normal holliday dna

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4 years 10 months ago #3967 by dave
holliday dna was created by dave
Hi All,

This is my first mail and new to coarse-grain, and thus martini.

There is Martini for ssDNA and dsDNA and am sure it must have been extensively tested for these cases. I am just wondering how do I consider cases like holliday junctions in which structure has helical structure but each helix is formed by more than two ssDNA compared to normal helical dsDNA (having just two ssDNA).

Also is there any documentation/published paper available for martini DNA, like for proteins (so many papers for proteins). It will be of interest to know which properties were tested and compared experimentally.

best regards
Dave

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4 years 10 months ago #3978 by jaakko
Replied by jaakko on topic holliday dna
Hi Dave,

Martini DNA is still in beta and we have not looked into holliday junctions. You can model these by using a stiff elastic network that is provided with the beta version but it won't allow the structure to change. The paper about Martini DNA is not published yet, as soon as it is we will put the final parameters here on the website and add a reference to the publication.

- Jaakko

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4 years 10 months ago #3979 by helgi
Replied by helgi on topic holliday dna
Jaakko just beat me to the answer :)

So yes so far no one has looked at holliday junctions with Martini and the initial paper (ssDNA and dsDNA) is not out yet (but nearly ready and should be submitted any day now).

If you are interested in exploring them with Martini currently it would require some scripting on your part. You can use the DNA Martinize (provided in the Martini DNA beta) to construct the CG topologies for the different parts (x4 dsDNAs and x4 ssDNAs) then you would shift the indexes of the different parts and carefully merge them into one topology (in theory not difficult but very easy to make mistakes). This would allow you to tune the level of elastic use for each part, the heavy stiff network would maintain the initial structure well but not allow for much dynamics, so you might want to keep a stiff elastic network on the dsDNA parts but then a less stiff network on the middle part of the holliday junctions allowing more flexibility, but this depends on what you want to explore.

Great to hear you are interested in Martini DNA.
Cheers,
- Helgi

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4 years 10 months ago #3980 by dave
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Hi Jaakko, Hi Helgi

I will try small test case and I will ask few more things soon.

Thanks
Dave

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