Nucleic acid nanotechnology

Abstract:

The negative-tone epoxy photoresist, SU-8, expands ≈1% by volume after postexposure baking. However, if the maximum optical fl uence is comparable to that at the insolubility threshold, as in a holographic exposure, the developed resist shrinks ( ≈35% by volume) due to the removal of light oligomers not incorporated into the polymeric network. IR spectroscopy shows that, at this level of exposure, only 15% of the epoxy groups in the insoluble polymer have reacted; consequently microstructural elements soften and collapse at > 100 °C. When the light oligomers are removed, the sensitivity of the resist is unchanged, provided that 5% (w/w) of a high-molecular-weight reactive plasticizer (glycidoxy-terminated polyethylene glycol) is added, but it shrinks less on development and, when used as a photonic crystal template, shows improved uniformity with less cracking and buckling. Reinforcing the polymer network by reaction with the polyfunctional amine (bis- N , N′ -(3-aminopropyl) ethylenediamine) increases the extent of cross-linking and the thermal stability, allowing inverse replicas of photonic crystal templates to be fabricated from both Al:ZnO and Zr3N4 using atomic layer deposition at temperatures up to 200 °C. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Abstract:

We have developed a programmable and auton-omous molecular robot whose motion is fueled by DNA hybridization. Instructions determining the path to be followed are programmed into the fuel molecules, allowing precise control of cargo motion on a branched track.

Abstract:

The efficiencies of DNA-templated acyl transfer reactions between a thioester modified oligonucleotide and a series of amine and thiol based nucleophiles are directly compared. The reactivity of the nucleophile, reaction conditions (solvent, buffer, pH) and linker length all play important roles in determining the efficiency of the transfer reaction. Careful optimisation of the system enables the use of DNA-templated synthesis to form stable peptide-like bonds under mild aqueous conditions close to neutral pH.

Abstract:

Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor and fuel, all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold, and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.

Abstract:

Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes. © 2011 American Chemical Society.