Chi (χ) torsion angle characterizes base/sugar relative orientation

Except for pseudouridine, a nucleoside in DNA/RNA contains an N-glycosidic bond that connects the base to the sugar. The chi (χ) torsion angle, which characterizes the relative base/sugar orientation, is defined by O4'-C1'-N1-C2 for pyrimidines (C, T and U), and O4'-C1'-N9-C4 for purines (A and G).

Normally (as in A- and B-form DNA/RNA duplex), χ falls into the ranges of +90° to +180°;  –90° to –180° (or 180° to 270°), corresponding to the anti conformation (Figure below, top). Occasionally, χ has values in the range of –90° to +90°, referring to the syn conformation (Figure below, bottom). Note that in left-handed Z-DNA with CG repeating sequence, the purine G is in syn conformation whilst the pyrimidine C is anti.

Presumably, the χ-related anti/syn conformation is a very basic and simple concept. In essence, though, the N-glycosidic bond and the corresponding χ torsion angle illustrate that the base and sugar are two separate entities, i.e. there is an internal degree of freedom between them. In this respect, it is worth noting that the Leontis-Westhod sugar edge for base-pair classification corresponds to the anti form only. When a base is flipped over into the syn conformation,  the "sugar edge", defined in connection with the minor (shallow) groove side of a nitrogenous bases, simply does not exist.

Base-flipping (anti/syn conformation switch) is one of the factors associated with the two possible relative orientations in a base pair, characterized explicitly in 3DNA as of type M+N or M–N since the 2003 NAR paper (Figure 2, linked below). I reemphasized this distinction in our 2010 GpU dinucleotide platform paper (in particular, see supplementary Figure S2). Unfortunately, this subtle (but crucial, in my opinion) point has never been taken seriously (or at all) by the RNA community, even with 3DNA's wide adoption. However, as people know 3DNA deeper/better and take RNA base-pair classification more rigorously, I have no doubt they will begin to appreciate the simplicity of this explicit distinction and the resultant full quantification of each and every possible base pair using standard geometric parameters.

On a related issue, current versions of 3DNA (v1.5 and v2.0) output only the χ torsion angle without providing the anti/syn classification. This defect, and many others, will hopefully be rectified in future releases of 3DNA.