Fig. 56. Schematics of DNA-templated cyanine (Cy) aggregates and associated optical spectra. (A) Type 1 DNA–dye constructs formed by mixing two complementary Cy5-labeled oligonucleotide strands in an aqueous buffer solution in the absence (left) and presence (right) of added MgCl2. Duplex DNA is the primary nanostructure in the absence of added MgCl2, whereas DNA HJs are formed when MgCl2 is added. There is one Cy5 dye per strand, and therefore, the duplex and HJ template the aggregation of a Cy5 dimer and tetramer, respectively. (B) Normalized absorption spectra of the duplex dimer and “mobile” HJ tetramer. The lower part of panel (B) depicts schematic illustrations of the duplex dimer and HJ tetramer, where cyan circles indicate the approximate location of Cy5 dyes. (C) Type 2 DNA–dye constructs formed by mixing four mutually complementary oligonucleotide strands in an aqueous buffer solution with MgCl2 added. The solutions primarily consist of “immobile” HJs. Cy5 dyes are covalently tethered to two, three, or four positions within the HJ. (D) Normalized absorption spectra of the two dimer species (adjacent and transverse), trimer, and tetramer formed via “immobile” Hjs. The lower part of panel (D) depicts schematic illustrations of the dimer, trimer, and tetramer structures, where cyan circles indicate the approximate location of Cy5 dyes. The schematic depictions of the dye-labeled duplex and HJ structures are not meant to imply specific geometric configurations of the dye or DNA backbone. Reproduced with permission from ref. 402 Copyright 2021 American Chemical Society.
