Quantifying base stacking interactions

[chubetty]

Hi Xiang-Jun,

I am analyzing the base stacking interactions, which I generated using the --non-pair option, in my DNA model. If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2? And would you define these numbers as area of overlap of the bases?

Thank you!

Betty Chu

[xiangjun]

Hi Betty,

If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2?

Yes, the unit is in Ų. The numbers outside () take consideration of the exocyclic atoms, while those within () use only the 6- (pyrimidines) or 9- (purines) membered base rings (polygons). You may use a Jmol/PyMOL or other molecular viewer to see how the numbers match intuitive observations.

And would you define these numbers as area of overlap of the bases?

Yes. The reported area is the overlapped polygon of the two corresponding rings projected onto the mean plane of the base normals.

Here is the relevant portion excerpt from the 2003 3DNA NAR paper:

The stacking interactions are quantified in 3DNA by the shared overlap area, in Ų, of closely associated base rings, i.e. the nine-membered ring of a purine R (A or G) and the six- membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. ... To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, ... an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1'-O2-N3-N4-C5-C6-C1' atomic sequence.

HTH,

Xiang-Jun