Fig. 10. Molecular dynamic (MD) analysis of a DNA block scaffolded multi-dye structure. (A) Dye positions as estimated from the MD simulation with the small spheres representing the dyes. In the ideal crystal the planes would be flat and the vertical lines (that approximate every other constituent duplexes in the block) would be straight. The axes dimensions are in nm. See Fig. 27 for a schematic of the structure. MD estimated distribution of (B) distances and (C) dipole orientation factor between a central Cy3.5 and the plane of Cy5.5 dyes. Reproduced with permission from ref. 103 Copyright 2021 American Chemical Society.
