The development of light harvesting systems for directed, efficient control of energy transfer at the biomolecular level has generated considerable interest in the past decade. Molecular fluorophores provide a straightforward mechanism for determining nanoscale distance changes through Förster resonance energy transfer (FRET), and many systems seek to build off of this simple yet powerful principle to provide additional functionality. The use of DNA-based integrated biomolecular devices offer many unique advantages towards this end. DNA itself is an excellent engineering material – it is innately biocompatible, quickly and cheaply synthesized, and complex structures can be readily designed in silico. It also provides an excellent scaffold for the precise patterning of various biomolecules. Here, we discuss the systems that have been recently developed which add to this toolbox, including nanostructural dye patterning, photonic wires, and the incorporation of alternative energy propagation modalities, such as semiconductor quantum dots (QD) and the bioluminescent protein luciferase. In particular, we explore the incorporation of luciferase into various nanostructural conformations, providing the capability to efficiently control energy flow directionality. We discuss the nature of this system, including unexpected spectral complexities, in the context of the field.
KEYWORDS: Nanostructures, Luminescence, Molecules, Energy transfer, Energy harvesting, Resonance energy transfer, Fluorescence resonance energy transfer, Dendrimers, Light harvesting, Molecular photonics
DNA is a biocompatible scaffold that allows for the design of a variety of nanostructures, from straightforward double stranded DNA to more complex DNA origami and 3-D structures. By modifying the structures, with dyes, nanoparticles, or enzymes, they can be used to create light harvesting and energy transfer systems. We have focused on using Förster resonance energy transfer (FRET) between organic fluorophores separated with nanometer precision based on the DNAs defined positioning. Using FRET theory we can control the direction of the energy flow and optimize the design parameters to increase the systems efficiency. The design parameters include fluorophore selection, separation, number, and orientation among others. Additionally the use of bioluminescence resonance energy transfer (BRET) allowed the use of chemical energy, as opposed to photonic, to activate the systems. Here we discuss a variety of systems, such as the longest reported DNA-based molecular photonic wires (> 30 nm), dendrimeric light harvesting systems, and semiconductor nanocrystals integrated systems where they act as both scaffold and antennae for the original excitation. Using a variety of techniques, a comparison of different types of structures as well as heterogeneous vs. homogenous FRET was realized.
KEYWORDS: Nanostructures, Energy efficiency, Luminescence, Energy transfer, Energy harvesting, Resonance energy transfer, Fluorescence resonance energy transfer, Photosynthesis, Molecular photonics, Anisotropy
Molecular photonic wires (MPWs) present interesting applications in energy harvesting, artificial photosynthesis, and nano-circuitry. MPWs allow the directed movement of energy at the nanoscopic level. Extending the length of the energy transfer with a minimal loss in efficiency would overcome an important hurdle in allowing MPWs to reach their potential. We investigated Homogenous Förster Resonance Energy Transfer (HomoFRET) as a means to achieve this goal. We designed a simple, self-assembled DNA nanostructure with specifically placed dyes (Alexa488-Cy3-Cy3.5-Alexa647-Cy5.5) at a distance of 3.4 nm, a separation at which energy transfer should theoretically be very high. The input of the wire was at 466 nm with an output up to 697 nm. Different structures were studied where the Cy3.5 section of the MPW was extended from one to six repeats. We found that though the efficiency cost is not null, HomoFRET can be extended up to six repeat dyes with only a 22% efficiency loss when compared to a single step system. The advantage is that these six repeats created a MPW which was 17 nm longer, almost 2.5 times the initial length. To confirm the existence of HomoFRET between the Cy3.5 repeats fluorescence lifetime and fluorescence lifetime anisotropy was measured. Under these conditions we are able to demonstrate the energy transfer over a distance of 30.4 nm, with an end-to-end efficiency of 2.0%, by utilizing a system with only five unique dyes.
The “spectroscopic ruler” based on fluorescence resonance energy transfer (FRET) is explored as a method for detailed
structural characterization of DNA nanostructures in solution. The approach is most directly useful for assessing the
positional relationships among chromophores organized by the DNA, but it can also be used to characterize the geometry
and kinematics of the DNA scaffold itself. By accumulating data for the distances separating various donor-acceptor
pairs, and correlating them with the expected distances, one can quantify the shape and deformability of the structure. A
8x16nm “mini-origami” rectangle is used as the model test structure and the dye-pairs are chosen to investigate
anisotropy in the origami’s mechanical properties. Not unexpectedly, our analysis finds a strong anisotropy in the
stiffness, with the measured spacing across the origami weave deviating much more from expectation than the spacing
aligned along the weave pattern.
There is considerable research in the area of manipulating light below the diffraction limit, with potential applications ranging from information processing to light-harvesting. In such work, a common problem is a lack of efficiency associated with non-radiative losses, e.g., ohmic loss in plasmonic structures. From this point of view, one attractive method for sub-wavelength light manipulation is to use Förster resonance energy transfer (FRET) between chromophores. Although most current work does not show high efficiency, biology suggests that this approach could achieve very high efficiency. In order to achieve this goal, the geometry and spacing of the chromophores must be optimized. For this, DNA provides an easy means for the self-assembly of these complex structures. With well established ligation chemistries, it is possible to create facile hierarchical assemblies of quantum dots (QDs) and organic dyes using DNA as the platform. These nanostructures range from simple linear wires to complex 3-dimensional structures all of which can be self-assembled around a central QD. The efficiency of the system can then be tuned by changing the spacing between chromophores, changing the DNA geometry such that the donor to acceptor ratio changes, or changing the number of DNA structures that are self-assembled around the central QD. By exploring these variables we have developed a flexible optical system for which the efficiency can be both controlled and optimized.