Structure-based model for light-harvesting properties of nucleic acid nanostructures

Abstract

Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.

Spectroscopic studies of the mechanism of reversible photodegradation of 1-substituted aminoanthraquinone-doped polymers

“…Understanding the mechanism of energy transfer between dye and polymer will provide a new perspective to design desirable dye-doped polymer materials. For example, Förster resonance energy transfer theory has been applied to simulate the dynamics of dye excitation and energy transfer in nanostructured DNA-dye assemblies for light-harvesting applications [112]. The study in kinetics of reversible photodegradation of dye-doped polymers is currently ongoing.…”

Long‐Distance Electronic Energy Transfer in Light‐Harvesting Supramolecular Polymers

“…Polymeric and dendritic materials appear particularly promising in this context, due to the covalent joining of large numbers of light absorbing molecules. [24][25][26][27][28][29][30][31][32][33][34][35][36] Alternatively, DNA has been used as a supramolecular scaffold [37][38][39][40][41][42][43][44][45][46][47][48][49] for the construction and the study of light-harvesting antenna systems. We have recently reported on the assembly of water soluble linear [50,51] and two-dimensional [52] supramolecular polymers [53][54][55][56][57] from short amphiphilic pyrene oligomers (oligopyrenotides).…”

Implementation of Probabilistic Algorithms by Multi‐chromophoric Molecular Networks with Application to Multiple Travelling Pathways

“…Figures C and D show the total arrival probability, the maximum value of the probability density and the corresponding arrival time starting from the two different locations (Paris or Milan) as a function of the distance between the Yellow and the Red chromophores r . The modulation of this distance is only one of the parameters that can be changed to simulate several situations affecting the relative transfer rates . Other distances, the chemical nature of the chromophores, the presence of quenchers and changes in the chemical environment represents other controllable parameters that can be used to program the Markov chain that is implemented by the system.…”