Creating Intercalation Site in the canonical DNA

[pooja]

Hi,

I am Pooja and would like to thank for creating such a great forum.

I have been working on the study of Intercalators. Currently I am working on the docking of ligands at the intercalation site ( using the DNA structures from PDB after removing the ligand). But most of the complexes deposited in PDB are limited to hexanucleotide sequence and mostly the ligand intercalated in the terminal dinucleotide step.

For my study, I want to dock the ligand molecule at the centre and of different sequences for which I thought of constructing canonical DNA and then creating the intercalation site. Since the rebuild in 3DNA reads the base pair step parameters, I increased the rise value to 6.8A without changing other parameters (of regular BDNA). But for attaching the sugar phosphate backbone I cannot use the bases with sugar-phosphate that are in ATOMIC folder.

I tried to superimpose the sugar phosphate backbone of the dinucleotide steps (intercalation site)  of DNA extracted from the crystal structures but only few of them were superimposing well others were not. Can you please suggest me how can I get the parameters for sugar phosphate backbone? And I also the twist and buckle values differ depending on the ligand, so how should I take care of that thing while passing the parameters in rebuild?

Thanks in anticipation,
Pooja

[xiangjun]

Hi Pooja,

Thanks for using 3DNA and writing such a thoughtful post. I think I understand your question, even though I do not have (or know of) a straight answer to it.

As you tried out, '[mono:1hmzqauk]rebuild[/mono:1hmzqauk]' with the [mono:1hmzqauk]-atomic[/mono:1hmzqauk] option does not generate proper sugar-phosphate backbone geometry for intercalated dinucleotide steps. Meanwhile, the available "complexes deposited in PDB are limited to hexanucleotide sequence and mostly the ligand intercalated in the terminal dinucleotide step." However, by combining the two, plus other utilities in 3DNA, it'd be possible to achieve approximately what you want.

You could start with a PDB complex with an intercalated dinucleotide step and then extend both ends with desired sequence in B-DNA fiber conformation. The intercalated dinucleotide can then be mutated to whatever bases you like, using [red:1hmzqauk]mutate_bp[/red:1hmzqauk] or [red:1hmzqauk]mutate_bases[/red:1hmzqauk] (see my reply to "change one base pair in a double-strand DNA structure file").

Surely, this is not an automatic process; there is no GUI-driven menu and mouse clicks to achieve 'magic'  -- you have to know what to do for each step. However, if you cannot find a better method elsewhere, 3DNA may prove useful. Please share your experience and thought. If you decide to try the 3DNA route, please provide a specific example.

HTH,

Xiang-Jun

[pooja]

Hi Xiang-Jun,

thanks a lot for providing one solution. And that seems to be a pretty good one and thinking of trying this out.

Actually I was using ver1.5 and I want to get access to 3dna v2.0. Can I get the newer version? As you mentioned in one of the post on how to download v2.0? I have already mailed in that regard. Can you tell me by what time can I get the access or there is some other criteria for getting v2.0?

thanks a lot for your help.

Regards,
Pooja Khurana

[xiangjun]

Thanks for following the instructions in post "How to download 3DNA v2.0?". At this summer time, Dr. Olson may be at a meeting or on vocation. It helps to send her a follow up message, and hopefully the problem will be solved soon.

Xiang-Jun

[hr:1tj7d3n5][/hr:1tj7d3n5]PS: If things go well, future releases of 3DNA would be more easily accessible, and with 'formal' support.