Nucleic acid nanotechnology

Abstract:

We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.

Abstract:

We present a study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices. The rate of spontaneous hybridization between complementary hairpins can be reduced by increasing the neck length or decreasing the loop length. Hairpins with larger loops rapidly form long-lived kissed complexes. Hairpin loops may be opened by strand displacement using an opening strand that contains the same sequence as half of the neck and a "toehold" complementary to a single-stranded domain adjacent to the neck. We find loop opening via an external toehold to be 10-100 times faster than via an internal toehold. We measure rates of loop opening by opening strands that are at least 1000 times faster than the spontaneous interaction between hairpins. We discuss suitable choices for loop, neck, and toehold length for hairpin loops to be used as fuel for autonomous DNA devices.

Abstract:

A range of techniques employed for 3D optical lithography including atomic layer deposition (ALD) and holographic lithography has been demonstrated. A 3D photonic crystal structure can be written by holographic lithography which makes use of a periodic interference pattern generated by a multiple-beam interferometer to expose a thick layer of photoresist. 3D microstructures can also be generated by point-to-point exposure of the resist by two-photon absorption at a laser focus. The potential of ALD has been explored to develop a well-controlled infiltration technique for optically fabricated 3D microstructures used for the formation of single- and multicomponent inverse opals. A high quality photonic crystal in amorphous TiO2 was produced by conformal infiltration followed by etching of holographically defined polymeric templates. The results show that the combination of holographic lithography and ALD allows rapid and flexible fabrication of 3D photonic crystals.