areas of the polygons used to calculate base overlap

[bhmmooers]

Dear Xiang-Jun,

What are the areas (with and without the exocyclic atoms) of the polygons used to calculate base overlap?
I failed to find these values in the user manual (v. 1.5) or on the forum.

Best regards,

Blaine
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center

[xiangjun]

Hi Blaine,

Thanks for using 3DNA and posting on the Forum. The following is quoted from the 2003 3DNA NAR paper. Hopefully, it would answer your question.

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. For example, the overlap areas between base rings on the left strands of the dimer steps shown in Figure 6 are 0.63 Ų (C3···G2), 0 Ų (G4···C3) and 1.11 Ų (A5···G4). To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, e.g. the overlap of the amino N4 atom of residue C3 with the five‐membered pyrrole ring of base G2 in Figure 6, 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. The overlap areas of the bases on the left strand of Figure 6 increase, respectively, to 2.95, 2.66 and 3.94 Ų when these and other exocyclic atoms are included in the calculations. The sum of the intra‐ and inter strand stacking overlaps is provided for each dinucleotide step in the 3DNA output.

Best regards,

Xiang-Jun