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Molecular Interconnect for NanoTechnology

Deliverables

Tessellated RNA was utilised as a templating agent for metallic nano-deposition. A poly (m-aminophenol) polymer was produced using standard electrochemical methodology. The polymer film displayed various properties, most notably, pinhole free, biocompatible and insulating to metal deposition conditions. The polymer film was deemed to be 13.4nm thick, via AFM imaging in accordance with the estimated size of the tessellated RNA. After polymer deposition the RNA was removed by standard techniques and an incomplete polymer layer remained. A series of benign, simple inorganic salt electrochemical baths were developed as to minimise interference with the biological agent. Metals investigated include copper, silver, and palladium. AFM imaging after the removal of the polymer layer showed metal deposits of approximately 100x150nm. The presence of copper was determined using Energy Dispersive X-ray Spectroscopy. Copper deposition was achieved using various RNA templates including tessellated and non-tessellated RNA molecules. RNA modified with phosphothioate at each c group was found to be the most time effective templating agent. Focused Ion Beam Milling and E-Beam arrays were fabricated to investigate metal deposition in nanometre dimensions. The two approaches were compared using AFM imaging and whilst the e-beam arrays revealed a smoother substrate surface both methods were deemed acceptable. The optimised poly (m-aminophenol) film was used in investigations using FIB milling and commonly used resists for the fabrication of e-beam arrays. Standard electrochemical sweep methods were employed to obtain the optimum conditions for metal deposition for each electrochemical bath tested. These optimised conditions lead to a well-controlled plating process from simple inorganic, benign, pH neutral plating baths and the subsequent copper, silver, and palladium deposits were imaged using AFM. Overall a process has been determined and optimised for the nano-electro deposition of metals on areas of a gold substrate that have been templated using tessellated RNA, from plating solutions compatible with the chosen polymer layer.
High resolution scanning probe microscopy has been used to image tecto RNA structures synthesised in this project. Imaging of both thiolated and non-thiolated RNA fibres was achieved with atomic force microscopy with low tip-sample interactions. The resolution of the images enabled us to distinguish individual fibres on the mica surface and determine fibre length for individual fibres, association of fibres and also to estimate fibre width.
Self-assembled structures that have been placed on to electrode systems have been characterised electrically as a function of temperature. Evidence of Coulomb blockade and activated conduction has been identified. A variety of different samples made using different techniques have been evaluated, including nanowires made from Au nanoparticles that have been assembled using RNA. The impact of this work is likely to be in nanofabrication of small electrical devices since there is potential to provide a low cost manufacturing process.
A spectrum of planar fabrication processes have been developed to enable nanoelectrodes to be made for use in nanotechnology experiments requiring electrical contact to be made. Typical dimensions are electrode width 20nm, tip radius 10nm, and electrode separation of 20nm. The electrodes can be made on a range of substrates using electron beam lithography in a routine manner. Typical materials are Ti:Pd:Au, deposited in that order in a carousel based electron beam evaporator. Ti is used to promote adhesion and Pd acts as a barrier layer between the Ti and the Au. The principal metal is Au, but other materials such as Pt are available. A process has also been developed for nanofluidics based on e-beam lithography in conjunction with UV3 resist. Tube IDs of 50nm with ODs of 200nm are achievable. Interconnect and branching technologies on planar substrates have been demonstrated.
A reliable method has been developed for attaching gold nano-particles of various sizes (generally 15 or 30nm), to self-assembling RNA molecules. Attachment of the gold particles to the RNA was performed by initially attaching short oligodeoxynucleotides (ODNs), which were complementary to single-stranded regions of the RNA motifs. Using this procedure up to approximately 75 RNA molecules can be attached to a 15nm gold particle. The number of RNA molecules per particle can also be reduced in a controllable manner by means of ODNs that competed with the RNA hybridisation sites. In the simplest case, nanoparticle association has been demonstrated between small and large particles, each carrying a specific partner of a Mg2+-dependent, RNA tetraloop-receptor interaction. Control experiments were also able to demonstrate that the association was both Mg2+-dependent and sequence specific. These Mg2+-dependent loop-receptor interactions have been used to position gold particles between two modified electrodes. This work has been submitted for publication and clearly has the potential to create nanoscale wires in a controlled and predictable fashion.
Methods have been developed to specifically immobilise and quantify the amount of functionalised oligonucleotides and RNA oligomers on the surface of both gold and reactive polymer modified electrodes. The reactive polymer can be either an activated ester of a poly (pyrrole) derivative or an amine terminated poly (pyrrole) derivative. In both cases a variety of coupling strategies can be used to selectively deposit different sequence oligos on to different electrodes within a lithographically patterned array (described in other another e-tip result). (The polymers are deposited onto lithographically patterned electrodes using electrochemical techniques.) Assessment of the specificity and degree of oligo and RNA immobilisation is performed using XPS and QCM techniques. Using these methods, optimisation of both solution parameters and conjugation strategies has been perform. Having immobilised the oligonucleotides and RNA, it is then possible to immobilise on the modified electrode surface, gold nanoparticles that have been decorated with appropriate oligonucleotide and RNA motifs. This immobilisation takes place through the Mg2+ mediated association of structural motifs in the tertiary structure of specific RNA sequences. Currently this work is being prepared for dissemination in scientific journals and is of potential use in the controlled creation of nanoscale wires and interconnections between nanoparticles having particular functionalities.
A suite of self-assembling RNA molecules, based on the tecto-RNA molecules developed by Luc Jaeger have been designed and characterized. The designs are broadly of two kinds: pairs of molecules that heterodimerise through two tertiary RNA, Mg2+-dependent loop-receptor interactions, and four way junction molecules, each containing two loops and two receptors, which assemble into one-dimensional fibres in the presence of magnesium ions. Each of these designs has been derivatised in a number of ways to enable specific and non-specific attachment of the RNA molecules to gold nanoparticles, gold nanoelectrodes or surfaces, either through specific hybridisation of and RNA tail designed into the molecule to a DNA oligonucleotide immobilized on the desired gold partner, or by substitution of phosphorothioate linkages between ribonucleotides in place of the natural phosphodiesters, to allow direct attachment to gold partners. The molecules have been synthesized using molecular biological methods: Polymerase chain reaction, in vitro run-off transcription, and their interactions have been characterized by denaturing and native polyacrylamide gel electrophoresis, as well as by physical methods including surface plasmon resonance. The dimerising molecules have been used by other partners for the controlled assembly of gold nanoparticles both in solution and in combination with attachment to gold nanoelectrodes, where they have been used to assemble nanowires, whose construction is controlled by the Mg2+-dependent assembly of the RNA molecules. Such assembly is the first such controlled assembly of this type. In addition, the RNA fibres have also been decorated with gold nanoparticles, and have been used as a template for the electrochemical deposition of metal on a gold surface, with the intention of forming nano-interconnects. This work has been submitted for publication and, although at the level of basic science has the potential for use in the specific creation of nano-interconnections between particles and other components with specific functionalities.

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