Influence of N7 Protonation on the Mechanism of the N-Glycosidic Bond Hydrolysis in 2‘-Deoxyguanosine. A Theoretical Study

Rios-Font, Raquel; Rodrı́guez-Santiago, Luis; Bertrán, Juan; Sodupe, Mariona

doi:10.1021/jp070822j

Cited by 42 publications

(71 citation statements)

References 47 publications

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“…Optimized geometries for reactants and their transition states were in agreement with structures previously reported. 19,33,34 In particular, in agreement with the literature data, 35,36 the minimum energy structure of dG and 8-Oxo-dG was in the anti conformation, whereas that of 8-Me-dG was measured in the syn conformation (Figure 9). Evidently, S -cdG and ddcdG are locked in the anti orientation (Figure 9).…”

Section: Resultssupporting

confidence: 89%

Stability of N-Glycosidic Bond of (5′S)-8,5′-Cyclo-2′-deoxyguanosine

Das

Samaraweera

Morton

et al. 2012

Chem. Res. Toxicol.

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8,5′-Cyclopurine deoxynucleosides are unique tandem lesions containing an additional covalent bond between the base and the sugar. These mutagenic and genotoxic lesions are repaired only by nucleotide excision repair. The N-glycosidic (or C1′-N9) bond of 2′-deoxyguanosine (dG) derivatives is usually susceptible to acid hydrolysis, but even after cleavage of this bond of the cyclopurine lesions, the base would remain attached to the sugar. Here, the stability of the N-glycosidic bond and the products formed by formic acid hydrolysis of (5′S)-8,5′-cyclo-2′-deoxyguanosine (S-cdG) were investigated. For comparison, the stability of the N-glycosidic bond of 8,5′-cyclo-2′,5′-dideoxyguanosine (ddcdG), 8-methyl-2′-deoxyguanosine (8-Me-dG), 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-Oxo-dG), and dG was also studied. In various acid conditions, S-cdG and ddcdG exhibited similar stability to hydrolysis. Likewise, 8-Me-dG and dG showed comparable stability, but the half lives of the cyclic dG lesions were at least 5-fold higher than dG or 8-Me-dG. NMR studies were carried out to investigate the products formed after the cleavage of the C1′-N9 bond. 2-Deoxyribose generated α and β anomers of deoxyribopyranose and deoxyribopyranose oligomers following acid treatment. S-cdG gave α and β deoxyribopyranose linked guanine as the major products, but α and β anomers of deoxyribofuranose linked guanine and other products were also detected. The N-glycosidic bond of 8-Oxo-dG was found exceptionally stable in acid. Computational studies determined that both the protonation of the N7 atom and the rate constant in the bond breaking step control the overall kinetics of hydrolysis, but both varied for the molecules studied indicating a delicate balance between the two steps. Nevertheless, the computational approach successfully predicted the trend observed experimentally. For 8-Oxo-dG, the low pKa of O8 and N3 prevented appreciable protonation, making the free energy for N-glycosidic bond cleavage in the subsequent step very high.

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Section: Resultssupporting

confidence: 89%

Stability of N-Glycosidic Bond of (5′S)-8,5′-Cyclo-2′-deoxyguanosine

Das

Samaraweera

Morton

et al. 2012

Chem. Res. Toxicol.

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“…This indicated that the cationic T(6–4)T NH2 was successfully formed by the intramolecular Paterno-Büchi reaction and the following spontaneous oxetane splitting, similar to the formation of the (6–4) photoproduct of TpT (18,23). However, as observed in the FAB MS and NMR analyses, this product was extremely unstable even under neutral conditions, probably due to the electron deficiency of the cationic base, which induces the hydrolysis of the N -glycosidic bond (Scheme S1) (24). This instability supports the cationic structure of the 2-aminopyrimidinium photoproduct.…”

Section: Discussionmentioning

confidence: 91%

Role of the Carbonyl Group of the (6−4) Photoproduct in the (6−4) Photolyase Reaction

et al. 2009

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The (6–4) photoproduct, which is one of the major UV-induced DNA lesions, causes carcinogenesis with high frequency. The (6–4) photolyase is a flavoprotein that can restore this lesion to the original bases, but its repair mechanism has not been elucidated. In this study, we focused on the interaction between the enzyme and the 3’ pyrimidone component of the (6–4) photoproduct, and prepared a substrate analog in which the carbonyl group, a hydrogen-bond acceptor, was replaced with an imine, a hydrogen-bond donor, to investigate the involvement of this carbonyl group in the (6–4) photolyase reaction. UV irradiation of oligodeoxyribonucleotides containing a single thymine–5-methylisocytosine site yielded products with absorption bands at wavelengths longer than 300 nm, similar to those obtained from the conversion of the TT site to the (6–4) photoproduct. The nuclease digestion, MALDI-TOF mass spectrometry, and the instability of the products indicated the formation of the 2-iminopyrimidine-type photoproduct. Analyses of the reaction and the binding of the (6–4) photolyase using these oligonucleotides revealed that this imine analog of the (6–4) photoproduct was not repaired by the (6–4) photolyase, although the enzyme bound to the oligonucleotide with considerable affinity. These results indicate that the carbonyl group of the 3’ pyrimidone ring plays an important role in the (6–4) photolyase reaction. Based on these results, we discuss the repair mechanism.

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“…13,16,27 Other studies that examine both the S N 1 and S N 2 mechanisms report prohibitively large activation energies for the S N 1 dissociation step, and thus conclude that the synchronous mechanism is favored. 25,26,29 In addition, most studies do not contain the empirically proposed oxacarbenium cation intermediate. [24][25][26]29 For example, two studies have reported a reaction intermediate where the nucleobase reattaches to the sugar through a different connectivity compared with the corresponding natural nucleoside, 26,29 such as O2 of thymine glycol bound to C1′ of the sugar moiety.…”

Section: Introductionmentioning

confidence: 99%

“…40 In all of the uncatalyzed hydrolysis computational studies mentioned above, [25][26][27]29 and many of the enzyme-catalyzed studies, 21,23,24,31,32 environmental effects (if included) were treated as a correction to the energy. Indeed, this is still the most common methodology for studying reaction mechanisms using computational chemistry in the literature, although microsolvation and large-scale models with explicit solvation are increasing in frequency.…”

Section: Introductionmentioning

confidence: 99%

Modeling the Dissociative Hydrolysis of the Natural DNA Nucleosides

Przybylski

Wetmore

2009

J. Phys. Chem. B

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Two-dimensional PCM-B3LYP/6-31+G(d) potential energy surfaces for the hydrolysis of the four natural 2'-deoxyribonucleosides (2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and thymidine) are characterized using a model that includes both implicit (bulk) solvent effects and (three or four) explicit water molecules in the optimization routine. For the first time, the experimentally predicted dissociative (S(N)1) mechanism is found to be favored over the synchronous (S(N)2) pathway for all nucleosides studied. Due to the success of our model in stabilizing the charge-separated intermediates along the S(N)1 pathway, it is proposed that the new model presented here is the smallest system capable of generating the experimentally predicted oxacarbenium cation intermediate. We therefore stress that dissociative mechanisms should be studied with methodologies that account for the (bulk) environment in the optimization routine, where these effects are often only included as a correction to the energy in the current literature. In addition to accounting for charge stabilization through implicit solvation, nucleophile activation and leaving group stabilization should also be explicitly introduced into the model to further stabilize the system. Our work also emphasizes the importance of studying the Gibbs surface, which in some cases provides a better description of chemically important regions of the reaction surface or changes the calculated trend in the magnitude of dissociative barriers. In addition, it is proposed that the methodology presented in this study can be used to calculate uncatalyzed deglycosylation barriers for a range of DNA nucleosides, which when compared to the corresponding enzyme-catalyzed reactions, will allow the prediction of the rate enhancement (barrier reduction) due to the enzyme.

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Influence of N7 Protonation on the Mechanism of the N-Glycosidic Bond Hydrolysis in 2‘-Deoxyguanosine. A Theoretical Study

Cited by 42 publications

References 47 publications

Stability of N-Glycosidic Bond of (5′S)-8,5′-Cyclo-2′-deoxyguanosine

Stability of N-Glycosidic Bond of (5′S)-8,5′-Cyclo-2′-deoxyguanosine

Role of the Carbonyl Group of the (6−4) Photoproduct in the (6−4) Photolyase Reaction

Modeling the Dissociative Hydrolysis of the Natural DNA Nucleosides

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