3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: xiaolei on May 14, 2017, 11:25:11 am

Title: global DNA curvature analysis
Post by: xiaolei on May 14, 2017, 11:25:11 am: Dear Dr. Lu,
I know you have answered many times in the topic of how to calculate global DNA curvature, as my background is largely biology with almost none computational background, I feel hard to understand when you explain it in a computational or mathematical way about this topic in the forum. I am asking simply that: Is it a way to input a protein/DNA complex structure coordinate (PDB) into w3DNA server or 3DNA program on user's computer and get a global DNA curvature (DNA bending) results, for example such as in protein/DNA complexes papers phrases like "The X-ray structure shows that the DNA is bent overall to 17 􏰆degree", I'd like to know how to get the overall bent number ( the "17 degree" in my example) from w3DNA or 3DNA program.

Thanks ahead!
Title: Re: global DNA curvature analysis
Post by: xiangjun on May 14, 2017, 11:45:55 am: Does the FAQ item "How to calculate DNA bending angle?" (http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/) help? See also the 2008 3DNA Nature Protocols paper which contains a concrete example with detailed script/datafile on exectly this topic.

HTH,

Xiang-Jun
Title: Re: global DNA curvature analysis
Post by: bciezah1 on July 17, 2017, 04:03:35 pm: Dear Dr. Xiang-Jun,

I hope this email finds you well. I have a question. I was a following the 3DNA USER GUIDE (http://www.csb.yale.edu/userguides/datamanip/3dna/x3dna.pdf), by the way is very useful, and in page 14 I found this statement: The G+C rich end adopts the A-DNA conformation while the A+T rich part has the B-DNA conformation. As a consequence, this DNA is non-linear, i.e., curved. . Regarding this statement, the USER GUIDE refers to the work of Pouderoyen et al (1997) but I reviewed the paper and they did not mentioned this statement. I wonder if maybe you can give me a reference about this statement please, to be honest, for my work this information will be very important.

Thank you very much,

Basilio.
Title: Re: global DNA curvature analysis
Post by: xiangjun on July 17, 2017, 06:38:33 pm: Hi Basilio,

I'm surprised to know that Yale is still holding a version of the 3DNA v1.5 User Manual I wrote well more than ten years ago.

The Pouderoyen et al.publication (https://www.ncbi.nlm.nih.gov/pubmed/9312061) referred to there is about 1tc3 (http://www.rcsb.org/pdb/explore/explore.do?structureId=1tc3), which contains a A-B junction. See also the paper "A-form conformational motifs in ligand-bound DNA structures (https://www.ncbi.nlm.nih.gov/pubmed/10891271)" where 1tc3 is analyzed from a different perspective.

HTH,

Xiang-Jun
Title: Re: global DNA curvature analysis
Post by: bciezah1 on July 17, 2017, 07:18:52 pm: Really nice paper! Thank you very much!

Best wishes,

Basilio.