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 simple geometric concept. Nevertheless, the N-glycosidic bond and the corresponding χ torsion angle illustrate that the base and the 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 (as applied to RNA) 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 of the two bases in a pair, characterized explicitly in 3DNA as of type M+N or M–N since the 2003 NAR paper (Figure 2, linked below). I re-emphasized 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 that the simplicity of this explicit distinction and the resultant full quantification of each and every possible base pair using standard geometric parameters will gradually be appreciated.
As of 3DNA v2.1, the output of the χ torsion angle is also associated with its classification in anti / syn conformation, among other new features (see for example the output for 6tna).
