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.
Abstract: The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological “nanomachines” in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks.
Pub.: 23 Feb '16, Pinned: 29 Jun '17
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
Abstract: The extent of photon energy transfer through individual DNA-based molecular wires composed of five dyes is investigated at the single molecular level. Combining single-molecule spectroscopy and pulse interleaved excitation imaging, we have directly resolved the time evolution spectral response of individual constructs, while simultaneously probing DNA integrity. Our data clearly show that intact wires exhibit photon-transfer efficiencies close to 100% across five dyes. Dynamical and multiple pathways for the photon emission resulting from conformational freedom of the wire are readily uncovered. These results provide the basis for guiding the synthesis of DNA-based supramolecular arrays with improved photon transport at the nanometer scale.
Pub.: 22 Dec '06, Pinned: 07 Jun '17
Abstract: Using the principle of self-assembly, a fluorescence-based photonic network is constructed with one input and two spatially and spectrally distinct outputs. A hexagonal DNA nanoassembly is used as a scaffold to host both the input and output dyes. The use of DNA to host functional groups enables spatial resolution on the level of single base pairs, well below the wavelength of light. Communication between the input and output dyes is achieved through excitation energy transfer. Output selection is achieved by the addition of a mediator dye intercalating between the DNA base pairs transferring the excitation energy from input to output through energy hopping. This creates a tool for selective excitation energy transfer on the nanometer scale with spectral and spatial control. The ability to direct excitation energy in a controlled way on the nanometer scale is important for the incorporation of photochemical processes in nanotechnology.
Pub.: 09 Sep '11, Pinned: 07 Jun '17
Abstract: Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.
Pub.: 10 Mar '12, Pinned: 07 Jun '17
Abstract: Obtaining quantitative information about molecular assemblies with high spatial and temporal resolution is a challenging task in fluorescence microscopy. Single-molecule techniques build on the ability to count molecules one by one. Here, a method is presented that extends recent approaches to analyze the statistics of coincidently emitted photons to enable reliable counting of molecules in the range of 1-20. This method does not require photochemistry such as blinking or bleaching. DNA origami structures are labeled with up to 36 dye molecules as a new evaluation tool to characterize this counting by a photon statistics approach. Labeled DNA origami has a well-defined labeling stoichiometry and ensures equal brightness for all dyes incorporated. Bias and precision of the estimating algorithm are determined, along with the minimal acquisition time required for robust estimation. Complexes containing up to 18 molecules can be investigated non-invasively within 150 ms. The method might become a quantifying add-on for confocal microscopes and could be especially powerful in combination with STED/RESOLFT-type microscopy.
Pub.: 25 Jun '13, Pinned: 07 Jun '17
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
Abstract: Taking inspiration from photosynthetic mechanisms in natural systems, a light-sensitive photo protective quenching element was introduced into an artificial light-harvesting antenna model to control the flow of energy as a function of light intensity excitation. The Orange Carotenoid Protein (OCP) is a non-photochemical quencher in cyanobacteria: under high light conditions the protein undergoes a spectral shift, and by binding to the phycobilisome it absorbs excess light and dissipates it as heat. By using DNA as a scaffold, an antenna system made of organic dyes (Cy3, Cy5) was constructed, and OCP was assembled on it as a modulated quenching element. By controlling the illumination intensity it is possible to switch the direction of excitation energy transfer from the donor Cy3 to either of two acceptors. Under low light conditions energy is transferred from Cy3 to Cy5, and under intense illumination, energy is partially transferred to OCP as well. These results demonstrate the feasibility of controlling the pathway of energy transfer using light intensity systems.
Pub.: 14 Jan '17, Pinned: 07 Jun '17
Abstract: An efficient artificial light-harvesting system is fabricated from a cyclic polysaccharide, sulfato-β-cyclodextrin (SCD); an aggregation-induced emission molecule, an oligo(phenylenevinylene) derivative (OPV-I); and a fluorescent dye, nile red (NiR), via noncovalent interactions in an aqueous solution. In this system, the OPV-I/SCD supramolecular assembly acts as a donor, and NiR that is loaded into the OPV-I/SCD assembly acts as an acceptor. Significantly, an efficient energy-transfer process occurs between the OPV-I/SCD assembly and the loaded NiR, leading to an extremely high antenna effect.
Pub.: 07 Jun '17, Pinned: 07 Jun '17