3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ovelha on December 02, 2008, 01:11:48 pm

Title: Continuous polymer
Post by: ovelha on December 02, 2008, 01:11:48 pm: Dear all,

I am trying to build a continuous polymer of A-DNA from a 8 base pair structure in a crystal.
In fact, using the rebuild I have managed to create a 32 bp structure (analyse the pdb, changed the bp_step file and rebuild -atomic).
However, I would like to know if it is possible to build such a structure but keeping the ions and waters (around the helix) that I have in my original pdb?
I would really appreciate your help.
Thanks in advance for your replies.
Regards,
Ricardo
Title: Re: Continuous polymer
Post by: xiangjun on December 03, 2008, 11:05:08 pm: This is a good question! Unfortunately, 3DNA do not have a direct answer for it (yet). Does anyone know of a general solution to this problem (say, from a commercial or freely available software package)?

In principle, though, one would image to keep each repeating unit (8-bps here) as a rigid body and perform transformations (rotations + translations) to get the next and so on. One way to achieve it is by properly setting coordinate frames.

Xiang-Jun
Title: Re: Continuous polymer
Post by: ghzheng on December 09, 2008, 01:00:26 pm: Since you changed the base-pair step parameters and connected repeating crystal structures, you changed the relative association of waters, ions with DNA atoms. It seems that you would need to refine the model by conducting minimization if you want to keep waters and ions with sense. To do this, you may follow:
1) After analysis, express ions and waters onto a specific frame, e.g. the middle base-pair frame. You would need to perform rotations + translations as suggested by Dr. Lu. You will have 4 such frames ( 4 pieces of 8-bp DNA)

2) After rebuilding, analyze again to find the 4 frames that you just used in Step 1.

3) Insert waters and ions relating to each of the reference frames in Step 2. So far, you have a model with 32-bp structure with waters and ions.

Then, you would need to conduct minimization, which I am not very familiar with. But I guess, those X-ray/NMR software will do, such as CNS (Crystallography & NMR System), or maybe Amber will do as well.

HTH.

Guohui Zheng