Hi RG community,
I'm looking for a little clarification. Hofreiter et al. (2001) discusses the hydrolytic deamination of nucleotides and the generation of C->T and G->A transitions due to the deamination of cytosine to uracil. The specific text in question reads as follows: "When DNA containing [deaminated cytosine] is used as a template for PCR, C->T and G->A transitions in the DNA sequences recovered will result, since deoxyuridine residues in the template DNA strand cause DNA polymerases to incorporate deoxyadenosine residues at positions where a deoxyguanosine would normally have been incorporated."
I understand that hydrolytic deamination of cytosine generates uracil on the template stand, thus an adenosine is added in place of a guanine on the daughter/coding strand. Am I correct in interpreting this as meaning the transition mutation is perceived in the daughter strand? If so, I am clear on the mechanism yielding C->T transitions.
Cytosine methylation yields thymine, which pairs with adenosine in the daughter/coding strand. Employing the logic from above the mutation in this scenario would still be a C->T transition, correct?
Oxidative deamination of guanine yields xanthine, which pairs with a modified cytosine in the daughter/coding strand. My interpretation may be incorrect, in which case I am curious of the process that causes a G->A transition.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC96698/
Update: I've confirmed that the process described above regarding the mechanism of C->T transitions via hydrolytic deamination is correct and recognize the G->A substitution occurs in subsequent replications due to the C->T mutation. This effectively resolves the primary question posed. I am still interested if my interpretation of the effect of cytosine methylation is accurate.
It is perhaps worth mentioning that in living organisms, endogenous or exogenous exposure to agents that can directly or indirectly cause alkylation damage to DNA will often generate lesions that, on replication, cause the same G->A transitions. Perhaps the most frequent is alkylation of the O6-position of guanine, which on replication can result in misincorporation of thymine into the opposite strand. A further round of DNA replication thus converts the original G to A (and C to T on the opposite strand).
You may distinguish in which sequence context mutations occur, since the activity of cytosine deamination is essentially limited to 5mCpG dinucleotides.
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