Surface probe immobilisation is a complex and time consuming task undertaken prior to microfluidic integration, this requires surface functionalisation, biomolecule spotting, incubation and blocking steps. Traditional bonding techniques (anodic, thermal, etc.) or adhesives (UV cured) used to seal fluidic systems may denature biomolecules due to high temperature or vapour effects, thus bonding techniques such as thin film laminate or PDMS are used to seal systems, with substrate-fluidic alignment required prior to bonding. We propose a technique allowing probe DNA molecules to be immobilised in a sealed microfluidic system using (3D) hydrogel structures without any alignment steps. A prepolymer solution is introduced to the channels where photo-polymerisation is undertaken forming 3D structures covalently attached to the channel surface. We use a photo-initiated prepolymer material poly-ethyleneglycol (PEG) to form structures containing probe DNA. This process is fast compared to conventional biomolecule immobilisation techniques and is also biocompatible, this direct write approach removes overnight immobilisation/incubation of the probe DNA, it also facilitates immobilisation within a sealed fluidic system where conventionally DNA probe spots must be immobilised prior to channel sealing. We consider the transport of target DNA from bulk analyte to the 3D gel structure and evaluate hybridisation within the microfluidic system. (C) 2009 Elsevier B.V. All rights reserved.