build dna bulge via 3dna?

[Randy Bin Lin]

I have been trying to build a DNA duplex with bulges with -1, -2 up to -3 deletion, such as in PDB 1AX6 (-2 deletion). I searched online, there is no protocol detailing how to build them in silico with desired DNA sequence. 3DNA and NAB are the two nucleic acid manipulation tool I have been using. but it is not obvious how to do it in both of them. Any advices on that? thanks!

[xiangjun]

Thanks for using 3DNA. As to your question "to build a DNA duplex with bulges with -1, -2 up to -3 deletion, such as in PDB 1AX6 (-2 deletion)", I do not think 3DNA can do the magic automatically in a general sense -- there are so many possible variabilities to introduce bulges with -1, -2 or -3 deletions. Nevertheless, some components of 3DNA can help to some extent in the modeling process:

• Starting from a known structure, e.g. 1ax6, you can use "mutate_bases" to change the bases to your desired DNA sequence while preserving the backbone conformation and base orientation.
• By using "find_pair -s your.pdb stdout | analyze stdin", (manually) editing the generated file "bp_step.par" and then running "rebuild -atomic", you can build any DNA structure with your prescribed sequence and step parameters, but only approximate sugar-phosphate backbone.

HTH,

Xiang-Jun

[Randy Bin Lin]

xiangjun, thank you for the suggestions. I will definitely give it a try. I will let you know how it goes.

Randy Bin Lin