A pinboard by
James Banal

Postdoctoral Research Associate, Massachusetts Institute of Technology


Creating synthetic light-harvesting units mimicking photosynthesis using DNA

Photosynthetic light-harvesting is a hallmark for nanoscale engineering of chromophores to achieve efficient photon absorption, transport, and energy conversion. The orientation, precise localization, and separation of these pigments are determined by the association of the pigments to protein scaffolds. The hierarchical and dense molecular organization of photosynthetic pigments lead to the formation of a manifold of delocalized excited states useful for long-range energy transfer. Creating artificial light-harvesting devices that implement the design principles of pigment organization typically found in photosynthetic light-harvesting systems requires a scaffold that can control the formation of chromophore aggregates in a robust manner. DNA is a potential scaffold to assemble light-harvesting units due to its programmable sequence design. This sequence programmability allows for precise positioning of dyes in space. Assembling light-harvesting units can be further extended into more complex structures through DNA origami — a method by which a large piece of DNA is being folded into specific shape by short complementary DNA strands. Combining the sequence precision of DNA with the ability to create arbitrary geometric shapes using DNA origami, a myriad of exciton networks can be designed and investigated, similar to a nanoscale breadboard, which can provide insight to nanoscale light-harvesting and energy transport in unprecedented detail.


Self-assembled nanoscale DNA-porphyrin complex for artificial light harvesting.

Abstract: Mimicking green plants' and bacteria's extraordinary ability to absorb a vast number of photons and harness their energy is a longstanding goal in artificial photosynthesis. Resonance energy transfer among donor dyes has been shown to play a crucial role on the overall transfer of energy in the natural systems. Here, we present artificial, self-assembled, light-harvesting complexes consisting of DNA scaffolds, intercalated YO-PRO-1 (YO) donor dyes and a porphyrin acceptor anchored to a lipid bilayer, conceptually mimicking the natural light-harvesting systems. A model system consisting of 39-mer duplex DNA in a linear wire configuration with the porphyrin attached in the middle of the wire is primarily investigated. Utilizing intercalated donor fluorophores to sensitize the excitation of the porphyrin acceptor, we obtain an effective absorption coefficient 12 times larger than for direct excitation of the porphyrin. On the basis of steady-state and time-resolved emission measurements and Markov chain simulations, we show that YO-to-YO resonance energy transfer substantially contributes to the overall flow of energy to the porphyrin. This increase is explained through energy migration along the wire allowing the excited state energy to transfer to positions closer to the porphyrin. The versatility of DNA as a structural material is demonstrated through the construction of a more complex, hexagonal, light-harvesting scaffold yielding further increase in the effective absorption coefficient. Our results show that, by using DNA as a scaffold, we are able to arrange chromophores on a nanometer scale and in this way facilitate the assembly of efficient light-harvesting systems.

Pub.: 29 Jan '13, Pinned: 07 Jun '17

Achieving effective terminal exciton delivery in quantum dot antenna-sensitized multistep DNA photonic wires.

Abstract: Assembling DNA-based photonic wires around semiconductor quantum dots (QDs) creates optically active hybrid architectures that exploit the unique properties of both components. DNA hybridization allows positioning of multiple, carefully arranged fluorophores that can engage in sequential energy transfer steps while the QDs provide a superior energy harvesting antenna capacity that drives a Förster resonance energy transfer (FRET) cascade through the structures. Although the first generation of these composites demonstrated four-sequential energy transfer steps across a distance >150 Å, the exciton transfer efficiency reaching the final, terminal dye was estimated to be only ~0.7% with no concomitant sensitized emission observed. Had the terminal Cy7 dye utilized in that construct provided a sensitized emission, we estimate that this would have equated to an overall end-to-end ET efficiency of ≤ 0.1%. In this report, we demonstrate that overall energy flow through a second generation hybrid architecture can be significantly improved by reengineering four key aspects of the composite structure: (1) making the initial DNA modification chemistry smaller and more facile to implement, (2) optimizing donor-acceptor dye pairings, (3) varying donor-acceptor dye spacing as a function of the Förster distance R0, and (4) increasing the number of DNA wires displayed around each central QD donor. These cumulative changes lead to a 2 orders of magnitude improvement in the exciton transfer efficiency to the final terminal dye in comparison to the first-generation construct. The overall end-to-end efficiency through the optimized, five-fluorophore/four-step cascaded energy transfer system now approaches 10%. The results are analyzed using Förster theory with various sources of randomness accounted for by averaging over ensembles of modeled constructs. Fits to the spectra suggest near-ideal behavior when the photonic wires have two sequential acceptor dyes (Cy3 and Cy3.5) and exciton transfer efficiencies approaching 100% are seen when the dye spacings are 0.5 × R0. However, as additional dyes are included in each wire, strong nonidealities appear that are suspected to arise predominantly from the poor photophysical performance of the last two acceptor dyes (Cy5 and Cy5.5). The results are discussed in the context of improving exciton transfer efficiency along photonic wires and the contributions these architectures can make to understanding multistep FRET processes.

Pub.: 13 Jul '13, Pinned: 07 Jun '17