A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 31-May-2023 number of released structures: 12820
Search for released structures

Correspondence of Leontis/Westhof names to Saenger numbering*

  Proposed nomenclature Saenger Recent designation
1. Cis Watson–Crick/Watson–Crick G·A cis W.C./W.C. VIII GA Imino
C·C cis W.C./W.C. (wobble)   CC N3(+)-carbonyl, amino-N3
G·U cis W.C./W.C. (wobble) XXVIII  
U·C cis W.C./W.C. XVIII UC 4-carbonyl-amino
U·U cis (wobble) W.C./W.C. XVI UU imino-carbonyl
2. Trans Watson–Crick/Watson–Crick A·U trans W.C./W.C. XXI AU Reverse Watson–Crick
A·A trans W.C./W.C. I AA N1-amino, symmetric
G·G trans W.C./W.C. III GG N1-carbonyl, symmetric
G·C trans W.C./W.C. XXII GC Reverse Watson–Crick
· trans W.C./W.C. XXVI AC Reverse Wobble
· trans W.C./W.C. XXVII GU Reverse Wobble
· trans W.C./W.C. XVII  
· trans W.C./W.C. XIV, XV  
· trans W.C./W.C. XII, XIII UU 4(2)-carbonyl-imino, symmetric
3. Cis Watson–Crick/Hoogsteen G·G cis W.C./Hoogsteen VI GG N1-carbonyl, N7-amino
U·A cis W.C./Hoogsteen XXIII AU Hoogsteen
G·A cis W.C./Hoogsteen   GA N1-N7, carbonyl-amino
A+·G cis W.C./Hoogsteen   GA+ carbonyl-amino, N7-N1
4. Trans Watson–Crick/Hoogsteen A·A trans W.C./Hoogsteen V AA N7-amino
G·G trans W.C./Hoogsteen VII GG N7-imino
U·A trans W.C./Hoogsteen XXIV AU Reverse Hoogsteen
C·A trans W.C./Hoogsteen XXV AC Reverse Hoogsteen
5. Cis Watson–Crick/Sugar-edge A·G cis W.C./Sugar-edge   GA N3-amino (1 bond)
A·U cis W.C./Sugar-edge   AU amino-2-carbonyl
6. Trans Watson–Crick/Sugar-edge A·G trans W.C./Sugar-edge X GA N3-amino, amino-N1
A·U cis W.C./Sugar-edge   GC N3-amino, amino-N3
7. Cis Hoogsteen/Hoogsteen      
8. Trans Hoogsteen/Hoogsteen A·A trans Hoogsteen/Hoogsteen II AA N7-amino, symmetric
10. Trans Hoogsteen/Sugar-edge A·G trans Hoogsteen/Sugar-edge XI GA Sheared
A·A trans Hoogsteen/Sugar-edge   AA N3-amino
C·U trans Hoogsteen/Sugar-edge   UC 2-carbonyl-amino (1 bond)
12. Trans Sugar-edge/Sugar-edge G·G trans Sugar-edge/Sugar-edge IV GG N3-amino, symmetric

Correspondence of proposed names to the numbering of Saenger (1984) and the nomenclature used in a recent compilation (Nagaswamy et al., 2000).

* Leontis N, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs.
  RNA 7:499-512.