Nucleic acid nanotechnology

Abstract:

The second law of thermodynamics requires that directed motion be accompanied by dissipation of energy. Here we demonstrate the working principles of a bipedal molecular motor. The motor is constructed from DNA and is driven by the hybridization of a DNA fuel. We show how the catalytic activities of the feet can be coordinated to create a Brownian ratchet that is in principle capable of directional and processive movement along a track. This system can be driven away from equilibrium, demonstrating the potential of the motor to do work.

Abstract:

We have registered the position and wavelength of a single InGaAs quantum dot using an innovative cryogenic laser lithography technique. This approach provides accurate marking of the location of self-organized dots and is particularly important for realizing any solid-state cavity quantum electrodynamics scheme where the overlap of the spectral and spatial characteristics of an emitter and a cavity is essential. We demonstrate progress in two key areas towards efficient single quantum dot photonic device implementation. Firstly, we show the registration and reacquisition of a single quantum dot with 50 and 150 nm accuracy, respectively. Secondly, we present data on the successful fabrication of a photonic crystal L3 cavity following the registration process.

Abstract:

We demonstrate the use of a one-dimensional template to control the shape of a two-dimensional array self-assembled from a minimal set of DNA tiles. A periodic single-stranded template seeds tile assembly. A unique vertex tile at the 5′ end of the template controls the positioning of edge and body tiles to create a wedge-shaped array. The vertex angle of the array is approximately 12°; edge lengths are of the order of 1 μm. © 2008 Elsevier Ltd. All rights reserved.

Abstract:

DNA nanotechnology makes use of the exquisite self-recognition of DNA in order to build on a molecular scale. Although static structures may find applications in structural biology and computer science, many applications in nanomedicine and nanorobotics require the additional capacity for controlled three-dimensional movement. DNA architectures can span three dimensions and DNA devices are capable of movement, but active control of well-defined three-dimensional structures has not been achieved. We demonstrate the operation of reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals. Shape changes are confirmed by gel electrophoresis and by bulk and single-molecule Förster resonance energy transfer measurements. DNA tetrahedra are natural building blocks for three-dimensional construction; they may be synthesized rapidly with high yield of a single stereoisomer, and their triangulated architecture conveys structural stability. The introduction of shape-changing structural modules opens new avenues for the manipulation of matter on the nanometre scale.

Abstract:

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.