Problems with mutations on DNA

[lolthedoctor]

Hi 3DNA users and xiangjun in particular for your effort to make possible to use 3DNA and to discuss about possible problems and solutions.
I'm trying to use 3DNA to mutate one base pair of a protein-DNA complex, but I don't understand how to make this operation, if possible.
I have tried the examples and the tutorial, but there I haven't found any similar example.
I have just the template structure with the double strand sequence GCGT and I want, for example, to mutate the base pair CG with TA but I haven't found a similar example in the tutorial or in the examples.                                                                                   CGCA
Anyone uses/used 3DNA for this particular operation? COuld you please give me an advice about this work?
Thank you!
Rubben

[xiangjun]

I have just the template structure with the double strand sequence GCGT and I want, for example, to mutate the base pair CG with TA but I haven't found a similar example in the tutorial or in the examples.

Conceivably, there are two ways to do what you want with 3DNA:

• Use the "[mono:2j91smsb]analyze/rebuild[/mono:2j91smsb]" pair, as follows (assuming your PDB file is named [mono:2j91smsb]sample.pdb[/mono:2j91smsb]):
  [pre:2j91smsb]find_pair sample.pdb stdout | analyze
  [red:2j91smsb]# In addition to sample.out file, the above will also generate a text file named "bp_step.par".
  # Manually edit it as you see fit, e.g., change a C-G pair to T-A, and name it "new_step.par"[/red:2j91smsb]
  rebuild -atomic new_step.par sample_new.pdb
  [red:2j91smsb]# Refer to FAQ #5 if you want to build a structure with sugar-phosphate backbone.[/red:2j91smsb][/pre:2j91smsb]
  If you have many mutations to perform, it should be straightforward to write a script to automate the process. The possible issue with this approach is that the sugar-phosphate backbone conformation is approximate, and will certainly be different from what you start with.
  
• For a more general approach where the backbone is kept untouched, see the thread "mutating DNA in DNA protein complex". The problem here is that the procedure is not automated (yet). Three years later, I still have the same question:
  

  ... the possibility of performing base mutations while keeping the backbone unchanged. Given this is such a common and clearly defined function, it is hard to imagine there is no such a handy standalone utility program from so many other resources to get the job done. Am I missing something here?

  I'd consider to write a script to automate the task, if there is still enough interest in this functionality and no other available tools are handy enough for this task.

Alternatively, another tool you could try is mutateNA.pl within MMTSB.

HTH, and I hope to see your feedback.

Xiang-Jun
(added June 5, 2011):
Please see the thread "change one base pair in a double-strand DNA structure file"
where the Perl script mutate_bp and the ANSI C program mutate_bases are introduced.

[lolthedoctor]

Thank you xiangjun for your very exhaustive explanation..
I need to perform a lot of mutation so perhaps I need to make a script to make this process automatic..
Thank you again for all the suggestions and I promise you to update about my progresses..