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. Author manuscript; available in PMC: 2014 Feb 21.
Published in final edited form as: J Phys Chem A. 2013 Feb 12;117(7):1560–1568. doi: 10.1021/jp308364d

Figure 1.

Figure 1

Definitions of the vectors and centroid of the A) purine and B) pyrimidine bases used to describe the relative orientation of the stacked bases, including an illustration of stacked monomers. X-axis (red): C4 and N1 for purines or C6 and N3 for pyrimidines; Y-axis (blue): perpendicular axis to the x-axis in the plane of the base; and Z-axis (green): perpendicular vector to the plane of the base originating from the centroid of the reference base. The base centroid is the midpoint connecting C4 and N1 for purines or C6 and N3 for pyrimdines. Based on these definitions, risesm corresponds to the length of the green vector, both slidesm and shiftsm are zero, the twistsm angle is approximately −30° and both the tiltsm and the rollsm are 0°.