium anchored on guanidine-terminated magnetic dendrimer (G3-Gu-Pd): An efficient nano-sized catalyst for phosphorous-free Mizoroki-Heck and copper-free Sonogashira couplings in water. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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6
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Theoretical study of hydrogen bonds and electronic properties in hexagonal arrangements composed of self-assembled DNA analogues. Struct Chem 2020. [DOI: 10.1007/s11224-020-01545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Sun Y, Moe MM, Liu J. Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues. Phys Chem Chem Phys 2020; 22:24986-25000. [DOI: 10.1039/d0cp04243a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Non-statistical dissociation of a protonated guanine–cytosine Watson–Crick base pair.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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8
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Khalili B. Structural and energetic quantum chemical investigations into how the bioactive thiazolidinedione and rhodanine scaffolds interact with cytosine to form part of DNA. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Khalili B. A quantum chemical insight to intermolecular hydrogen bonding interaction between cytosine and nitrosamine: Structural and energetic investigations. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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10
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Cerón-Carrasco JP, Requena A, Zúñiga J, Jacquemin D. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair. Front Chem 2015; 3:13. [PMID: 25798437 PMCID: PMC4351615 DOI: 10.3389/fchem.2015.00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/16/2015] [Indexed: 12/04/2022] Open
Abstract
We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.
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Affiliation(s)
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR Centre National de la Recherche Scientifique, Université de Nantes Nantes, France ; Institut Universitaire de France Paris, France
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11
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Ming X, Matter B, Song M, Veliath E, Shanley R, Jones R, Tretyakova N. Mapping structurally defined guanine oxidation products along DNA duplexes: influence of local sequence context and endogenous cytosine methylation. J Am Chem Soc 2014; 136:4223-35. [PMID: 24571128 PMCID: PMC3985951 DOI: 10.1021/ja411636j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Indexed: 02/07/2023]
Abstract
DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated (Me)CG dinucleotides and at 5' Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of (Me)CG sequences may be caused by a lowered ionization potential of guanine bases paired with (Me)C and the preferential intercalation of riboflavin photosensitizer adjacent to (Me)C:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational "hotspots" at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer.
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Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brock Matter
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew Song
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elizabeth Veliath
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ryan Shanley
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Roger Jones
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Bass PD, Gubler DA, Judd TC, Williams RM. Mitomycinoid alkaloids: mechanism of action, biosynthesis, total syntheses, and synthetic approaches. Chem Rev 2013; 113:6816-63. [PMID: 23654296 PMCID: PMC3864988 DOI: 10.1021/cr3001059] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Phillip D Bass
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
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13
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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14
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Hume PA, Brimble MA, Reynisson J. DNA adduct formation of mitomycin C. A test case for DFT calculations on model systems. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Xiao S, Wang L, Liu Y, Lin X, Liang H. Theoretical investigation of the proton transfer mechanism in guanine-cytosine and adenine-thymine base pairs. J Chem Phys 2012. [DOI: 10.1063/1.4766319] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Bueren-Calabuig JA, Negri A, Morreale A, Gago F. Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity. Org Biomol Chem 2012; 10:1543-52. [PMID: 22222915 DOI: 10.1039/c1ob06675g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mitomycin C (MMC) is a potent antitumour agent that forms a covalent bond with the 2-amino group of selected guanines in the minor groove of double-stranded DNA following intracellular reduction of its quinone ring and opening of its aziridine moiety. At some 5'-CG-3' (CpG) steps the resulting monofunctional adduct can evolve towards a more deleterious bifunctional lesion, which is known as an interstrand crosslink (ICL). MMC reactivity is enhanced when the cytosine bases are methylated (5 MC) and decreased when they are replaced with 5-F-cytosine (5FC) whereas the stereochemical preference of alkylation changes upon decarbamoylation. We have studied three duplex oligonucleotides of general formula d(CGATAAXGCTAACG) in which X stands for C, 5MC or 5FC. Using a combination of molecular dynamics simulations in aqueous solution, quantum mechanics and continuum electrostatics, we have been able to (i) obtain a large series of snapshots that facilitate an understanding in atomic detail of the distinct stereochemistry of monoadduct and ICL formation by MMC and its decarbamoylated analogue, (ii) provide an explanation for the altered reactivity of MMC towards DNA molecules containing 5MC or 5FC, and (iii) show the distinct accommodation in the DNA minor groove of the different covalent modifications, particularly the most cytotoxic C1α and C1β ICLs.
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Affiliation(s)
- Juan A Bueren-Calabuig
- Departamento de Farmacología, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
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19
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Cerón-Carrasco JP, Jacquemin D, Cauët E. Cisplatin cytotoxicity: a theoretical study of induced mutations. Phys Chem Chem Phys 2012; 14:12457-64. [DOI: 10.1039/c2cp40515f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Paz MM, Pritsos CA. The Molecular Toxicology of Mitomycin C. ADVANCES IN MOLECULAR TOXICOLOGY VOLUME 6 2012. [DOI: 10.1016/b978-0-444-59389-4.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Cerón-Carrasco JP, Jacquemin D. Interplay between hydroxyl radical attack and H-bond stability in guanine–cytosine. RSC Adv 2012. [DOI: 10.1039/c2ra22389a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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22
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Cerón-Carrasco JP, Jacquemin D. Influence of Mg2+ on the Guanine-Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer. Chemphyschem 2011; 12:2615-23. [DOI: 10.1002/cphc.201100264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/28/2011] [Indexed: 01/01/2023]
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23
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Guza R, Kotandeniya D, Murphy K, Dissanayake T, Lin C, Giambasu GM, Lad RR, Wojciechowski F, Amin S, Sturla SJ, Hudson RH, York DM, Jankowiak R, Jones R, Tretyakova NY. Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA. Nucleic Acids Res 2011; 39:3988-4006. [PMID: 21245046 PMCID: PMC3089471 DOI: 10.1093/nar/gkq1341] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023] Open
Abstract
Endogenous 5-methylcytosine ((Me)C) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational 'hotspots' for smoking induced lung cancer. (Me)C enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5'-CCCGGCACCC GC[(15)N(3),(13)C(1)-G]TCCGCG-3', + strand) were prepared containing [(15)N(3), (13)C(1)]-guanine opposite unsubstituted cytosine, (Me)C, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2'-deoxynucleosides, N(2)-BPDE-dG adducts formed at the [(15)N(3), (13)C(1)]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N(2)-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N(2) position of guanine.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- Base Pairing
- Chromatography, High Pressure Liquid
- Cytosine/analogs & derivatives
- DNA Adducts/chemistry
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Genes, p53
- Guanine/chemistry
- Isotope Labeling
- Models, Molecular
- Oligodeoxyribonucleotides/chemical synthesis
- Oligodeoxyribonucleotides/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Rebecca Guza
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Thakshila Dissanayake
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chen Lin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - George Madalin Giambasu
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Rahul R. Lad
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Filip Wojciechowski
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shantu Amin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shana J. Sturla
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Robert H.E. Hudson
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ryszard Jankowiak
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Roger Jones
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Cerón-Carrasco JP, Zúñiga J, Requena A, Perpète EA, Michaux C, Jacquemin D. Combined effect of stacking and solvation on the spontaneous mutation in DNA. Phys Chem Chem Phys 2011; 13:14584-9. [DOI: 10.1039/c1cp20946a] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Acosta-Silva C, Branchadell V, Bertran J, Oliva A. Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers. J Phys Chem B 2010; 114:10217-27. [PMID: 20684646 DOI: 10.1021/jp103850h] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain
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26
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Jiang YL, Patel P, Klein SM. A fluorescein-containing, small-molecule, water-soluble receptor for cytosine free bases. Bioorg Med Chem 2010; 18:7034-42. [PMID: 20801661 DOI: 10.1016/j.bmc.2010.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/02/2010] [Accepted: 08/04/2010] [Indexed: 11/15/2022]
Abstract
In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using (15)N NMR spectroscopy and partially labeled cytosine-2,4-(13)C-1,3,4-(15)N-cytosine. Binding with the receptor 6a (the disodium form of 6) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.
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Affiliation(s)
- Yu Lin Jiang
- Department of Chemistry, College of Arts and Sciences, East Tennessee State University, Johnson City, TN 37614, United States.
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27
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Villani G. Theoretical Investigation of Hydrogen Atom Transfer in the Cytosine-Guanine Base Pair and Its Coupling with Electronic Rearrangement. Concerted vs Stepwise Mechanism. J Phys Chem B 2010; 114:9653-62. [DOI: 10.1021/jp102457s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Giovanni Villani
- Istituto per i Processi Chimico-Fisici, IPCF-CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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28
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Roy RK, Saha S. Studies of regioselectivity of large molecular systems using DFT based reactivity descriptors. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b811052m] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Rationalizing the Strength of Hydrogen-Bonding of Molybdate-Phosphonic Acid Complex: Density Functional Theory Studies. REV INORG CHEM 2009. [DOI: 10.1515/revic.2009.29.3.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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30
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Moser A, Guza R, Tretyakova N, York DM. Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine. Theor Chem Acc 2009; 122:179-188. [PMID: 19890472 PMCID: PMC2771868 DOI: 10.1007/s00214-008-0497-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The present study employs density-functional electronic structure methods to investigate the effect of chemical modification at the C5 position of cytosine. A series of experimentally motivated chemical modifications are considered, including alkyl, halogen, aromatic, fused ring, and strong σ and π withdrawing functional groups. The effect of these modifications on cytosine geometry, electronic structure, proton affinities, gas phase basicities, cytosine-guanine base-pair hydrogen bond network and corresponding nucleophilicity at guanine are examined. Ultimately, these results play a part in dissecting the effect of endogenous cytosine methylation on the reactivity of neighboring guanine toward carcinogens and DNA alkylating agents.
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Affiliation(s)
- Adam Moser
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455–0431, USA
| | - Rebecca Guza
- Department of Medicinal Chemistry and the Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darrin M. York
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455–0431, USA. E-mail:
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31
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Zhang AG, Qin M, Zhou ZY, Jia ZK, Hou RY. A density functional theory study of interaction between formamide and guanine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2008. [DOI: 10.1134/s0036024408070169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Han SY, Lee SH, Chung J, Oh HB. Base-pair interactions in the gas-phase proton-bonded complexes of C+G and C+GC. J Chem Phys 2007; 127:245102. [DOI: 10.1063/1.2817604] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Saha S, Roy RK. “One-into-Many” Model: An Approach on DFT Based Reactivity Descriptor to Predict the Regioselectivity of Large Systems. J Phys Chem B 2007; 111:9664-74. [PMID: 17658783 DOI: 10.1021/jp070417s] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present work consists of the development of a new model (named "one-into-many") to predict the regioselectivity of large chemical and biological systems. Large chemical and biological systems with multiple reactive sites are proposed to be broken into small fragments having at least one reactive site in each fragment. The environment around each reactive site is mimicked by incorporating a buffer zone. Local reactivity descriptor (i.e., local hardness), originally proposed by Berkowitz et al. (J. Am.Chem. Soc. 1985, 107, 6811) and later implemented by Langenaeker et al. (J. Phys. Chem. 1995, 99, 6424), is evaluated for each reactive site adopting a new modified approach (i.e., without neglecting kinetic energy and exchange energy parts). When the model is applied to predict the regioselectivity (toward an electrophilic attack) of the base pairs in DNA (PDB ID: 1BNA) (Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 2179) the generated results are found to be satisfactory in most cases.
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Affiliation(s)
- Soumen Saha
- Department of Chemistry, Birla Institute of Technology and Science, Pilani-330 331, Rajasthan, India
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34
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Dong H, Hua W, Li S. Estimation on the individual hydrogen-bond strength in molecules with multiple hydrogen bonds. J Phys Chem A 2007; 111:2941-5. [PMID: 17388581 DOI: 10.1021/jp0709860] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A simple atom-replacement approach is proposed for estimating the individual contributions of each intermolecular hydrogen bond (HB) in multiple hydrogen-bonded systems. The approach is validated by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers. With the help of this method, it is easy to distinguish the relative strength of each HB, and identify the main factors contributing to the total binding energies of multiple HBs.
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Affiliation(s)
- Hao Dong
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Chemistry, Nanjing University, Nanjing, 210093, People's Republic of China
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The Structures and Proton Transfer Barriers in Proton-bound Homodimers of Aromatic Molecular Bases: Implication of Zero-point Energies for the Proton-transfer Reaction. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.11.1903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Carcinogenicity of benzo[a]pyrene diol epoxide stereoisomers: A linear free energy relationship study. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Ziegel R, Shallop A, Upadhyaya P, Jones R, Tretyakova N. Endogenous 5-methylcytosine protects neighboring guanines from N7 and O6-methylation and O6-pyridyloxobutylation by the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Biochemistry 2004; 43:540-9. [PMID: 14717610 DOI: 10.1021/bi035259j] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All CG dinucleotides along exons 5-8 of the p53 tumor suppressor gene contain endogenous 5-methylcytosine (MeC). These same sites (e.g., codons 157, 158, 245, 248, and 273) are mutational hot spots in smoking-induced lung cancer. Several groups used the UvrABC endonuclease incision assay to demonstrate that methylated CG dinucleotides of the p53 gene are the preferred binding sites for the diol epoxides of bay region polycyclic aromatic hydrocarbons (PAH). In contrast, effects of endogenous cytosine methylation on the distribution of DNA lesions induced by tobacco-specific nitrosamines, e.g., 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), have not been elucidated. In the work presented here, a stable isotope labeling HPLC-ESI-MS/MS approach was employed to analyze the reactivity of the N7 and O6 positions of guanines within hemimethylated and fully methylated CG dinucleotides toward NNK-derived methylating and pyridyloxobutylating species. 15N3-labeled guanine bases were placed within synthetic DNA sequences representing endogenously methylated p53 codons 154, 157, and 248, followed by treatment with acetylated precursors to NNK diazohydroxides. HPLC-ESI-MS/MS analysis was used to determine the relative yields of N7- and O6-guanine adducts at the 15N3-labeled position. In all cases, the presence of MeC inhibited the formation of N7-methylguanine, O6-methylguanine, and O6-pyridyloxobutylguanine at a neighboring G, with the greatest decrease observed in fully methylated dinucleotides and at guanines preceded by MeC. Furthermore, the O6-Me-dG/N7-Me-G molar ratios were decreased in the presence of the 5'-neighboring MeC, suggesting that the observed decline in O6-alkylguanine adduct yields is, at least partially, a result of an altered reactivity pattern in methylated CG dinucleotides. These results indicate that, unlike N2-guanine adducts of PAH diol epoxides, NNK-induced N7- and O6-alkylguanine adducts are not preferentially formed at the endogenously methylated CG sites within the p53 tumor suppressor gene.
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Affiliation(s)
- Rebecca Ziegel
- Department of Medicinal Chemistry, University of Minnesota School of Pharmacy, Minneapolis, Minnesota 55455, USA
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39
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Freccero M, Gandolfi R, Sarzi-Amadè M. Selectivity of purine alkylation by a quinone methide. Kinetic or thermodynamic control? J Org Chem 2003; 68:6411-23. [PMID: 12895079 DOI: 10.1021/jo0346252] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alkylation reaction of 9-methyladenine and 9-methylguanine (as prototype substrates of deoxy-adenosine and -guanosine), by the parent o-quinone methide (o-QM), has been investigated in the gas phase and in aqueous solution, using density functional theory at the B3LYP/6-311+G(d,p) level. The effect of the medium on the reactivity, and on the stability of the resulting adducts, has been investigated by using the C-PCM solvation model to assess which adduct arises from the kinetically favorable path, or from an equilibrating process. The calculations indicate that the most nucleophilic site of the methyl-substituted nucleobases in the gas phase is the guanine oxygen atom (O(6)) (DeltaG()(gas) = 5.6 kcal mol(-)(1)), followed by the adenine N1 (DeltaG)(gas) = 10.3 kcal mol(-)(1)), while other centers exhibit a substantially lower nucleophilicity. The bulk effect of water as a solvent is the dramatic reduction of the nucleophilicity of both 9-methyladenine N1 (DeltaG)(solv) = 14.5 kcal mol(-)(1)) and 9-methylguanine O(6) (DeltaG)(solv) = 17.0 kcal mol(-)(1)). As a result there is a reversal of the nucleophilicity order of the purine bases. While O(6) and N7 nucleophilic centers of 9-methylguanine compete almost on the same footing, the reactivity gap between N1 and N7 of 9-methyladenine in solution is highly reduced. Regarding product stability, calculations predict that only two of the adducts of o-QM with 9-methyladenine, those at NH(2) and N1 positions, are lower in energy than reactants, both in the gas phase and in water. However, the adduct at N1 can easily dissociate in water. The adducts arising from the covalent modification of 9-methylguanine are largely more stable than reactants in the gas phase, but their stability is markedly reduced in water. In particular, the oxygen alkylation adduct becomes slightly unstable in water (DeltaG(solv) = +1.4 kcal mol(-)(1)), and the N7 alkylation product remains only moderately more stable than free reactants (DeltaG(solv) = -2.8 kcal mol(-)(1)). Our data show that site alkylations at the adenine N1 and the guanine O(6) and N7 in water are the result of kinetically controlled processes and that the selective modification of the exo-amino groups of guanine N2 and adenine N6 are generated by thermodynamic equilibrations. The ability of o-QM to form several metastable adducts with purine nucleobases (at guanine N7 and O(2), and adenine N1) in water suggests that the above adducts may act as o-QM carriers.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, Viale Taramelli 10, 27100 Pavia, Italy.
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40
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Asensio A, Kobko N, Dannenberg JJ. Cooperative Hydrogen-Bonding in Adenine−Thymine and Guanine−Cytosine Base Pairs. Density Functional Theory and Møller−Plesset Molecular Orbital Study. J Phys Chem A 2003. [DOI: 10.1021/jp0344646] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amparo Asensio
- Department of Chemistry, City University of New York−Hunter College and The Graduate School, 695 Park Avenue, New York, New York 10021
| | - Nadya Kobko
- Department of Chemistry, City University of New York−Hunter College and The Graduate School, 695 Park Avenue, New York, New York 10021
| | - J. J. Dannenberg
- Department of Chemistry, City University of New York−Hunter College and The Graduate School, 695 Park Avenue, New York, New York 10021
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Freccero M, Di Valentin C, Sarzi-Amadè M. Modeling H-bonding and solvent effects in the alkylation of pyrimidine bases by a prototype quinone methide: a DFT study. J Am Chem Soc 2003; 125:3544-53. [PMID: 12643716 DOI: 10.1021/ja028732+] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilicity of NH(2), N3, and O(2) centers of cytosine toward a model quinone methide (o-QM) as alkylating agent has been studied using DFT computational analysis [at the B3LYP/6-311+G(d,p) level]. Specific and bulk effects of water (by C-PCM model) on the alkylation pathways have been evaluated by analyzing both unassisted and water-assisted reaction mechanisms. An ancillary water molecule, H-bonded to the alkylating agent, may interact monofunctionally with the o-QM oxygen atom (passive mechanisms) or may participate bifunctionally in cyclic hydrogen-bonded structures as a proton shuttle (active mechanisms). A comparison of the unassisted with the water-assisted reaction mechanisms has been made on the basis of activation Gibbs free energies (DeltaG(++)). The gas-phase alkylation reaction at N3 does proceed through a passive mechanism that is preferred over both the active (by -6.3 kcal mol(-1)) and the unassisted process. In contrast, in the gas phase, the active assisted processes at NH(2) and O(2) centers are both favored over their unassisted counterparts by -4.0 and -2.2 kcal mol(-1), respectively. The catalytic effect of a water molecule, in gas phase, reduces the gap between the TSs of the O(2) and NH(2) reaction pathways, but the former remains more stable. Water bulk effect significantly modifies the relative importance of the unassisted and water-assisted alkylation mechanisms, favoring the former, in comparison to the gas-phase reactions. In particular, the unassisted alkylation becomes the preferred mechanism for the reaction at both the exocyclic (NH(2)) and the heterocyclic (N3) nitrogen atoms. By contrast, alkylation at the cytosine oxygen atom is a water-catalyzed process, since in water the active water-assisted mechanism is still favored. As far as competition, among all the possible mechanisms, our calculations unambiguously suggest that the most nucleophilic site both in gas phase (naked reagents: N3 >> O(2) >or= NH(2)) and in water solution (solvated reagents: N3 >> NH(2) >> O(2)) is the heterocyclic nitrogen atom (N3) (DeltaG(++)(gas) = +7.1 kcal mol(-1), and DeltaG(++)(solv) = +13.7 kcal mol(-1)). Our investigation explains the high reactivity and selectivity of the cytosine moiety toward o-QM-like structures both in deoxymononucleoside and in a single-stranded DNA, on the basis of strong H-bonding interactions between reactants and solvent bulk effect. It also offers two general reactivity models in water, uncatalyzed and active water-catalyzed mechanisms (for nitrogen and oxygen nucleophiles, respectively), which should provide a general tool for the planning of nucleic acid modification.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia Italy.
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42
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Li X, Cai Z, Sevilla MD. Energetics of the Radical Ions of the AT and AU Base Pairs: A Density Functional Theory (DFT) Study. J Phys Chem A 2002. [DOI: 10.1021/jp021322n] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xifeng Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Zhongli Cai
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - M. D. Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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43
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Lukin O, Leszczynski J. Rationalizing the Strength of Hydrogen-Bonded Complexes. Ab Initio HF and DFT Studies. J Phys Chem A 2002. [DOI: 10.1021/jp0145154] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oleg Lukin
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
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Effect of hydrogen bonding on the photo-oxidation of DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2002. [DOI: 10.1016/s1389-5567(02)00005-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejskova 3, 182 23 Prague, Czech Republic.
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McClelland RA, Sanchez C, Sauer E, Vukovic S. Reaction of the tamoxifen cation and the bis-(4-methoxyphenyl)methyl cation in aqueous solutions containing 2'-deoxyguanosine. CAN J CHEM 2002. [DOI: 10.1139/v02-011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The competition between 2'-deoxyguanosine (dG) and water has been quantitatively evaluated for the allylic carbocation derived from tamoxifen and for the stabilized diarylmethyl cation (bis-(4-methoxyphenyl)methyl). Both systems were examined by the competition kinetics method, in which the products were quantitatively analyzed after the SN1 solvolysis of the corresponding acetate esters in aqueous solutions containing the nucleoside. The principal product of the reaction of both cations with dG is the adduct at the NH2 group, a characteristic of delocalized carbocations. The tamoxifen cation was also examined by laser flash photolysis, with absolute rate constants for the reaction with dG and water being obtained and converted into rate constant ratios. The principal result of this study is that there is a three orders of magnitude difference in the reactivity of these cations towards the neutral form of dG and its conjugate base. Under acidic conditions where the reaction occurs with neutral dG, the guaninewater selectivity is low. Even at relatively high concentrations of dG, the majority of the product is alcohol derived from the water reaction. At pH 10 to 11, in contrast, dG is present as the anion and this is highly competitive. Yields of adduct as high as 90% can be attained. A consequence of the large difference in reactivities is that at neutral pH the majority of the reaction of the cation with dG is actually occurring via the small amount of conjugate base present. A further feature of the results is that the NH2 adduct is the predominant stable product from the anion. To explain the high rate constant for the reaction forming this product, a mechanism is proposed whereby one of the protons of the NH2 group is transferred to N1 as the N2-cation bond is forming.Key words: guanine, DNA adduct, carbocation, tamoxifen.
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Li VS, Tang MS, Kohn H. The effect of C(5) cytosine methylation at CpG sequences on mitomycin-DNA bonding profiles. Bioorg Med Chem 2001; 9:863-73. [PMID: 11354669 DOI: 10.1016/s0968-0896(00)00301-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent studies have documented that cytosine C(5) methylation of CpG sequences enhances mitomycin C (1) adduction. The reports differ on the extent and uniformity of 1 modification at the nucleotide level. We have determined the bonding profiles for mitomycin monoalkylation in two DNA restriction fragments where the CpG sequences were methylated. Three mitomycin substrates were used and two different enzymatic assays employed to monitor the extent of drug modification at the individual base sites. Drug DNA modification was accomplished with I and 10-decarbamoylmitomycin C (2) under reductive (Na2S2O4) condilions and with N-methyl-7-methoxyaziridinomitosene (3) under nonreductive conditions. The UvrABC incision assay permitted us to quantitate the sites of drug adduction, and the lambda-exonuclease stop assay provided a qualitative estimation of drug-DNA modification consistent with the UvrABC data. We learned that C(5) cytosine methylation (m5C) enhanced the extent of overall DNA modification. Using the UvrABC endonuclease assay, we found that modification by 1 increased 2.0 and 7.4 times for the two DNA restriction fragments. Analysis of the modification sites at the nucleotide sequence level revealed that guanine (G) was the only base modified and that the overall increased level of DNA adduction was due to enhanced modification of select m5CpG* (G* = mitomycin (mitosene) adduction sites) loci compared with CpG* sites: the largest differences reached two orders of magnitude. Significantly, not all CpG* sites underwent increased drug adduction upon C(5) cytosine methylation. The effect of C(5) cytosine methylation on the drug adduction profiles was less pronounced for G* sites located within dinucleotide sequences other than CpG*. We observed that DNA methylation often led to slightly diminished adduction levels at these sites. The different m5CpG* adduction patterns provided distinctive sequence-selective bonding profiles for 1-3. We have attributed the large differences in guanine reactivity to DNA structural factors created, in part, by C(5) cytosine methylation. The significance of these findings in cancer chemotherapy is briefly discussed.
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Affiliation(s)
- V S Li
- Department of Chemistry, University of Houston, TX 77204-5641, USA
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Veldhuyzen WF, Lam YF, Rokita SE. 2'-Deoxyguanosine reacts with a model quinone methide at multiple sites. Chem Res Toxicol 2001; 14:1345-51. [PMID: 11559052 DOI: 10.1021/tx0101043] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quinone methides and related intermediates have been implicated in a range of beneficial and detrimental processes in biology and effectively alkylate a variety of cellular components despite the ubiquitous presence of water. As a prerequisite to understanding the origins of their specificity, the major products generated by DNA and its components with an unsubstituted ortho quinone methide under aqueous conditions were recently characterized [Pande, P., Shearer, J., Yang, J., Greenberg, W. A., and Rokita, S. E. (1999) J. Am. Chem. Soc. 121, 6773-6779]. Investigations currently focus on the complete range of derivatives formed by deoxyguanosine (dG) and guanine residues in duplex DNA through product isolation and structure determination using reversed-phase chromatography and a range of one and two-dimensional NMR techniques. Previous construction of a synthetic standard for dG alkylation is now shown to have yielded the N1-linked adduct rather than the N(2)-linked adduct. This later adduct has also now been characterized and confirmed to be the major product of reaction between the quinone methide and both duplex DNA and dG under neutral conditions. An N7 adduct of guanine has additionally been identified under these conditions and appears to result from spontaneous deglycosylation of the corresponding N7 adduct of dG. A combination of steric and electronic properties of duplex DNA likely contribute to the enhanced selectivity of the quinone methide for its guanine N(2) position (7.8:3.2:1.0 for adducts of N(2):N7:N1) relative to that of dG (4.7:3.5:1.0 for adducts of N(2):N7:N1).
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Affiliation(s)
- W F Veldhuyzen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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Teixidó J, Borrell JI, Colominas C, Deupí X, Matallana JL, Falcó JL, Martinez-Teipel B. Selective hydrolysis of 2,4-diaminopyrimidine systems: a theoretical and experimental insight into an old rule. J Org Chem 2001; 66:192-9. [PMID: 11429899 DOI: 10.1021/jo0056390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolysis of the amino groups in condensed 2,4-diaminopyrimidine systems (1) has been used as a common method for the synthesis of oxo-substituted pyrimidines. In particular, the treatment with 6 M HCl usually yields exclusively the 2-amino-4-oxopyrimidine isomer (2). During our work, we found that the hydrolysis of the amino groups present in some condensed 2,4-diaminopyrimidine systems unexpectedly afforded exclusively the 4-amino-2-oxopyrimidine isomer (3). In this paper, we present the experimental work and ab initio calculations carried out to understand this discrepancy. As a part of such study, eight compounds containing a 2,4-diaminopyrimidine moiety were calculated in gas phase and in aqueous solution, and some acid hydrolyses were reexamined. Results showed that the presence of an electron-donating nitrogen linked to C6 of the 2,4-diaminopyrimidine ring changes the preferred hydrolysis site to yield the 4-amino-2-oxopyrimidine isomer.
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Affiliation(s)
- J Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain.
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Rauhut G. Recent Advances in Computing Heteroatom-Rich Five- and Six-Membered Ring Systems. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)81010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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