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Given a strain that is expressing proteins of a restriction-modification system (like EcoRI), is there data to measure the fraction of metylated target sites? I am just looking for an approximation, so in vitro assays also should work.

For EcoRI, I have seen people measuring kinetic constants for the methyltranferase and couting number of molecules in a cell. But from that I do not think I am able to predict the fraction of modified sites, only the fraction of enzyme bound to DNA at a time.

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  • $\begingroup$ I find it difficult to understand your question. When you refer to target sites, which DNA are you referring to — E.coli DNA or invading bacteriophage DNA? And why would you expect not all EcoRI sites in Ecoli to be methylated, if that is what you mean? Or in a phage infection, that would be related to the number of progeny phage. Or are you thinking of restriction enzymes in cloning? If so the problem is one of enzyme kinetics. $\endgroup$
    – David
    Commented Aug 2 at 13:24
  • $\begingroup$ By target sites I mean the sites recognized by the Methyltransferase in the own bacteria DNA. I would expect almost all of them to be methylated, but probably a small percentage may remain unmethylated due to loss of the methyl group, or DNA replication before division. I expect this percentage to be small, but I have not been able to find any data about that. $\endgroup$
    – Alicia Cantero
    Commented Aug 2 at 15:03
  • $\begingroup$ Ok. That’s a fair question (to which I don’t have an answer). Perhaps you could edit the question to make that clear, or I will do it for you if you wish. $\endgroup$
    – David
    Commented Aug 2 at 18:00

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