Abstract
We present data to explain the sequence dependence of alkylation at the O 6 position of guanine. Both methylation and ethylation of O 6 -guanine occur at either the first or the second position of the middle codon, GGA, in the DNA double helix d(5′-GGCGCTGGAGGCGTG-3′). From our molecular dynamics studies, parameters such as hydrogen bonding, surface accessibility and root-mean-square deviation, provide an atomic rationale for the fact that the second guanine of the middle codon of the sequence is the preferred site for alkylation in this sequence. Furthermore, the recognition and repair by O 6 -alkylguanine-DNA alkyl transferase (AGT) is less effective for alkylation at the second position than the first, and is also less effective for O 6 -ethylguanine (O 6 -etG) than for O 6 -methylguanine (O 6 -meG).
Published Version
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