single-stranded base stacking

[liu4gre]

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.

[temizna]

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

[xiangjun]

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" 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