Synthesis and Structure of Duplex DNA Containing the Genotoxic Nucleobase Lesion N7-Methylguanine

Lee, Seongmin; Bowman, Brian R.; Ueno, Yoshihito; Wang, Shuyu; Verdine, Gregory L.

doi:10.1021/ja8025328

Cited by 58 publications

(72 citation statements)

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“…N7-methylguanine has no discernible effect on the conformation of duplex DNA (46) and slightly stabilizes it thermodynamically (52). The structural and thermodynamic effects of m3A are not known, but there is no reason to expect them to be significant, because m3A has the same base-pairing functionality as A, and the methyl group creates no obvious clash.…”

Section: Discussionmentioning

confidence: 99%

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Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Bowman

Lee

Wang

et al. 2010

Journal of Biological Chemistry

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Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.The integrity of covalent structure in the genome is essential for normal cellular function and for faithful transmission of the heritable information reposited therein. DNA inside cells is under constant attack by exogenous environmental toxins and endogenous reactive cellular constituents, giving rise to nucleobase modifications such as oxidation, hydrolytic deamination, and alkylation (1, 2). If left uncorrected, these lesions and the products of their mismanagement by the cell can cause mutations and also interfere with essential cellular processes including transcription, recombination, and DNA replication, events that are causally linked with cancer (3, 4).Although several repair pathways exist for eliminating aberrant nucleobases from the genome, BER 4 is the primary cellular response for the repair of single lesion bases in DNA. The proteins responsible for initiating BER are DNA glycosylases, enzymes that recognize aberrant nucleoside lesions and catalyze scission of their glycosidic linkage. Most BER glycosylases are characterized by high specificity for one particular lesion, or at most a few closely related ones, with this specificity arising from binding interactions between the lesion nucleobase and residues within the enzyme active site (5, 6). There does exist, however, a class of BER enzymes, the 3-methyladenine DNA glycosylases, many members of which exhibit the ability to repair a highly diverse array of nucleoside lesions (7) mostly resulting from DNA alkylation. Prototypical members of this class of enzymes include the Saccharomyces cerevisiae Mag1, human alkyladenine glycosylase AAG, and Escherichia coli 3-methyladenine glycosylase II AlkA. In E. coli, the expression of AlkA is under the control of the adaptive response and the ada regulon, which induces transcription of the alkA gene some hundredfold upon exposure to certain DNA alkylating agents (8 -10). Among the remarkably broad range of AlkA substrates are the alkylated purines N3-and N7-methylguanine and -ad...

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Section: Discussionmentioning

confidence: 99%

“…5, B and C). As a negative control, we examined the lesion analog Fm 7 G, which is known to act as an inhibitor of the AlkA glycosylase reaction (46); as shown in Fig. 5B, Fm 7 G is not cleaved to any appreciable extent by AlkA.…”

Section: Crystal Structure Of Complexes Having Alka Bound Tomentioning

confidence: 99%

Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Bowman

Lee

Wang

et al. 2010

Journal of Biological Chemistry

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“…1 The N7 position of guanine is known as the most nucleophilic site within the heterocyclic bases of DNA. 2 Accordingly, N7-methylguanine (7MeG) is the one of the most prevailing forms of the methylated guanine.…”

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“…Recently, a DNA double helical structure of a 25-mer containing a 7MeG was reported, which revealed the base pairing characteristics of 7MeG. 1 Information on the acid dissociation constants and the relative populations of various tautomers would provide valuable clues toward optimizing analysis of 7MeG and to understand the biological consequences of the modified base.…”

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Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method

Hwang¹,

Jang²,

Cho³

et al. 2010

Bulletin of the Korean Chemical Society

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Methylation of DNA by endogenous methylating agents generates a variety of genotoxic adducts.1 The N7 position of guanine is known as the most nucleophilic site within the heterocyclic bases of DNA.2 Accordingly, N7-methylguanine (7MeG) is the one of the most prevailing forms of the methylated guanine. 7MeG is also generated by methylation in order to be used as a probe of protein-DNA interactions and DNA sequencing. Recently, a DNA double helical structure of a 25-mer containing a 7MeG was reported, which revealed the base pairing characteristics of 7MeG.1 Information on the acid dissociation constants and the relative populations of various tautomers would provide valuable clues toward optimizing analysis of 7MeG and to understand the biological consequences of the modified base.We have developed a scheme based on density-functional theoretical calculations in combination with the Poisson-Boltzmann continuum solvation model for water to predict pKa values and the major tautomeric forms of a number of nucleobases, their oxidative damage products, 3-5 and heteronuclear aromatic compounds. 6,7 As well as macroscopic pKa values, we reproduced the micro pKa values of individual protonation sites of purine nucleobases.8 Hydrogen transfer between paired nucleobases was also investigated using the same computational model. Among methylated guanine species, we have already reported computations on the tautomerism and pK a values of 9-methylguanine (9MeG) and 7,9-dimethylguanine.8 Gas-phase vibrational experiments and computation results on 1,7-dimethylguanine, 7MeG, and 9MeG were also reported. 10In the current work, we report calculated relative stabilities of the tautomers of 7MeG at each ionization stage and the pKa values of 7MeG in aqueous solution.pKa calculations on the nucleobases and their derivatives are complicated due to the presence of multiple tautomers with different site-specific microscopic pKa values. A way to estimate the overall macroscopic pKa from the site-specific pKa's of the tautomers devised in our previous studies and the details of the computation scheme have been presented elsewhere. 3,4For a deprotonation process leading the i-th tautomer of an acid HA into the j-th tautomer of the conjugate base A -, the Gibbs energy of deprotonation reaction is calculated as (1) and the corresponding micro pKa ij values is given bywhere R is the gas constant and T is 298.15 K. From this micro pK a ij value, the partial population of the i-th tautomer out of all of the acid species ( fi), and the partial population of the j-th tautomer out of all of the conjugate base species ( fj ' ), the macro pKa value is estimated as 4 pKa = pKa ij -log fi + log fj ' .The standard free energy of each species (HA, A -, and H + ) in water, ∆Ga 0 q, can be written as the sum of the gas-phase standard Gibbs energy ∆Gg 0 and the standard Gibbs energy of solvation in water ∆Gs 0 olv:The standard Gibbs energy of each species in the gas phase, ∆Gg 0 , is obtained byThe total energy of the molecule at 0 K (E0 K) is calculated ...

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Replication of N²,3‐Ethenoguanine by DNA Polymerases

et al. 2012

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Das instabile DNA‐Addukt N2,3‐Ethenoguanin (N2,3‐εG), das durch Einwirkung von kanzerogenem Vinylchlorid oder durch oxidativen Stress entsteht, wurde mithilfe einer Isosteren‐Strategie zur Stabilisierung der glycosidischen Bindung in ein Oligonukleotid eingebaut. Diese Modifikation wurde dann genutzt, um die Replikation von N2,3‐εG durch verschiedene DNA‐Polymerasen zu untersuchen (siehe Schema).

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Synthesis and Structure of Duplex DNA Containing the Genotoxic Nucleobase Lesion N7-Methylguanine

Cited by 58 publications

References 23 publications

Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method

Replication of N²,3‐Ethenoguanine by DNA Polymerases

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Synthesis and Structure of Duplex DNA Containing the Genotoxic Nucleobase Lesion N7-Methylguanine

Cited by 58 publications

References 23 publications

Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Structure of Escherichia coli AlkA in Complex with Undamaged DNA

Study of 7-Methylguanine on pKaValues by Using Density Functional Theoretical Method

Replication of N2,3‐Ethenoguanine by DNA Polymerases

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Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method

Replication of N²,3‐Ethenoguanine by DNA Polymerases