Leontis / Westhof Classification Legend

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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)
5. Cis Watson–Crick/Sugar-edge	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
6. Trans Watson–Crick/Sugar-edge	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.