The ability to detect and interrogate DNA sequences allows further understanding and diagnosis of genetic disease. The ability to perform such analysis of genetic material requires highly selective and reliable technologies. Furthermore techniques which can use simple and cheap equipment allow the use of such technologies for point of care analysis. Described in this thesis are two novel DNA probe systems designed for mutation discrimination and sequence recognition of PCR products. A homogenous PCR system using HyBeacons® which utilise FRET to produce a three probe multiplex system and surface enhanced Raman detection method. Both of these systems allow multiplex detection of PCR products and mutation discrimination by melting temperature analysis. The research reported includes investigations into the effects of different modifications to improve the performance of HyBeacon® probes as well as the effect of different dyes in a FRET system, including unique changes in the optical properties of such dyes. Also a novel method of performing melting temperature analysis using an electrochemical potential is reported. In addition to the detection methods described this thesis includes initial work into the stabilisation of quantum dot nanoparticles for their use in aqueous systems as a potential alternative to fluorescent organic molecules.