1
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Hinz DJ, Krajewski AE, Lee JK. Carbon-Fluorine Activation in the Gas Phase: The Reactions of Benzyl C-F Bonds and Silyl Cations. J Org Chem 2024. [PMID: 39239936 DOI: 10.1021/acs.joc.4c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The activation of C-F bonds figures largely in both fundamental and applied chemical processes. Herein the activation of benzyl C-F bonds by silyl cations is examined both computationally and experimentally in the gas phase. The experimental rate constant values obtained herein have not heretofore been measured and provide insight into the intrinsic ability of silyl cations to activate C-F bonds. Trends in reactivity and correlations between theoretical and experimental data are discussed in the context of C-F bond cleavage.
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Affiliation(s)
- Damon J Hinz
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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2
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Zhang L, Ding X, Kratka CR, Levine A, Lee JK. Gas Phase Experimental and Computational Studies of AlkB Substrates: Intrinsic Properties and Biological Implications. J Org Chem 2023; 88:13115-13124. [PMID: 37651719 DOI: 10.1021/acs.joc.3c01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The gas phase acidity and proton affinity of nucleobases that are substrates for the DNA repair enzyme AlkB have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data that help benchmark the theoretical results. We also use our gas phase results to lend insight into the AlkB mechanism, particularly in terms of the role AlkB plays in DNA repair, versus its complementary enzyme AlkA.
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Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Xiao Ding
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Catherine R Kratka
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Alec Levine
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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3
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Zhang L, Kiruba GSM, Lee JK. Gas-Phase Studies of Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase (HG(X)PRT) Substrates. J Org Chem 2023. [PMID: 37220241 DOI: 10.1021/acs.joc.3c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The gas-phase acidity and proton affinity of nucleobases that are substrates for the enzyme Plasmodium falciparum hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (Pf HG(X)PRT) have been examined using both computational and experimental methods. These thermochemical values have not heretofore been measured and provide experimental data to benchmark the theoretical results. Pf HG(X)PRT is a target of interest in the development of antimalarials. We use our gas-phase results to lend insight into the Pf HG(X)PRT mechanism, and also propose kinetic isotope studies that could potentially differentiate between possible mechanisms.
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Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - G S M Kiruba
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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4
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Lotsof ER, Krajewski AE, Anderson-Steele B, Rogers J, Zhang L, Yeo J, Conlon SG, Manlove AH, Lee JK, David SS. NEIL1 Recoding due to RNA Editing Impacts Lesion-Specific Recognition and Excision. J Am Chem Soc 2022; 144:14578-14589. [PMID: 35917336 DOI: 10.1021/jacs.2c03625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A-to-I RNA editing is widespread in human cells but is uncommon in the coding regions of proteins outside the nervous system. An unusual target for recoding by the adenosine deaminase ADAR1 is the pre-mRNA of the base excision DNA repair enzyme NEIL1 that results in the conversion of a lysine (K) to arginine (R) within the lesion recognition loop and alters substrate specificity. Differences in base removal by unedited (UE, K242) vs edited (Ed, R242) NEIL1 were evaluated using a series of oxidatively modified DNA bases to provide insight into the chemical and structural features of the lesion base that impact isoform-specific repair. We find that UE NEIL1 exhibits higher activity than Ed NEIL1 toward the removal of oxidized pyrimidines, such as thymine glycol, uracil glycol, 5-hydroxyuracil, and 5-hydroxymethyluracil. Gas-phase calculations indicate that the relative rates in excision track with the more stable lactim tautomer and the proton affinity of N3 of the base lesion. These trends support the contribution of tautomerization and N3 protonation in NEIL1 excision catalysis of these pyrimidine base lesions. Structurally similar but distinct substrate lesions, 5-hydroxycytosine and guanidinohydantoin, are more efficiently removed by the Ed NEIL1 isoform, consistent with the inherent differences in tautomerization, proton affinities, and lability. We also observed biphasic kinetic profiles and lack of complete base removal with specific combinations of the lesion and NEIL1 isoform, suggestive of multiple lesion binding modes. The complexity of NEIL1 isoform activity implies multiple roles for NEIL1 in safeguarding accurate repair and as an epigenetic regulator.
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Affiliation(s)
- Elizabeth R Lotsof
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Brittany Anderson-Steele
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - JohnPatrick Rogers
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Jongchan Yeo
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Savannah G Conlon
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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5
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Hinz DJ, Zhang L, Lee JK. Mass spectrometry in organic and bio-organic catalysis: Using thermochemical properties to lend insight into mechanism. MASS SPECTROMETRY REVIEWS 2022. [PMID: 35899315 DOI: 10.1002/mas.21797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this review, we discuss gas phase experimentation centered on the measurement of acidity and proton affinity of substrates that are useful for understanding catalytic mechanisms. The review is divided into two parts. The first covers examples of organocatalysis, while the second focuses on biological catalysis. The utility of gas phase acidity and basicity values for lending insight into mechanisms of catalysis is highlighted.
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Affiliation(s)
- Damon J Hinz
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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6
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Zhang L, Hinz DJ, Kiruba GSM, Ding X, Lee JK. Gas‐phase experimental and computational studies of human hypoxanthine‐guanine phosphoribosyltransferase substrates: Intrinsic properties and biological implications. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | - Damon J. Hinz
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | | | - Xiao Ding
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
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7
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Krajewski AE, Lee JK. Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications. J Org Chem 2021; 86:6361-6370. [PMID: 33891415 DOI: 10.1021/acs.joc.1c00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase acidity and proton affinity (PA) of 5-halouracils (5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil) have been examined using both theoretical and experimental methods. This work represents a comprehensive study of the thermochemical properties of these nucleobases. Other than 5-fluorouracil acidity, the intrinsic acidity and PA of these halouracils have not been heretofore measured; these new experimental data provide a benchmark for the computational values. Furthermore, we examine these 5-halouracils in the context of the enzyme thymine DNA glycosylase (TDG), which is an enzyme that protects the genome by cleaving these substrates from DNA. Our gas-phase results are compared and contrasted to TDG excision rates to afford insights into the TDG mechanism.
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Affiliation(s)
- Allison E Krajewski
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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8
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Majumdar C, McKibbin PL, Krajewski AE, Manlove AH, Lee JK, David SS. Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY. J Am Chem Soc 2020; 142:20340-20350. [PMID: 33202125 DOI: 10.1021/jacs.0c06767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediatedadenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogues of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analogue substrates with their experimental and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogues that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogues paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analogue duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogues to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analogue SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.
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Affiliation(s)
- Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Paige L McKibbin
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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9
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Kaur R, Nikkel DJ, Wetmore SD. Computational studies of DNA repair: Insights into the function of monofunctional DNA glycosylases in the base excision repair pathway. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
| | - Dylan J. Nikkel
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge Alberta Canada
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10
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Wang N, Lee JK. Gas-Phase and Ionic Liquid Experimental and Computational Studies of Imidazole Acidity and Carbon Dioxide Capture. J Org Chem 2019; 84:14593-14601. [PMID: 31647232 DOI: 10.1021/acs.joc.9b02193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The capture and storage of carbon dioxide are pressing environmental concerns. Nucleophilic capture by anions in ionic liquids, such as imidazolates, is a promising strategy. Herein, the gas-phase acidity of a series of imidazoles is examined both experimentally and computationally. The intrinsic acidity of these imidazoles has not heretofore been measured; these experimental data provide a benchmark for the computational values. The relationship between imidazole acidity and carbon dioxide capture is explored computationally, both in the gas phase and in ionic liquid. The improved understanding of imidazolate properties provided herein is important for the design and development of improved systems for carbon dioxide capture.
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Affiliation(s)
- Ning Wang
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 United States
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11
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Xu J, Krajewski AE, Niu Y, Kiruba GSM, Lee JK. Kinetic hydricity of silane hydrides in the gas phase. Chem Sci 2019; 10:8002-8008. [PMID: 31853355 PMCID: PMC6837013 DOI: 10.1039/c9sc02118c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/09/2019] [Indexed: 12/01/2022] Open
Abstract
Herein, gas phase studies of the kinetic hydricity of a series of silane hydrides are described. An understanding of hydricity is important as hydride reactions figure largely in many processes, including organic synthesis, photoelectrocatalysis, and hydrogen activation. We find that hydricity trends in the gas phase differ from those in solution, revealing the effect of solvent. Calculations and further experiments, including H/D studies, were used to delve into the reactivity and structure of the reactants. These studies also represent a first step toward systematically understanding nucleophilicity and electrophilicity in the absence of solvent.
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Affiliation(s)
- Jiahui Xu
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Yijie Niu
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - G S M Kiruba
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
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12
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Xu J, Mieres-Perez J, Sanchez-Garcia E, Lee JK. Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements. J Org Chem 2019; 84:7685-7693. [PMID: 31008604 DOI: 10.1021/acs.joc.9b00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many fundamental properties of carbenes, particularly basicity, remain poorly understood. Herein, an experimental and computational examination of the deprotonation of a series of benzhydryl cations has been undertaken. These studies represent the first attempt at providing experimental values for diarylcarbene basicities. Pathways to deprotonation, including whether the singlet or triplet carbene is formed, are probed. Because diarylcarbenes are expected to be among the strongest organic bases known, assessing the energetics of protonation of these species is of fundamental importance for a wide range of chemical processes.
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Affiliation(s)
- Jiahui Xu
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology , University of Duisburg-Essen , D-45141 Essen , Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology , University of Duisburg-Essen , D-45141 Essen , Germany
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
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13
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Lenz SAP, Wetmore SD. QM/MM Study of the Reaction Catalyzed by Alkyladenine DNA Glycosylase: Examination of the Substrate Specificity of a DNA Repair Enzyme. J Phys Chem B 2017; 121:11096-11108. [PMID: 29148771 DOI: 10.1021/acs.jpcb.7b09646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a nonspecific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a nonsubstrate (G), or a cationic substrate (7-methylguanine (7MeG)) and probe changes in the reaction pathway that occur when AAG targets different nucleotides. We reveal that subtle differences in protein-DNA contacts upon binding different substrates within the flexible AAG active site can significantly affect the deglycosylation reaction. Notably, we predict that AAG excises Hx in a concerted mechanism that is facilitated through correct alignment of the (E125) general base due to hydrogen bonding with a neighboring aromatic amino acid (Y127). Hx departure is further stabilized by π-π interactions with aromatic amino acids and hydrogen bonds with active site water. Despite possessing a similar structure to Hx, G is not excised since the additional exocyclic amino group leads to misalignment of the general base due to disruption of the key E125-Y127 hydrogen bond, the catalytically unfavorable placement of water within the active site, and weakened π-contacts between aromatic amino acids and the nucleobase. In contrast, cationic 7MeG does not occupy the same position within the AAG active site as G due to steric clashes with the additional N7 methyl group, which results in the correct alignment of the general base and permits nucleobase excision as observed for neutral Hx. Overall, our structural data rationalizes the observed substrate specificity of AAG and contributes to our fundamental understanding of enzymes with flexible active sites and broad substrate specificities.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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14
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Niu Y, Wang N, Muñoz A, Xu J, Zeng H, Rovis T, Lee JK. Experimental and Computational Gas Phase Acidities of Conjugate Acids of Triazolylidene Carbenes: Rationalizing Subtle Electronic Effects. J Am Chem Soc 2017; 139:14917-14930. [PMID: 29039669 DOI: 10.1021/jacs.7b05229] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, triazolylidene carbenes have come to the forefront as important organocatalysts for a wide range of reactions. The fundamental properties of these species, however, remain largely unknown. Herein, the gas phase acidities have been measured and calculated for a series of triazolium cations (the conjugate acids of the triazolylidene carbenes) that have not been heretofore examined in vacuo. The results are discussed in the context of these species as catalysts. We find correlations between the gas phase acidity and selectivity in two Umpolung reactions catalyzed by these species; such correlations are the first of their kind. We are able to use these linear correlations to improve reaction enantioselectivity. These results establish the possibility of using these thermochemical properties to predict reactivity in related transformations.
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Affiliation(s)
- Yijie Niu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , New Brunswick, New Jersey 08901, United States
| | - Ning Wang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , New Brunswick, New Jersey 08901, United States
| | - Alberto Muñoz
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Jiahui Xu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , New Brunswick, New Jersey 08901, United States
| | - Hao Zeng
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , New Brunswick, New Jersey 08901, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , New Brunswick, New Jersey 08901, United States
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15
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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16
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Wincel H. Microhydration of Deprotonated Nucleobases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1383-92. [PMID: 27178262 PMCID: PMC4942500 DOI: 10.1007/s13361-016-1411-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
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17
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Kiruba GSM, Xu J, Zelikson V, Lee JK. Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates. Chemistry 2016; 22:3881-90. [DOI: 10.1002/chem.201505003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/08/2022]
Affiliation(s)
- G. S. M. Kiruba
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Jiahui Xu
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Victoria Zelikson
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
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18
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Lenz SAP, Wetmore SD. Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization. Biochemistry 2016; 55:798-808. [PMID: 26765542 DOI: 10.1021/acs.biochem.5b01179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair (BER) pathway by cleaving the N-glycosidic bond that connects nucleobases to the sugar-phosphate backbone in DNA. AAG targets a range of structurally diverse purine lesions using nonspecific DNA-protein π-π interactions. Nevertheless, the enzyme discriminates against the natural purines and is inhibited by pyrimidine lesions. This study uses molecular dynamics simulations and seven different neutral or charged substrates, inhibitors, or canonical purines to probe how the bound nucleotide affects the conformation of the AAG active site, and the role of active site residues in dictating substrate selectivity. The neutral substrates form a common DNA-protein hydrogen bond, which results in a consistent active site conformation that maximizes π-π interactions between the aromatic residues and the nucleobase required for catalysis. Nevertheless, subtle differences in DNA-enzyme contacts for different neutral substrates explain observed differential catalytic efficiencies. In contrast, the exocyclic amino groups of the natural purines clash with active site residues, which leads to catalytically incompetent DNA-enzyme complexes due to significant reorganization of active site water. Specifically, water resides between the A nucleobase and the active site aromatic amino acids required for catalysis, while a shift in the position of the general base (E125) repositions (potentially nucleophilic) water away from G. Despite sharing common amino groups, the methyl substituents in cationic purine lesions (3MeA and 7MeG) exhibit repulsion with active site residues, which repositions the damaged bases in the active site in a manner that promotes their excision. Overall, we provide a structural explanation for the diverse yet discriminatory substrate selectivity of AAG and rationalize key kinetic data available for the enzyme. Specifically, our results highlight the complex interplay of many different DNA-protein interactions used by AAG to facilitate BER, as well as the crucial role of the general base and water (nucleophile) positioning. The insights gained from our work will aid the understanding of the function of other enzymes that use flexible active sites to exhibit diverse substrate specificity.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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19
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Lu S, Wen Y, Bai L, Liu G, Chen Y, Du H, Wang X. pH-controlled voltammetric behaviors and detection of phytohormone 6-benzylaminopurine using MWCNT/GCE. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.05.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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20
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Drohat AC, Maiti A. Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA. Org Biomol Chem 2015; 12:8367-78. [PMID: 25181003 DOI: 10.1039/c4ob01063a] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA glycosylases remove damaged or enzymatically modified nucleobases from DNA, thereby initiating the base excision repair (BER) pathway, which is found in all forms of life. These ubiquitous enzymes promote genomic integrity by initiating repair of mutagenic and/or cytotoxic lesions that arise continuously due to alkylation, deamination, or oxidation of the normal bases in DNA. Glycosylases also perform essential roles in epigenetic regulation of gene expression, by targeting enzymatically-modified forms of the canonical DNA bases. Monofunctional DNA glycosylases hydrolyze the N-glycosidic bond to liberate the target base, while bifunctional glycosylases mediate glycosyl transfer using an amine group of the enzyme, generating a Schiff base intermediate that facilitates their second activity, cleavage of the DNA backbone. Here we review recent advances in understanding the chemical mechanism of monofunctional DNA glycosylases, with an emphasis on how the reactions are influenced by the properties of the nucleobase leaving-group, the moiety that varies across the vast range of substrates targeted by these enzymes.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
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21
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Chen M, Lee JK. Computational Studies of the Gas-Phase Thermochemical Properties of Modified Nucleobases. J Org Chem 2014; 79:11295-300. [DOI: 10.1021/jo502058w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mu Chen
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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22
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Brovarets’ OO, Zhurakivsky RO, Hovorun DM. A QM/QTAIM microstructural analysis of the tautomerisationviathe DPT of the hypoxanthine·adenine nucleobase pair. Mol Phys 2014. [DOI: 10.1080/00268976.2013.877170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Šebera J, Trantírek L, Tanaka Y, Nencka R, Fukal J, Sychrovský V. The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG. RSC Adv 2014. [DOI: 10.1039/c4ra08278h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NLMOs of lone-pair electrons at N9 nitrogen and Fukui indexesf2of N9.
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Affiliation(s)
- Jakub Šebera
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology – Masaryk University
- 625 00 Brno, Czech Republic
| | - Yoshiyuki Tanaka
- Division of Pharmaceutical Chemistry
- Tohoku University
- Sendai, Japan
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Jiří Fukal
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i
- 16610 Praha, Czech Republic
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24
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Brovarets’ OO, Hovorun DM. Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis. J Biomol Struct Dyn 2013; 31:913-36. [PMID: 22962845 DOI: 10.1080/07391102.2012.715041] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Wang K, Chen M, Wang Q, Shi X, Lee JK. 1,2,3-Triazoles: Gas Phase Properties. J Org Chem 2013; 78:7249-58. [PMID: 23805820 DOI: 10.1021/jo4012738] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kai Wang
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Mu Chen
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Qiaoyi Wang
- C. Eugene Bennett Department
of Chemistry, West Virginia University,
Morgantown, West Virginia 26506, United States
| | - Xiaodong Shi
- C. Eugene Bennett Department
of Chemistry, West Virginia University,
Morgantown, West Virginia 26506, United States
| | - Jeehiun K. Lee
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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26
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Brovarets' OO, Zhurakivsky RO, Hovorun DM. The physico-chemical "anatomy" of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives. J Mol Model 2013; 19:4119-37. [PMID: 23292249 DOI: 10.1007/s00894-012-1720-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
Abstract
The biologically important tautomerization of the Hyp·Cyt, Hyp·Thy and Hyp·Hyp base pairs to the Hyp·Cyt, Hyp·Thy and Hyp·Hyp base pairs, respectively, by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ε = 4) corresponding to hydrophobic interfaces of protein-nucleic acid interactions by combining theoretical investigations at the B3LYP/6-311++G(d,p) level of QM theory with QTAIM topological analysis. Based on the sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), it was proved that the tautomerization through the DPT is concerted and asynchronous process for the Hyp·Cyt and Hyp·Thy base pairs, while concerted and synchronous for the Hyp·Hyp homodimer. The continuum with ε = 4 does not affect qualitatively the course of the tautomerization reaction for all studied complexes. The nine key points along the IRC of the Hyp·Cyt↔Hyp·Cyt and Hyp·Thy↔Hyp·Thy tautomerizations and the six key points of the Hyp·Hyp↔Hyp·Hyp tautomerization have been identified and fully characterized. These key points could be considered as electron-topological "fingerprints" of concerted asynchronous (for Hyp·Cyt and Hyp·Thy) or synchronous (for Hyp·Hyp) tautomerization process via the DPT. It was found, that in the Hyp·Cyt, Hyp·Thy, Hyp·Hyp and Hyp·Hyp base pairs all H-bonds are significantly cooperative and mutually reinforce each other, while the C2H…O2 H-bond in the Hyp·Cyt base pair and the O6H…O4 H-bond in the Hyp·Thy base pair behave anti-cooperatively, i.e., they become weakened, while two others become strengthened.
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Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str, 03680, Kyiv, Ukraine
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27
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Michelson AZ, Rozenberg A, Tian Y, Sun X, Davis J, Francis AW, O'Shea VL, Halasyam M, Manlove AH, David SS, Lee JK. Gas-phase studies of substrates for the DNA mismatch repair enzyme MutY. J Am Chem Soc 2012; 134:19839-50. [PMID: 23106240 PMCID: PMC4204490 DOI: 10.1021/ja309082k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The gas-phase thermochemical properties (tautomeric energies, acidity, and proton affinity) have been measured and calculated for adenine and six adenine analogues that were designed to test features of the catalytic mechanism used by the adenine glycosylase MutY. The gas-phase intrinsic properties are correlated to possible excision mechanisms and MutY excision rates to gain insight into the MutY mechanism. The data support a mechanism involving protonation at N7 and hydrogen bonding to N3 of adenine. We also explored the acid-catalyzed (non-enzymatic) depurination of these substrates, which appears to follow a different mechanism than that employed by MutY, which we elucidate using calculations.
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Affiliation(s)
- Anna Zhachkina Michelson
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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28
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Zhang N, Meng F. Theoretical study of the deamination of 1-(2-hydroxy-1-phenylethyl)adenine. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Michelson AZ, Chen M, Wang K, Lee JK. Gas-Phase Studies of Purine 3-Methyladenine DNA Glycosylase II (AlkA) Substrates. J Am Chem Soc 2012; 134:9622-33. [DOI: 10.1021/ja211960r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Zhachkina Michelson
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Mu Chen
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Kai Wang
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
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30
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LIU XINLIN, ZENG HUI, MENG FANCUI, LIU JUNXIANG. THE HYDROLYTIC DEAMINATION MECHANISM OF PROTONATED ADENINE: A DFT STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633611006463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hydrolytic deamination mechanism of protonated adenine has been studied using density functional theory method. There are five pathways according to adenine protonated at N1, N3 and N7, respectively. As for the N1 protonated adenine only one pathway has been found, while for N3 and N7 protonated adenine two pathways have been found. Pathway c2 is preferred due to lowest activation free energy barrier of 53.02 kcal/mol. In this pathway, the hydroxyl group of water attacks C6 atom and hydrogen atom attacks N10 atom to produce enol form of protonated hypoxanthine and ammonia, then hydrogen transfer occurs to cause enol-keto tautomerization of protonated hypoxanthine with the assistance of ammonia. Adenine deamination is easier to take place under acidic condition than under neutral condition owing to lower activation energy barrier.
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Affiliation(s)
- XINLIN LIU
- Institute of Cardiovascular Disease, Pingjin Hospital, Medical College of Chinese People's, Armed Police Forces, Tianjin, 300162, P. R. China
| | - HUI ZENG
- Department of Pathology, Chinese People's Armed, Police Corps Hospital of Qinghai Province, Xining, 810000, P. R. China
| | - FANCUI MENG
- Tianjin Key Lab of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - JUNXIANG LIU
- Institute of Cardiovascular Disease, Pingjin Hospital, Medical College of Chinese People's, Armed Police Forces, Tianjin, 300162, P. R. China
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31
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Villabona-Monsalve JP, Noria R, Matsika S, Peón J. On the Accessibility to Conical Intersections in Purines: Hypoxanthine and its Singly Protonated and Deprotonated Forms. J Am Chem Soc 2012; 134:7820-9. [DOI: 10.1021/ja300546x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Juan. P. Villabona-Monsalve
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
| | - Raquel Noria
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, 13th and
Norris Streets, Philadelphia
Pennsylvania 19122, United States
| | - Jorge Peón
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
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32
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Michelson AZ, Petronico A, Lee JK. 2-Pyridone and Derivatives: Gas-Phase Acidity, Proton Affinity, Tautomer Preference, and Leaving Group Ability. J Org Chem 2011; 77:1623-31. [DOI: 10.1021/jo201991y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Anna Zhachkina Michelson
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
| | - Aaron Petronico
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
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33
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Zubkov AS, Artyukhov VI, Chernozatonskii LA, Nedelina OS. A model of single-electron transport. Calculation of the thermodynamic parameters for electron capture by the bound proton of oxyacids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111090259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Rutledge LR, Wetmore SD. Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines. J Am Chem Soc 2011; 133:16258-69. [PMID: 21877721 DOI: 10.1021/ja207181c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) initiates the repair of a wide variety of (neutral or cationic) alkylated and deaminated purines by flipping damaged nucleotides out of the DNA helix and catalyzing the hydrolytic N-glycosidic bond cleavage. Unfortunately, the limited number of studies on the catalytic pathway has left many unanswered questions about the hydrolysis mechanism. Therefore, detailed ONIOM(M06-2X/6-31G(d):AMBER) reaction potential energy surface scans are used to gain the first atomistic perspective of the repair pathway used by AAG. The lowest barrier for neutral 1,N(6)-ethenoadenine (εA) and cationic N(3)-methyladenine (3MeA) excision corresponds to a concerted (A(N)D(N)) mechanism, where our calculated ΔG(‡) = 87.3 kJ mol(-1) for εA cleavage is consistent with recent kinetic data. The use of a concerted mechanism supports previous speculations that AAG uses a nonspecific strategy to excise both neutral (εA) and cationic (3MeA) lesions. We find that AAG uses nonspecific active site DNA-protein π-π interactions to catalyze the removal of inherently more difficult to excise neutral lesions, and strongly bind to cationic lesions, which comes at the expense of raising the excision barrier for cationic substrates. Although proton transfer from the recently proposed general acid (protein-bound water) to neutral substrates does not occur, hydrogen-bond donation lowers the catalytic barrier, which clarifies the role of a general acid in the excision of neutral lesions. Finally, our work shows that the natural base adenine (A) is further inserted into the AAG active site than the damaged substrates, which results in the loss of a hydrogen bond with Y127 and misaligns the general base (E125) and water nucleophile to lead to poor nucleophile activation. Therefore, our work proposes how AAG discriminates against the natural purines in the chemical step and may also explain why some damaged pyrimidines are bound but are not excised by this enzyme.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada
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35
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Liu M, Tran NT, Franz AK, Lee JK. Gas-Phase Acidity Studies of Dual Hydrogen-Bonding Organic Silanols and Organocatalysts. J Org Chem 2011; 76:7186-94. [DOI: 10.1021/jo201214x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Ngon T. Tran
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Annaliese K. Franz
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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36
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Liu M, Chen M, Zhang S, Yang I, Buckley B, Lee JK. Reactivity of carbene•phosphine dimers: proton affinity revisited. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1890] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology; Rutgers, The State University of New Jersey; New Brunswick NJ 08901 U.S.A
| | - Mu Chen
- Department of Chemistry and Chemical Biology; Rutgers, The State University of New Jersey; New Brunswick NJ 08901 U.S.A
| | - Sisi Zhang
- Department of Chemistry and Chemical Biology; Rutgers, The State University of New Jersey; New Brunswick NJ 08901 U.S.A
| | - Ill Yang
- Environmental and Occupational Health Sciences Institute; Piscataway NJ 08854 U.S.A
| | - Brian Buckley
- Environmental and Occupational Health Sciences Institute; Piscataway NJ 08854 U.S.A
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology; Rutgers, The State University of New Jersey; New Brunswick NJ 08901 U.S.A
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37
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Xing D, Tan X, Jiang X, Wang B. Deprotonation studies of Cu+–guanine and Cu2+–guanine complexes by theoretical investigation. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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39
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Zhachkina A, Lee JK. Uracil and thymine reactivity in the gas phase: the S(N)2 reaction and implications for electron delocalization in leaving groups. J Am Chem Soc 2010; 131:18376-85. [PMID: 19928991 DOI: 10.1021/ja906814d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The gas-phase substitution reactions of methyl chloride and 1,3-dimethyluracil (at the N1-CH(3)) are examined computationally and experimentally. It is found that, although hydrochloric acid and 3-methyluracil are similar in acidity, the leaving group abilities of chloride and N1-deprotonated 3-methyluracil are not: chloride is a slightly better leaving group. The reason for this difference is most likely related to the electron delocalization in the N1-deprotonated 3-methyluracil anion, which we explore further herein. The leaving group ability of the N1-deprotonated 3-methyluracil anion relative to the N1-deprotonated 3-methylthymine anion is also examined in the context of an enzymatic reaction that cleaves uracil but not thymine from DNA.
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Affiliation(s)
- Anna Zhachkina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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40
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Sun X, Lee JK. Stability of DNA Duplexes Containing Hypoxanthine (Inosine): Gas versus Solution Phase and Biological Implications. J Org Chem 2010; 75:1848-54. [DOI: 10.1021/jo9023683] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xuejun Sun
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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41
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Wincel H. Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1900-1905. [PMID: 19665394 DOI: 10.1016/j.jasms.2009.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/28/2009] [Accepted: 06/29/2009] [Indexed: 05/28/2023]
Abstract
Thermochemical data, DeltaH(o)(n), DeltaS(o)(n), and DeltaG(o)(n), for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4-13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
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Zhachkina A, Liu M, Sun X, Amegayibor FS, Lee JK. Gas-Phase Thermochemical Properties of the Damaged Base O6-Methylguanine versus Adenine and Guanine. J Org Chem 2009; 74:7429-40. [DOI: 10.1021/jo901479m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Anna Zhachkina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Xuejun Sun
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - F. Sedinam Amegayibor
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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43
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Liu M, Li T, Amegayibor FS, Cardoso DS, Fu Y, Lee JK. Gas-Phase Thermochemical Properties of Pyrimidine Nucleobases. J Org Chem 2008; 73:9283-91. [DOI: 10.1021/jo801822s] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Tingting Li
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - F. Sedinam Amegayibor
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Daisy S. Cardoso
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Yunlin Fu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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Chen ECM, Wiley JR, Chen ES. The electron affinities of deprotonated adenine, guanine, cytosine, uracil, and thymine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:506-24. [PMID: 18569789 DOI: 10.1080/15257770802088985] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Electron attachment rates and gas phase acidities for the canonical tautomers of the nucleobases and electron affinities for thymine, deprotonated thymine, and cytosine are reported The latter are from a new analysis of published photoelectron spectra. The values for deprotonated thymine are (all in eV) keto-N1-H, 3.327(5); enol-N3-H, 3.250(5), enol-C2OH, 3.120(5) enol-N1-H, 3.013(5), and enol-C4OH,3.123(5). The values for deprotonated cytosine, keto-N1-H, 3.184(5); trans-NH-H, 3.008(5); cis-NH-H, 3.039(5); and enol-N1-H, 2.750(5) and enol-O-H, 2.950(5). The gas phase acidities from these values are obtained from these values using experimental or theoretical calculations of bond dissociation energies. Kinetic and thermodynamic properties for thermal electron attachment to thymine are obtained from mass spectrometric data. We report an activation energy of 0.60 eV and electron affinity of thymine, 1.0(1) eV.
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Affiliation(s)
- Edward C M Chen
- University of Houston Clear Lake, The Wentworth Foundation, Houston, TX 77025, USA.
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Trujillo C, Mó O, Yáñez M. Why Are Selenouracils as Basic as but Stronger Acids than Uracil in the Gas Phase? Chemphyschem 2008; 9:1715-20. [DOI: 10.1002/cphc.200800215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Liu M, Xu M, Lee JK. The Acidity and Proton Affinity of the Damaged Base 1,N6-Ethenoadenine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications. J Org Chem 2008; 73:5907-14. [DOI: 10.1021/jo800891c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Meng Xu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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