An Optically Modulated Self-Assembled Resonance Energy Transfer Pass Gate.

We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence. Without this excitation, exciton flow through the device is hindered by absorbing paths along the way, resulting in weak output fluorescence. In this Letter, we describe the design and fabrication of the pass gate. We perform a steady-state analysis revealing that the on/off fluorescence ratio for this particular implementation is ∼8.7. To demonstrate dynamic modulation of the pass gate, we toggle the gate excitation on and off and measure the corresponding change in output fluorescence. We characterize the rise and fall times of these transitions, showing that they are faster and/or more easily achieved than other methods of RET network modulation. The pass gate is the first dynamic RET-based logic gate exclusively modulated by dark states and serves as a proof-of-concept device for building more complex RET systems in the future.

DNA-enabled integrated molecular systems for computation and sensing.

CONSPECTUS: Nucleic acids have become powerful building blocks for creating supramolecular nanostructures with a variety of new and interesting behaviors. The predictable and guided folding of DNA, inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be co-opted for engineered and purposeful ends. This Account details a small portion of what can be engineered using DNA within the context of computer architectures and systems. Over a decade of work at the intersection of DNA nanotechnology and computer system design has shown several key elements and properties of how to harness the massive parallelism created by DNA self-assembly. This work is presented, naturally, from the bottom-up beginning with early work on strand sequence design for deterministic, finite DNA nanostructure synthesis. The key features of DNA nanostructures are explored, including how the use of small DNA motifs assembled in a hierarchical manner enables full-addressability of the final nanostructure, an important property for building dense and complicated systems. A full computer system also requires devices that are compatible with DNA self-assembly and cooperate at a higher level as circuits patterned over many, many replicated units. Described here is some work in this area investigating nanowire and nanoparticle devices, as well as chromophore-based circuits called resonance energy transfer (RET) logic. The former is an example of a new way to bring traditional silicon transistor technology to the nanoscale, which is increasingly problematic with current fabrication methods. RET logic, on the other hand, introduces a framework for optical computing at the molecular level. This Account also highlights several architectural system studies that demonstrate that even with low-level devices that are inferior to their silicon counterparts and a substrate that harbors abundant defects, self-assembled systems can still outperform conventional systems. Further, the domain, that is, the physical environment, in which such self-assembled computers can operate transcends the usual limitations of silicon machines and opens up new and exciting horizons for their application. This Account also includes a look at simulation tools developed to streamline the design process at the strand, device, circuit, and architectural levels. These tools are essential for understanding how to best manipulate the devices into systems that explore the fundamentally new computing domains enabled by DNA nanotechnology.

An enzymatically-sensitized sequential and concentric energy transfer relay self-assembled around semiconductor quantum dots.

The ability to control light energy within de novo nanoscale structures and devices will greatly benefit their continuing development and ultimate application. Ideally, this control should extend from generating the light itself to its spatial propagation within the device along with providing defined emission wavelength(s), all in a stand-alone modality. Here we design and characterize macromolecular nanoassemblies consisting of semiconductor quantum dots (QDs), several differentially dye-labeled peptides and the enzyme luciferase which cumulatively demonstrate many of these capabilities by engaging in multiple-sequential energy transfer steps. To create these structures, recombinantly-expressed luciferase and the dye-labeled peptides were appended with a terminal polyhistidine sequence allowing for controlled ratiometric self-assembly around the QDs via metal-affinity coordination. The QDs serve to provide multiple roles in these structures including as central assembly platforms or nanoscaffolds along with acting as a potent energy harvesting and transfer relay. The devices are activated by addition of coelenterazine H substrate which is oxidized by luciferase producing light energy which sensitizes the central 625 nm emitting QD acceptor by bioluminescence resonance energy transfer (BRET). The sensitized QD, in turn, acts as a relay and transfers the energy to a first peptide-labeled Alexa Fluor 647 acceptor dye displayed on its surface. This dye then transfers energy to a second red-shifted peptide-labeled dye acceptor on the QD surface through a second concentric Förster resonance energy transfer (FRET) process. Alexa Fluor 700 and Cy5.5 are both tested in the role of this terminal FRET acceptor. Photophysical analysis of spectral profiles from the resulting sequential BRET-FRET-FRET processes allow us to estimate the efficiency of each of the transfer steps. Importantly, the efficiency of each step within this energy transfer cascade can be controlled to some extent by the number of enzymes/peptides displayed on the QD. Further optimization of the energy transfer process(es) along with potential applications of such devices are finally discussed.