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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!
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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 (http://forum.x3dna.org/programs/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 (http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/).
HTH,
Xiang-Jun
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xiangjun, thank you for the suggestions. I will definitely give it a try. I will let you know how it goes.
Randy Bin Lin
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University