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Core-shell molecularly imprinted particles (CS-MIPs) have been synthesised using the technique of emulsion polymerisation with caffeine and theophylline being used in the surface template polymerisation with ethylene glycol dimethacrylate and oleylphenyl hydrogen phosphate. A radiolabelling study with caffeine-8-14C showed that the template was completely located at the particle surface during polymerisation. Caffeine could be specifically bound to a caffeine-imprinted CS-MIP to give a biphasic Scatchard binding curve, whereas the binding profile to a theophylline-imprinted CS-MIP was monophasic. The nanoparticles have the potential to be used in the molecular recognition of small molecules in a complex biological matrix. Water soluble highly-branched imidazole end-chain functionalised polymers of nanodimensions have also been synthesised via reversible addition-fragmentation chain transfer polymerisation. The polymers have lower critical solution temperatures which occur at sub-ambient temperatures and have proven useful in the affinity precipitation of proteins which are particularly temperature sensitive, e.g. the histidine-tagged protein fragment BRCA1. An overview of both of these areas of research is described outlining the diversity of these aqueous compatible polymers in molecular recognition processes at the nanoscale.