Relieving ring strain
For a 5-membered ring with perfectly tetrahedral geometry of each atom in the ring, there is some strain if the ring were planar (355 degree rotation around the ring instead of 360). To relieve the strain, one or two atoms move out of the plane. The conformation with one atom out of the plane is called envelope (endo or exo depending on whether the atom is above or below the plane). The conformation with two consecutive atoms out of the plane, one above and one below, is called twist. More than two atoms are never out of plane because the remaining three atoms always define a plane.
Describing conformations with a pseudorotation angle
To classify conformations unambiguously, the pseudorotation angle and amplitude are used. There are two definitions in the literature that lead to very similar results.[1] Once the pseudoration angle is calculated, you can name the conformation and plot it in a pseudorotation diagram (see e.g. [2]).
Conformations of ribose rings
The two most common conformations are C3' endo and C2' endo. For ribose, endo refers to the side of the glycosidic bond (i.e. the direction of the nucleobase in nucleosides). It is also the direction of the 5'-OH group, whereas the 2'-OH and the 3'-OH are on the exo side. The animation shows a morph between a conformation. Use the buttons to toggle groups attached to the ring. Note how the distance between the 5'-OH and 3'-OH groups (or that of the attached phosphates, if displayed) changes when the conformation changes.
B-DNA vs A-DNA
