Sequence-Directed Control of Cyanine Dye Stacking Geometry within DNA Duplexes

High Resolution Image Download MS PowerPoint Slide The photophysical properties of dye aggregates are governed by their supramolecular stacking geometries, such as H- and J-type arrangements. Structural DNA nanotechnology provides a programmable platform for the spatially precise organization of chromophores, yet how nearest-neighbor base-pair sequences specifically regulate dye-stacking modes remains unclear. Here, we demonstrated that the nearest-neighbor base-pair sequence within a DNA duplex functions as a sequence-encoded regulator that directs the stacking geometry of covalently tethered cyanine-dye dimers. By systematically varying the local base-pair environment adjacent to internally incorporated Cy5 and Cy3 dyes, we show that C/G neighbors bias Cy5 dimers toward H-type cofacial stacking, whereas A/T base pairs promote J-type head-to-tail arrangements, and C/T neighboring sequences promote an oblique stacking geometry. In contrast, Cy3 dimers predominantly adopt J-type configurations irrespective of sequence context, revealing a pronounced dye-dependent selectivity in how local sequence controls stacking. These findings indicate that DNA can function not only as a passive scaffold but also as an active, sequence-dependent microenvironment that modulates supramolecular order through nearest-neighbor variation, providing a minimal and predictive strategy for engineering excitonic nanomaterials with tunable optical and chiroptical properties.