Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine

Journal Article · Mon Nov 03 04:00:00 EST 2008 · J. Am. Chem. Soc.

DOI:https://doi.org/10.1021/ja8025328· OSTI ID:1006820

Lee, S; Bowman, B R; Ueno, Y; Wang, S; Verdine, G L ^[1]

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1. Harvard

The predominant product of aberrant DNA methylation is the genotoxic lesion N7-methyl-2{prime}-deoxyguanosine (m{sup 7}dG). M{sup 7}dG is recognized and excised by lesion-specific DNA glycosylases, namely AlkA in E. coli and Aag in humans. Structural studies of m{sup 7}dG recognition and catalysis by these enzymes have been hampered due to a lack of efficient means by which to incorporate the chemically labile m{sup 7}dG moiety site-specifically into DNA on a preparative scale. Here we report a solution to this problem. We stabilized the lesion toward acid-catalyzed and glycosylase-catalyzed depurination by 2{prime}-fluorination and toward base-catalyzed degradation using mild, nonaqueous conditions in the DNA deprotection reaction. Duplex DNA containing 2{prime}-fluoro-m{sup 7}dG (Fm{sup 7}dG) cocrystallized with AlkA as a host-guest complex in which the lesion-containing segment of DNA was nearly devoid of protein contacts, thus enabling the first direct visualization of the N7-methylguanine lesion nucleobase in DNA. The structure reveals that the base-pairing mode of Fm{sup 7}dG:C is nearly identical to that of G:C, and Fm{sup 7}dG does not induce any apparent structural disturbance of the duplex structure. These observations suggest that AlkA and Aag must perform a structurally invasive interrogation of DNA in order to detect the presence of intrahelical m{sup 7}dG lesions.

• Research Organization: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
• Sponsoring Organization: USDOE
• OSTI ID: 1006820
• Journal Information: J. Am. Chem. Soc., Journal Name: J. Am. Chem. Soc. Journal Issue: (35) ; 09, 2008 Vol. 130; ISSN JACSAT; ISSN 0002-7863
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
CATALYSIS
DISTURBANCES
DNA
ENZYMES
METHYLATION
PROTEINS
SYNTHESIS