3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: liu4gre on September 10, 2010, 11:42:10 am

Title: single-stranded base stacking
Post by: liu4gre on September 10, 2010, 11:42:10 am: currently I am using your 3DNA software to analyse the 3D structure of RNA. I am wondering if this software provides the information of possible single-stranded base stacking? Thanks.
Title: Re: single-stranded base stacking
Post by: temizna on September 10, 2010, 02:17:31 pm: Hi Liu,

If you check the web3DNA site and enter a single stranded DNA/RNA PDB file such as 1S40 ( a SS DNA/protein complex) you will see that 3DNA can analyze a single stranded nucleic acid structure. Also check Lu's Nature Methods Paper for an example of how to analyze/make figures of base stacking.

Have fun,
Alpay
Title: Re: single-stranded base stacking
Post by: xiangjun on September 10, 2010, 11:28:18 pm: Quote from: "liu4gre"
I am wondering if this software provides the information of possible single-stranded base stacking?
In addition to what Alpay has suggested, you can also run 3DNA as follows:

Code: [Select]
find_pair -s your.pdb stdout | analyzewhich will generates a file named [mono:3vpvq2pu]your.outs[/mono:3vpvq2pu], containing overlap areas between neighboring base rings. As an example, see "RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions (http://http://www.ncbi.nlm.nih.gov/pubmed/20726568)" by Mohan et al. (J Am Chem Soc. 2010 Sep 15;132(36):12679-89).

Note that under the hook, w3DNA calls exactly the above commands.

HTH,

Xiang-Jun