Re: [DIYbio] Rolling circle replication-

In RCM, there's a dedicated enzyme called "rep" that's encoded usually
next to the origin nick site. In at least some plasmids (those I used as
a baseline for my designs), rep actually covalently bonds to the 5' end
of the DNA as it nicks, "lifting" the DNA as it nicks it to clearly
expose a loose 3' end for extension.

Although rep initially works as a monomer I think, I recall that in
order to work it needs a pair of reps: possibly the nicking process
requires a dimer, but a monomer is bound covalently? But the partner
monomer resumes its role later in finishing synthesis in such a way that
it permanently inactivates both monomers, preventing catalysis of
additional plasmids. I guess that means it's not an "enzyme" as it isn't
a catalyst, but rather is consumed in the reaction.

I had a paper describing this neatly, but I seem to have lost it. Do
some searching on RCM and rep dimers and you should find some good info.

On 08/02/13 04:25, Nathan McCorkle wrote:
> On Thu, Feb 7, 2013 at 5:48 PM, Koeng <koeng101@gmail.com> wrote:
>> Hey I was wondering what exactly makes the DNA "nicked" in the origin. Is it
>> just like that? Or is there other enzyme that makes it nicked? This question
>> has just been like an itch in my mind
>>
>
> Generally when I've heard about plasmids being nicked, it's referring
> to damage encountered during an extraction process.
>
> If you're asking how they coil and uncoil during/after replication,
> you probably want to start with topoisomerase.
>

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