Control of Indodicarbocyanine Dimer Geometry Using Variable-Length Linkers to DNA Scaffolds

In recent years, DNA scaffolds have been utilized to organize dye molecules into aggregates with tailored optical and photophysical properties. While dye separation can be controlled with nanometer-scale accuracy, controlling the relative dye orientation in an aggregate on DNA remains challenging. In this work, we investigate varying the length of the two-point linker between indodicarbocyanine (Cy5) dyes and the DNA template as a method to better control the resulting dimer geometry. To test this approach, we synthesize Cy5 with either 2-carbon or 4-carbon two-point linkers and compare their behavior to commercially available Cy5 with 3-carbon two-point linkers. Using experimental spectroscopy, theoretical modeling, and molecular dynamics simulations, we demonstrate that shortening the linker from 3-carbon to 2-carbon limits the π–π interactions between dyes, thereby promoting the formation of J-like Cy5 dimers. Conversely, increasing the linker length provides the dye more freedom of motion, allowing greater π–π interactions and yielding dimers with greater H-like character. Furthermore, shorter linkers can restrict dye accessible volume, which, under the driving force of π–π interactions, suppresses heterogeneity in dye packing for specific placements of Cy5 on double stranded DNA and DNA Holliday junction scaffolds. These results emphasize the importance of dye linker chemistry in determining important optical and photophysical properties of DNA-scaffolded dye aggregates. They also suggest that tuning the length of the dye linker is an effective strategy to overcome two challenges that currently limit DNA-scaffolded dye aggregates in photonics applications: gaining control of dye aggregate geometry and suppressing heterogeneity in dye packing.