Structure determination of DNA methylation lesions N 1 -meA and N 3 -meC in duplex DNA using a cross-linked protein–DNA system

Abstract

N1-meA and N3-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of SN2 type methylating agents. We report here the structural characterization of these base lesions in duplex DNA using a cross-linked protein–DNA crystallization system. The crystal structure of N1-meA:T pair shows an unambiguous Hoogsteen base pair with a syn conformation adopted by N1-meA, which exhibits significant changes in the opening, roll and twist angles as compared to the normal A:T base pair. Unlike N1-meA, N3-meC does not establish any interaction with the opposite G, but remains partially intrahelical. Also, structurally characterized is the N6-meA base modification that forms a normal base pair with the opposite T in duplex DNA. Structural characterization of these base methylation modifications provides molecular level information on how they affect the overall structure of duplex DNA. In addition, the base pairs containing N1-meA or N3-meC do not share any specific characteristic properties except that both lesions create thermodynamically unstable regions in a duplex DNA, a property that may be explored by the repair proteins to locate these lesions.