Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?
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$\begingroup$ Don't have sources at the moment, but as far as I know: Yes. Methylated DNA cannot only be replicated, but it can also be passed on to subsequent generations as part of the Epigenetic info inherited by the offspring. $\endgroup$– MCMCommented Aug 31, 2013 at 17:30
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Absolutely. It's a pretty cool process, actually. Most (well...) DNA methylation occurs in the context of what are called CpG; that is, a C (Cytosine) followed by a G (Guanine). Because C and G are the Watson-Crick pair for each other, the sequence on the opposite strand will also be CG. Usually, both Cs are methylated, which turns out to be rather critical for maintenance of methylation.
DNA replication occurs through a semi-conservative mechanism, which means each old, original strand is copied and paired with a new strand. The new strand has no methylation on it, however; it is at this point that the enzyme DNA methyltransferase (DNMT1, specifically) comes into play. DNMT1 finds the CpGs methylated on one strand ("hemimethylated") and methylates the other strand, providing complete inheritance. Here is a nice summary, and this is a review that (briefly) summarizes the evidence that CpGs may play a role in irigins of replication (the jury's still out).
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$\begingroup$ Thanks for the answer !In PCR ,do we always use methyated dna ? $\endgroup$– biogirlCommented Sep 1, 2013 at 15:10
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1$\begingroup$ @biogirl I dunno, do you? Theoretically your input sequence, if it's straight genomic DNA from an organism, could/should be methylated, but DNA polymerase does no methylation at all; that is done by DNMT1 and others, and is much slower than replication. After PCR, none of your product will be methylated. $\endgroup$– AmoryCommented Sep 2, 2013 at 20:48
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$\begingroup$ I have never done a PCR :) If I take DNA from an organism like human(whose DNA is naturally methylated) and then deliberately demethylate it, can it get replicated in PCR or in a cell ? $\endgroup$– biogirlCommented Sep 3, 2013 at 11:59
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$\begingroup$ Sorry, that's what I was trying to say above, you can't. PCR is pretty straightforward, it's basically just DNA polymerase. Each strand of DNA is split and copied, over and over. As I said above, DNMT1 adds methylation, not DNA polymerase, so none of your PCR product would be methylated. Adding in DNMT1 after each cycle would be prohibitively time consuming. $\endgroup$– AmoryCommented Sep 3, 2013 at 13:55