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Topics - Randy Bin Lin

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this is a step-by-step recipe about how to use 3dna to build a dna bulge based on a PDB structure and extend its sequence at both terminals. this is a collection of two posts and with much help from Xiang-Jun. Kudos to you!

here's the objective: PDB 1AX6 ( is a dna bulge of -2 deletion with its sequence as CTCGATGCCATC. I wish to build a similar dna bulge with CT at 5' terminal and AC at 3' terminal as extra. two things worth noting: the first is to preserve the backbone conformation (esp. the bulge region as solved by NMR in the PDB file). the second is essentially how to extend dna duplex (B-DNA in my case). I am sure there are many other ways to do the job (let me know if you know what they are). here's the way I used 3dna to achieve my goal.

1. use find_pair to generate ref_frames.dat for each base pair in 1ax6:
find_pair 1ax6.pdb stdout

2. re-orient 1ax6 based on the reference frame of its first 5' base pair, generate canonical B-DNA of CTC, re-orient it based on the reference frame of its last 3' base:
frame_mol -1 ref_frames.dat 1ax6.pdb 1ax6_ref_frames5.pdb
fiber -b -seq=ctc ctc.pdb
find_pair ctc.pdb ctc.bps
frame_mol -3 ref_frames.dat ctc.pdb ctc_ref_frames5.pdb

3. after step 2, 1ax6_ref_frames5.pdb and ctc_ref_frames5.pdb should superimpose based on the common base pair. cut the coordinates of CT in ctc_ref_frames5.pdb into 1ax6_ref_frames5.pdb and name the new pdb file as 1ax6_extend5.pdb. our sequence has two extra base pairs of CT at 5' terminal with canonical B DNA conformation matching that in 1ax6

4. do the same for the 3' terminal
find_pair 1ax6_extend5.pdb stdout
frame_mol -12 ref_frames.dat 1ax6_extend5.pdb 1ax6_extend5_ref_frames3.pdb
fiber -b -seq=cac cac.pdb
find_pair cac.pdb cac.bps
frame_mol -1 ref_frames.dat cac.pdb cac_ref_frames3.pdb

5. the newly extended pdb at both 5' and 3' terminal is 1ax6_extend53.pdb

6. generate bp_step.par by treating the whole structure as a continuous single helix, this way the bulge of 2 bases is preserved.
find_pair -s 1ax6_extend53.pdb stdout | analyze stdin

7. rebuild dna structure with extended terminals and dna bulge of -2 deletion:
x3dna_utils cp_std BDNA
rebuild -atomic bp_step.par bulge-2-full-3dna.pdb

the dna bulge I meant to build has slightly different sequence from 1ax6. just use mutate_bases in 3dna package to do the job. it's omitted here. but should be easy to do. do that before the first step.

hope it helps! feel free to contact me at if you have any questions. or post to the forum, Xiang-Jun knows better and he should be able to answer them fairly quickly.

Randy Bin Lin

General discussions (Q&As) / extend dna duplex at both terminals?
« on: June 01, 2012, 11:37:11 pm »
I have a DNA duplex with coordinates. But there are two base pairs missing at both terminals. I hope to use 3DNA to add the missing base pairs while they still maintain the alpha helix of B-DNA. Is it possible to do it via 3DNA?

Randy Bin Lin

General discussions (Q&As) / build dna bulge via 3dna?
« on: May 30, 2012, 08:19:06 pm »
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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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.