Fig. 5. DNA modification and multidye placement on increasingly complex structures. (A) ssDNA synthesized to display a primary amine (internal universal-link amino modifier) on the end of a 4 carbon linker. This would then be labeled by amino-reactive dyes such as those functionalized with N-hydroxysuccinimidyl esters. Other common groups inserted for chemical modification are also listed. (B) Dye (pink) insertion into complementary strands with the number of bps separating the dyes indicated to highlight the effect of dsDNA (silver) twist (C) Dye placement highlighted on increasing larger and complex DNA structures including a 1D ds, a 2D HJ, and a 3D DNA brick-based structure where the dyes are found across an internal plane. Models in (B) and (C) were created in UCSF Chimera.¹⁰².