Time-Gated DNA Photonic Wires with Förster Resonance Energy Transfer Cascades Initiated by a Luminescent Terbium Donor

Abstract

Functional DNA nanotechnology is a rapidly growing area of research with many prospective photonic applications, including roles as wires and switches, logic operators, and smart biological probes and delivery vectors. Photonic wire constructs are one such example and comprise a Forster resonance energy transfer (FRET) cascade between fluorescent dyes arranged periodically along a DNA scaffold. To date, the majority of research on photonic wires has focused on setting new benchmarks for efficient energy transfer over more steps and across longer distances, using almost exclusively organic fluorescent dyes and strictly DNA structures. Here, we expand the range of materials utilized with DNA photonic wires by demonstrating the use of a luminescent terbium complex (Tb) as an initial donor for a four-step FRET cascade along a ∼15 nm long DNA/locked nucleic acid (LNA) photonic wire. The inclusion of LNA nucleotides increases the thermal stability of the photonic wires while the Tb affords time-gated emission measurements and other optical benefits. Time-gating minimizes unwanted background emission, whether from direct excitation of fluorescent dyes along the length of the photonic wire, from excess dye-labeled DNA strands in the sample, or from a biological sample matrix. Observed efficiencies for Tb-to-dye energy transfer are also closer to the predicted values than those for dye-to-dye energy transfer, and the Tb can be used as an initial FRET donor for a variety of next-in-line acceptors at different spectral positions. We show that the key to using the Tb as an effective initial donor is to optimally position the next-in-line acceptor dye in a so-called "sweet spot" where the FRET efficiency is sufficiently high for practicality, but not so high as to suppress time-gated emission by shortening the Tb emission lifetime to within the instrument lag or delay time necessary for measurements. Overall, the initiation of a time-gated FRET cascade with a Tb donor is a very promising strategy for the design, characterization, and application of DNA-based photonic wires and other functional DNA nanostructures. D NA represents an exciting and promising approach to the bottom-up assembly of nanoscale devices for applications such as light harvesting, optical computing, and biological probes. 1−4 As a building block, DNA is advantageous because of its availability, versatility, and programmability. Long lengths of DNA can be obtained from natural sources, then amplified and modified enzymatically, whereas oligonucleotides can be made by solid-phase chemical synthesis or obtained from commercial vendors with terminal or internal modifications such as functional linkers and fluorescent dyes. Complementary DNA sequences predictably and spontaneously hybridize into relatively rigid double helical structures (persistence length ∼ 50 nm), and the rise of the helix (∼0.34 nm per base pair) affords subnanometer control over length. 1,4,5 Many years of research on DNA assembly have led to creation of a toolbox with concepts such as DN...

Toward the design of bio-solar cells: high efficiency cascade energy transfer among four donor–acceptor dyes self-assembled in a highly ordered protein–DNA matrix

“…The overall energy transfer efficiency depended on the highest energy donor concentration, which clearly indicated donor-donor and donor-acceptor FRET. 21 In another study, the efficiency of a DNA-porphyrin system was reported to be 0.55 from Förster theory. Donor-concentration dependence on FRET was attributed to donor-to-donor energy transfer.…”

“…Each of these lms was excited at 350 nm, and the emission from R at 650 nm was monitored. 20,21 In the case of tobacco mosaic virus coat protein-3 dye system, the efficiency was reported to be $0.90 based on the ratio of donor absorbance to donor excitation. 2A), while all other concentrations were kept constant.…”

“…Two boundary conditions were satised by the above equation. 21 Individual steps could be less than 100% efficient when the excitation of the system is quenched by non-radiative pathways or by emission from an intermediary jumper dye. Second, if the efficiency was 100%, then E must be 1.…”

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

“…Lanthanide ions have interesting fluorescent properties as compared to normal fluorophores, they present multiple sharp emission lines with large Stokes shifts and extremely long excited‐state lifetimes that are typically in the high µs to low ms range . Lanthanides have been used as fluorophores within multichromophore DNA nanophotonics systems, both within simple DNA MPWs as well as with hybrid lanthanide‐dye‐QD systems which have been applied to assays and diagnostics 59b,185. Due to the inherent long‐lifetimes of lanthanides as well as their generally small extinction coefficients found in the UV portion of the spectrum, they do not function well as relays or acceptors within energy transfer systems, rather they remain excellent initiators of energy cascades.…”

Utilizing HomoFRET to Extend DNA‐Scaffolded Photonic Networks and Increase Light‐Harvesting Capability

“…In pursuit of these same goals, we have explored a variety of DNA‐based architectures displaying different densities and combinations of fluorophore types . A purely linear double‐stranded (ds) DNA scaffold displaying single copies of seven sequential donor–acceptor dyes manifested poor end‐to‐end energy transfer efficiency ( E ee ) due to an intermediary dye acting as a strong energy sink rather than a viable relay .…”