Sequence-dependent alkylation of guanine residues in duplex DNA Molecular dynamics study
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).
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