RNA Basepair Families

No. Glycosidic Bond
Orientation		 Interacting Edges Symbol Default Local
Strand Orientation		 Link to Exemplars
1 Cis Watson-Crick/Watson-Crick Anti-Parallel
2 Trans Watson-Crick/Watson-Crick Parallel
3 Cis Watson-Crick/Hoogsteen Parallel
4 Trans Watson-Crick/Hoogsteen Anti-Parallel
5 Cis Watson-Crick/Sugar Edge Anti-Parallel
6 Trans Watson-Crick/Sugar Edge Parallel
7 Cis Hoogsteen/Hoogsteen Anti-Parallel
8 Trans Hoogsteen/Hoogsteen Parallel
9 Cis Hoogsteen/Sugar Edge Parallel
10 Trans Hoogsteen/Sugar Edge Anti-Parallel
11 Cis Sugar Edge/Sugar Edge Anti-Parallel
12 Trans Sugar Edge/Sugar Edge Parallel

1. Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512.  Abstract
2. Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497-3531. Abstract