The work conducted within the Centre for Molecular Nanometrology involving DNA sensing as part of this project has focussed on the use of light to direct the immobilisation of specific oligonucleotide sequences onto a number of different surfaces on a surface. The slides indicate that there are two current approaches to using light directed immobilisation of oligonucleotide probes in the construction of microarrays. These include the use of light generated acid which removes the standard protecting group to allow specific chemical reactions to take place, or the use of a unique protecting group which is removed by the action of light. In each of the current approaches the light activation results in the addition of a specific nucleotide in the sequence of choice on the surface.

In our approach we have devised a generic linking molecule which we can attach to the surface of the array and then specifically activate using light to generate a reactive nitrene which will then react with any primary amine group which can be introduced to the system. In the first approach, however, we decided to use a light cured polymer containing epoxy functionality. The light was directed to generate specific spots of epoxy polymer on glass and these epoxy polymers were then exposed to oligonucleotides containing a primary amine group and a fluorescent label. Confocal microscopy confirmed that the polymer spots were present and that the fluorescently labelled oligonucleotides were indeed attached to the polymer spots. In the more advanced approach a silane linker was used to derivatise glass and the light active linking molecule added to the glass through the formation of an amide bond. Activation of this using UV light followed by exposure to an amino linked oligonucleotide resulted in the immobilisation of specific oligonucleotide probes as directed by the light activation of the linker. Three different dye labels were used to confirm that we could get specific attachment chemistry to work and this is being investigated further for use in specific DNA detection using the UV LED’s as the light source for activation. In the final approach a range of new phosphoramidite monomers for DNA synthesis have been produced with a photo cleavable protecting group. This will allow synthesis of specific sequences on the surface using light directed chemistry. This work indicates the dependency of the novel chemistry on light directed synthesis and immobilisation of oligonucleotides on surfaces.