cloning: deletion in a primer

[Krys]

Hi
Recently, I cloned a 1000 pb gene in a pET25b+ plasmid. This
construction was transformed in DH5alpha. The insert was then
sequenced and shown a single nucleotide deletion in the forward primer
(It's not a primer problem cause it has been used for another reaction
without problem).
To repare this deletion, I used the Quick change mutagenesis kit (from
Stratagene) and transformed DH5alpha and XL1blue with the mix.
After mutagenesis: Insert sequences from DH5alpha show the same single
nucleotide deletion while insert sequences from XL1b show a single
nucleotide deletion 7 nd after the first (corresponding to the
mutagenesis primers).
To summerize: It's not a PCR or sequencing problem; certainly a
recombination from the host bacteria.
Questions I submit are:
1. What sort of mechanisms bacteria use to delete one nucleotide? Why
only one and not the same between two different strains (but in the
same area)?
2. This region contains a secondary structure; is it important??? but
the gene contains at least 50 secondary struct??
3. What do you think about Sure2 competent cell in this case?
Please send me informations or links.
If you need more information I'm available.
Thanks a lot
Christophe