DNA supercoiling

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fluciano
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DNA supercoiling

Post by fluciano » Thu Aug 25, 2016 10:37 am

Hello,

I find difficulties in understanding DNA supercoiling. In particular:
1. I found clear explanations about supercoiling in Prokaryotes: because of their covalently closed circular DNA, it acts as if the DNA molecule had two fixed extremities

(I found this video really useful.
https://www.youtube.com/watch?v=qj_eYWgQ90k
)

But talking about eukaryotes, we should consider a linear molecule of DNA: is there something like a mechanism used to "keep fixed" it extremities, just like in the previous model, in order to make supercoiling possible? Or am I not considering anything else important?


2. I didn't clearly understand how negative or positive supercoiling can be introduced into a DNA molecule: until now I found that
- topoisomerase often removes 1 or 2 supercoils
- gyrase introduces more supercoils.

But are there any other reasons (also non enzyme-linked) why a DNA molecule would undergo some supercoiling? For exeample I heard from my professor that when helicase opens a new replication fork, a new supercoiling is introduced; but honestly I didn't understand it and I didn't find some references or explanations about that.


Thank you for your attention and sorry for my poor english.

Best regards

Francesco

claudepa
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Re: DNA supercoiling

Post by claudepa » Thu Aug 25, 2016 3:04 pm

Hi. my souvenirs about DNA supercoiling are rather old. There are probably new data I do not know. I agree that it is clear for the circular bacterial DNA. In eukaryotes chromosome DNA is not circular. However there are sequences (MAR) of DNA which correspond to a nuclear matrix binding. This could correspond to fixed parts of DNA. Supercoiling can therefore take place between two MAR sequences. As far as I remember the aim of toposisomerases and gyrases is to reduce the number of superturns which can be positive or negative ones. The progress of the replication fork along the double helix generates positive supercoiling in front of the replication fork and negative supercoiling in the back of the replication fork. This is why topoisomerases and gyrases are associated to the replication fork. It is interesting to remark that inhibitors of topoisomerases and gyrases are pharmacological agents.

fluciano
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Post by fluciano » Thu Aug 25, 2016 3:36 pm

Thank you so much, you were really clear and helpful!

The only point which is not coherent to my notions is the role of gyrase: I know that it is different from other topoisomerases since it introduces new supercoils; in fact, it is ATP dependent.

Do you think my interpretation could be right?

http://www.ncbi.nlm.nih.gov/pubmed/1657531

claudepa
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Re: DNA supercoiling

Post by claudepa » Fri Aug 26, 2016 8:43 am

my feeling is that gyrase introduces new superturns to go from negative superturns to relaxed state. So it is logical the energy is needed to make superturns. I do not know if toposisomerases need ATP but if not it would not be surprising since they only need DNA cleavage and then the energy stored in the superturns is enough to relax DNA. If you have not the answer in the review I advise you to send a mail to the authors. Also you could contact Yves Pommier in the NCI. He is among the ones at the origin of the finding that topoisomerase 2 is the main target of anticancer DNA intercalating agents.

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Post by fluciano » Fri Aug 26, 2016 9:19 am

Thank you so much, in case I found a clear answer about gyrase I'll write it here.

Have a nice day.

Francesco

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Re: DNA supercoiling

Post by leesajohnson » Thu Sep 08, 2016 10:58 am

DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryote) is a difficult feat. Supercoiling of DNA reduces the space and allows for much more DNA to be packaged. In prokaryotes, plectonemic supercoils are predominant, because of the circular chromosome and relatively small amount of genetic material. In eukaryotes, DNA supercoiling exists on many levels of both plectonemic & solenoidal supercoils, with the solenoidal supercoiling proving most effective in compacting the DNA. Solenoidal supercoiling is achieved with histones to form a 10 nm fibre This fiber is further coiled into a 30 nm fiber, and further coiled upon itself numerous times more. https://en.wikipedia.org/wiki/DNA_supercoil
https://youtu.be/qj_eYWgQ90k

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