building a parallel stranded DNA

[subramanian]

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

[xiangjun]

Hi Subramanian,

Regarding your two questions on constructing models of parallel stranded (ps) DNA,

i) if it is possible to construct such a model using 3DNA and

3DNA does not have such a direct option. However, you may try fiber model 31 (or 32 for [red:3ckdzas2]Poly (U) : poly (A) : poly(U)[/red:3ckdzas2]), delete Us in chain B which form Watson-Crick base-pairs with As in chain A, then you get a parallel stranded Poly (U) : poly (A). You can then mutate bases to fit your needs (see below).

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.

The newly added utility program [red:3ckdzas2]mutate_bases[/red:3ckdzas2] should help. See thread "change one base pair in a double-strand DNA structure file". Please let me know if you want to have access to the program.

I may extend 3DNA's functionality to serve your specific purpose, if necessary; presumably such extension would turn out to be useful to other potential 3DNA users as well.

Xiang-Jun

[subramanian]

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

[xiangjun]

Hi Subbu,

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.

See my email. As I mentioned several times in the forum, it is users' feedbacks, like yours, that move the 3DNA project forward.

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.

Thanks for the info. Could you please provide an example of each? The new (ANSI C) program '[red:m67d7hlr]mutate_bases[/red:m67d7hlr]' preserves the base reference frame, and as a side effect, it retains "the glycosidic angle and position of the nitrogen forming the bond" as well.

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).

Excellent suggestion. I have long thought of consolidating the various source of information about 3DNA, but unable to get it done due to a lack of resources and time. This will change in the new future, so stay tuned.

Xiang-Jun

[subramanian]

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

[xiangjun]

Hi Bala,

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.

It seems that [red:27t8jes7]mutate_bases[/red:27t8jes7] serves your needs, right?

For the record, in fiber model #31, chains A and C form a parallel duplex with classic Hoogsteen A-U pairs. 3DNA has no problem in analyzing such structures. See the attached structure for an example:
[attachment=0:27t8jes7]fiber31_Hoogsteen.pdb[/attachment:27t8jes7]
[pre:27t8jes7]****************************************************************************
Structure classification:

This is a parallel duplex structure
****************************************************************************[/pre:27t8jes7]

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.

When you talk about the '[red:27t8jes7]swapna[/red:27t8jes7]' command with '[red:27t8jes7]preserve[/red:27t8jes7]' set to TRUE or FALSE, it would be helpful to be concrete by using examples. More specifically, you start with a structure in PDB format, and try to mutate a base to another one -- you have two results by setting '[red:27t8jes7]preserve[/red:27t8jes7]' to either TRUE or FALSE. If you attach these three PDB files, then things would be much clearer even for those who are not familiar with the UCSF chimera software.

Xiang-Jun

[subramanian]

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

[xiangjun]

Hi,

Thanks for attaching the three PDB files -- they indeed clarify the issues.

Do you know the rationale of the no preserve option? It appears there can be many ways to rotate around the glycosidic bond to orient the base.

Xiang-Jun

[subramanian]

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