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Author Topic: Meaning of base-pair id string e.g. 'U-**+-G'  (Read 2915 times)

Offline febos

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Meaning of base-pair id string e.g. 'U-**+-G'
« 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?

Offline xiangjun

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Re: Meaning of base-pair id string e.g. 'U-**+-G'
« Reply #1 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' 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 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".

HTH,

Xiang-Jun
« Last Edit: July 30, 2012, 08:36:31 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.