Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity

Abstract

DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the optical properties and associated electronic structures of these materials, less is known about their excited-state dynamics. For example, little is known about how the excited-state lifetime, a parameter essential to many applications, is influenced by structural factors, such as the number of dyes within the aggregate and their spatial arrangement. In this work, we use a combination of transient absorption spectroscopy and global target analysis to measure excited-state lifetimes in a series of DNA-templated cyanine dye aggregates. Specifically, we investigate six distinct dimer, trimer, and tetramer aggregates—based on the ubiquitous cyanine dye Cy5—templated using both duplex and Holliday junction DNA nanostructures. We find that these DNA-templated Cy5 aggregates all exhibit significantly reduced excited-state lifetimes, some by more than 2 orders of magnitude, and observe considerable variation among the lifetimes. We attribute the reduced excited-state lifetimes to enhanced nonradiative decay and proceed to discuss various structural factors, including exciton delocalization, dye separation, and DNA heterogeneity, that may contribute to the observed reduction and variability of excited-state lifetimes. Guided by insights from structural modeling, we find that the reduced lifetimes and enhanced nonradiative decay are most strongly correlated with the distance between the dyes. These results inform potential tradeoffs between dye separation, excitonic coupling strength, and excited-state lifetime that motivate deeper mechanistic understanding, potentially via further dye and dye template design.

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

“…Atomic charges for the dyes were calculated using the HF/6-31G* theory level [ 80 ]. The 26-basepair dsDNA duplex sequence and dye locations from Huff et al [ 29 ] was used. The dye–DNA structures were solvated in TIP3P water [ 81 ] in a truncated octahedron box with 1.2 nm between the dye–DNA structure and the box edge.…”

“…Mg 2+ ions were used to neutralize the system. Cannon et al and Huff et al showed, experimentally, that by adding excess MgCl 2 to solutions containing DNA duplexes with two pentamethine indocyanine Cy5 dyes, DNA Holliday junctions could be formed [ 28 , 29 ]. Because of this, no excess MgCl 2 was used in the MD simulations apart from replacing a necessary number of water molecules with Mg 2+ to achieve neutral charge.…”

“…One method of facilitating dye aggregation in a controlled and predictable manner is using DNA scaffolds. Dyes attached to DNA scaffolds, such as duplexes, Holliday junctions, and origami, have been shown to aggregate into dimers, trimers, and tetramers [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. Characterization of the optical properties of the aggregates reveals that the dyes can adopt various ideal orientations [ 22 , 24 , 26 , 40 ].…”

Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates

“…To gain additional insights into packing and coupling in the transverse dimer, we modeled its absorption and CD spectra. Specifically, we employed an approach based on Kühn–Renger–May (KRM) theory, 65 which we have previously used to derive information about packing and coupling in dimer, trimer, and tetramer aggregates of Cy5, 25 , 40 , 46 Square-660 (an indolenine-based squaraine), 52 and SeTau-670 (an aniline-based squaraine rotaxane). 38 Consistent with our expectations of H-aggregation, the modeling indicates that the “oblique” angle, α, between dyes (as the TDM is oriented along the long axis of the dye) is ∼22° ( section S9 ).…”

“…More broadly, the results indicate that the transverse heterodimer solution is heterogeneous and includes a small subpopulation of monomers, likely as a result of either static or dynamic heterogeneity. 25 Here, because of the optical selectivity of the constituent dye monomers, such heterogeneity—albeit not a major contributor for the 615 nm pumping experiment—is immediately apparent when pumping the transverse dimer solution at 650 and 690 nm.…”