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DNA polymerase III mis-insertion may, where not corrected by its 3′→ 5′ exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in  Escherichia coli , and its repair mechanism remains elusive. We present here  in vitro  evidence that C⋅C mismatch can be processed by base excision repair initiated by the  E. coli  formamidopyrimidine-DNA glycosylase (Fpg) protein. The  k  cat  for C⋅C is, however, 2.5 to 10 times lower than for its primary substrate 8-oxoguanine (oxo 8 G)⋅C, but approaches those for 5,6-dihydrothymine (dHT)⋅C and thymine glycol (Tg)⋅C. The  K  M  values are all in the same range, which indicates efficient recognition of C⋅C mismatches in DNA. Fpg activity was also exhibited for the thymine (T)⋅T mismatch and for  N  4 - and/or 5-methylated C opposite C or T, Fpg activity being enabled on a broad spectrum of DNA lesions and mismatches by the flexibility of the active site loop. We hypothesize that Fpg plays a role in resolving C⋅C in particular, but also other pyrimidine⋅pyrimidine mismatches, which increases survival at the cost of some mutagenesis.

Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein