Messages

1

General discussions (Q&As) / Re: constructing a modified sugar

« on: September 12, 2011, 04:28:05 am »

Dear Xiang-Jun,
Just want to update you that as of now, i am successful in making the modification using chimera software which has a menu called 'Build structure'. It would be nice to have this feature incorporated in 3DNA.

2

General discussions (Q&As) / Re: constructing a modified sugar

« on: September 09, 2011, 10:33:56 am »

Xiang-Jun,
I extracted chain A and B from the 2X2Q pdb, changed the residue names to A, T, G, and C instead of what is there in original pdb. I tried to run find_pair and analyze and i am able to get the output. So i guess i wont have a problem in analyzing such sugar modified DNA.

Just for curiosity, I looked in the fiber/str04 where there is a A.pdb, I guess this is the template Adenine structure used for building a fiber model with -4 option. I extracted the co-ordinates of just one sugar locked Adenine from the pdb and replaced A.pdb file. It has two extra atoms (O2' and C6') as compared to the standard Adenine. I then tried to constructed just a A:T base pair but i didnt find any change in the sugar, the result was a standard sugar.

I guess some more thing should be necessary. I read the discussion titled 'helical Parameters of a Modified nucleic acids' in the forum. What i understood was that they have tried analyzing a modified base by adding new residue names in baselist.dat and also Atomic_?.pdb files. Am i supposed to do a similar additions ?.

Cheers,
Bala

3

General discussions (Q&As) / constructing a modified sugar

« on: September 08, 2011, 01:40:02 pm »

Friends,
i want to incorporate a modified sugar into a canonical DNA duplex. Basically i am interested in incorporating a locked nucleic acid sugar, where the 2' oxygen and 4' carbon of the sugar has a methylene linkage. Such a structure is available in pdb:2X2Q. i would like to know the possibility of using 3DNA for replacing the normal sugar with such modified sugar in a DNA duplex.

Thanks,
Subbu

4

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 08, 2011, 09:28:12 am »

Hi,
I am not aware of the rotation but once you install the latest build of chimera. Pleases see the /UCSF-Chimera-2011-09-01/share/SwapRes/base.py script in the installation directory.

Hope this helps.
Subbu

5

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 07, 2011, 01:14:16 pm »

Hi,
Attached three pdb files.  org.pdb --> structure downloaded from pdb (1VT7.pdb)
                                     org_no_pre.pdb --> G in position 1 (chain A) is mutated with A with no preserve option
                                     org_pre.pdb --> mutation down with preserve option.

Hope this helps,
Subbu

6

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 07, 2011, 12:05:34 pm »

Xiang-Jun,

1) Firstly i tried by constructing the ps DNA from fiber model 31 but the structure i obtained was nt correct (in the sense the base pairs of chian A and C) were not in proper orientation. So i used the pdb structure as template to carry out mutation.

2) I am not getting what example you need, in case if it is related to chimera software, you can refer this page. It is freely down loadable.

http://plato.cgl.ucsf.edu/chimera/docs/ ... wapna.html

Thanks,
Bala

7

General discussions (Q&As) / Re: building a parallel stranded DNA

« on: September 06, 2011, 05:00:21 am »

Hi Xiang-Jun,
Thank you very much for the information. I read the related threads. Kindly provide me the script 'mutate_base'. I would like to try it. I think adding it in 3DNA package would be a good option.

I would like to share one information on this regard, USCF chimera software has a command called 'swapna' with which we can just replace the base moiety. In addition it has a parameter called 'preserve' with which you can retain the glycosidic angle and position of the nitrogen forming the bond too after replacement.

But it is always better to use a script like yours when we have to do many mutations. In case your script doesnt have preserve option, could you please see if you can incorporate this preserve option in your script. I guess a similar name swap_base would be more suitable for your script.

Also can you merge all these threads so that others can view all related information in one shot.  1) Problems with mutations on DNA (Feb. 2011) 2) mutating DNA in DNA protein complex (Oct. 2007).

Thanks,
Subbu

8

General discussions (Q&As) / building a parallel stranded DNA

« on: September 05, 2011, 11:59:36 am »

Friends,
I have to construct a duplex structure of 10mer oligo. I want to construct the model as parallel stranded (ps) DNA. I would like to know
i) if it is possible to construct such a model using 3DNA and
ii) there is an experimental structure of such ps duplex with completely different base composition, is there any way that i can use as am a template in 3DNA to model my structure. I am also planning to do a short simulation to optimize the model further.

Thanks,
Subramanian