Base-stacking interactions stabilize nucleic acid structures. Many ways exist to account for such interactions, including quantum chemical calculations (see for example the review by Sponer et al. [2008] on Nature and magnitude of aromatic stacking of nucleic acid bases.). In 3DNA, base-stacking interactions are assessed from planar projections of the ring and exocyclic atoms in consecutive bases or base pairs; the larger the overlap area, the stronger the stacking interactions, and vice versa.

Over the years, I’ve seen a few publications taking advantage of this 3DNA parameter. Here are two recent ones:

• Tamjar et al. (2012). Structural dynamics of double-helical RNAs composed of CUG/CUG- and CUG/CGG-repeats. J Biomol Struct Dyn. 30(5), 505-23.

To analyze the role of the sequence regularity for the double-helical structure, we calculated the overall overlapping of base pairs (stacking) at every step of the two duplexes of 20mer pG(CUG)6C and the duplex of 19mer pGG(CGG)3(CUG)2CC using the program 3DNA (Lu & Olson, 2003).

• Halder & Bhattacharyya (2012). Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis. J Phys Chem B. 116(39), 11845-56.

Basepair overlap values are calculated by 3DNA software.35

Hopefully, more 3DNA users would notice this ‘little’ feature and make good use of it.