As we all know, thermodynamic parameters for all possible double-helical nearest neighbors of Watson-Crick and GU wobble pairs have been determined by Turner's group. And, they also gave the thermodynamic values for the nearest neighbor interactions of terminal mismatches. However, I can not find the parameters for mismatches but not the terminal ones. Now, I need some parameters for mismatches, and what should I do? Could you help me? Thanks very much.
Please take a look here:
Kierzek et al., Biochemistry. 1999 Oct 26;38(43):14214-23
http://www.ncbi.nlm.nih.gov/pubmed/10571995
and here: Davis & Znosko, Biochemistry. 2007 Nov 20;46(46):13425-36
http://www.ncbi.nlm.nih.gov/pubmed/17958380
To Anna Pasternak,
Thank you very much for your answer. I have read the two papers, as well as other works about single/tandem (GA , AA or other) mismatches in internal loops. Yes, they are very helpful for me. However, is there some parameters, which is like the parameters for nearest neighbors of Watson-Crick and GU wobble pairs, could be used directly to predict RNA structures?
To the best of my knowledge the parameters published in:
Davis & Znosko, Biochemistry. 2007, 46,13425-36
and
Davis & Znosko, Biochemistry. 2010, 49, 8669
are rather the only detailed parameters concerning contributions of single, internal mismatches, and are really helpful to predict thermodynamic stability of mismatched duplexes.
If you will find some other papers with such comprehensive thermodynamic data for internal mismatches, then please just let me know :)
Good luck!
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