3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: febos on July 18, 2012, 10:48:33 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: Meaning of base-pair id string e.g. 'U-**+-G'
Post by: febos on July 18, 2012, 10:48:33 am
I'm sorry, but I don't have a list of problematic helices for these files. But, instead, I have a new question for you :). Could you please explain what symbols '*' and '+' mean in descriptions of bonds (for example 'U-**+-G')?. Again, I'm sorry if this question had been already discussed. I need to know which bonds can roughly be considered as WC-pairs. For example which of these pairs: A-*---U;A-**--U; A-**+-U - can I consider as A-----U?
Title: Re: Meaning of base-pair id string e.g. 'U-**+-G'
Post by: xiangjun on July 18, 2012, 11:13:04 am
Thanks for your new question :). I have split this post from the original thread 'Helices and Isolates in output of find_pair (http://forum.x3dna.org/general-discussions/helices-and-isolates-in-output-of-find_pair/)' to make each one focused on a specific topic, and not too lengthy.

I am sure I've answered this question before, maybe through priviate emails. I'll write a post on this issue on the 3DNA homepage (http://x3dna.org/articles/specification-of-base-pairs-in-3dna) soon [link added on 2012-07-30]. Here is the short answer to your question:

The general patten of a base-pair id string is M-XYZ-N for bases M and N. Only when XYZ equals --- would M and N be a possible Watson-Crick pair. If Z is '+', the two z-axes of bases are pointing the same direction and thus have a positive dot product. See my post "Hoogsteen and reverse Hoogsteen base pairs (http://x3dna.org/highlights/hoogsteen-and-reverse-hoogsteen-base-pairs)".

HTH,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.