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Nucleic Acids Research, 2000, Vol. 28, No. 1 375-376
© 2000 Oxford University Press

Database of non-canonical base pairs found in known RNA structures

Uma Nagaswamy, Neil Voss, Zhengdong Zhang and George E. Fox*

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5934, USA

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson–Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/ , contains infor-mation such as sequence context, sugar pucker conformation, anti/syn base conformations, chemical shift, pKa values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

* To whom correspondence should be addressed. Tel: +1 713 743 8363; Fax: +1 713 743 8351; Email: frox@uh.edu


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