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. 2008 May 30;95(6):2711–2721. doi: 10.1529/biophysj.107.126243

FIGURE 2.

FIGURE 2

Structures of AlexaFluor dyes. The geometry-optimized structures found in ab initio calculations are shown for (A) AF488 and (B) AF568. The direction of the transition moment is indicated by the arrow. (C) The length of the dyes, measured from the central oxygen in the headgroup to the furthest carbon in the linker is plotted during simulations in which AF488 (black) or AF568 (red) is immersed in water. Compact structures sampled during the molecular dynamics simulations are shown for (D) AF488 and (E) AF568.