Figure 13.

Relationship between 2′-OH orientation and ribose pucker. (A) A 2′-OH with a ‘sugar orientation’ (shown here is a κ angle in an ideal 180° ap conformation) combined with a C2′-endo pucker precludes short contacts to ribose H atoms and allows H-bonding between 2′-OH and O3′ (green double arrow). (B) A 2′-OH with a ‘sugar orientation’ (as in panel A, the κ angle is in an ideal 180° ap conformation) combined with a C3′-endo pucker results in a short contact (yellow flash) and precludes H-bonding between 2′-OH and O3′ (red cross). Selected atoms are labeled and relevant distances are shown in Å. Please see also the correlation between sugar pucker and 2′-OH orientation in an early MD study of RNA (Figure 1, C3′-endo, and Figure 5, C2′-endo (19)).