With the premise and potential of Lab-on-a-chip (LoC) devices well versed within popular literature, the pragmatic direction of work within the microfluidic community has shifted towards developing the engineering solutions required to realise and advance these powerful goals. Due to the requirement for in-line analytical techniques to be both stable and customisable within true LoC devices, much of this focus has been directed to the interfacing of complementary analytical techniques, which when combined produce a richer, more detailed, analytical framework. The initial portion of this thesis develops, demonstrates and benchmarks several on-chip analytical techniques, namely microchip capillary gel electrophoresis (μCGE) and droplet microfluidics. Through the careful on-chip integration of the developed platforms it is demonstrated that samples can be injected, separated and extracted utilizing a novel design structure put into practise. Underpinning this technique is the ability of the constructed platform to encapsulate and contain the band profile of separated analytes within discrete stable microdroplets suitable for use within further analytical processes. Subsequent to this work, the latter half of this thesis investigates both the potential applications and advantageous nuances specific to this novel technique. In particular, the design is shown to facilitate the production of characterizable sample dilution series from the injected and separated target analytes. Further applications are investigated through the deployment of the derived system and protocol to the separation, identification and encapsulation of dsDNA fragments from a composite sample.