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.

Permutation Machines.

We define a new inversion-based machine called a permuton of n genetic elements, which allows the n elements to be rearranged in any of the n·(n - 1)·(n - 2)···2 = n! distinct orderings. We present two design algorithms for architecting such a machine. We define a notion of a feasible design and use the framework to discuss the feasibility of the permuton architectures. We have implemented our design algorithms in a freely usable web-accessible software for exploration of these machines. Permutation machines could be used as memory elements or state machines and explicitly illustrate a rational approach to designing biological systems.

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.

Multiplexed method to calibrate and quantitate fluorescence signal for allergen-specific IgE.

Using a microarray platform for allergy diagnosis allows for testing of specific IgE sensitivity to a multitude of allergens, while requiring only small volumes of serum. However, variation of probe immobilization on microarrays hinders the ability to make quantitative, assertive, and statistically relevant conclusions necessary in immunodiagnostics. To address this problem, we have developed a calibrated, inexpensive, multiplexed, and rapid protein microarray method that directly correlates surface probe density to captured labeled secondary antibody in clinical samples. We have identified three major technological advantages of our calibrated fluorescence enhancement (CaFE) technique: (i) a significant increase in fluorescence emission over a broad range of fluorophores on a layered substrate optimized specifically for fluorescence; (ii) a method to perform label-free quantification of the probes in each spot while maintaining fluorescence enhancement for a particular fluorophore; and (iii) a calibrated, quantitative technique that combines fluorescence and label-free modalities to accurately measure probe density and bound target for a variety of antibody-antigen pairs. In this paper, we establish the effectiveness of the CaFE method by presenting the strong linear dependence of the amount of bound protein to the resulting fluorescence signal of secondary antibody for IgG, ß-lactoglobulin, and allergen-specific IgEs to Ara h 1 (peanut major allergen) and Phl p 1 (timothy grass major allergen) in human serum.