Both naturally occurring and synthetic small molecules play a significant role in a variety of applications. For example, small molecule food contaminants that occur infield or postharvest are of importance, both agriculturally and economically. Mycotoxins are toxic secondary metabolites produced by filamentous fungi that can potentially contaminate a variety of foodstuffs. Detection of these small molecules is required as mycotoxins pose multiple health-risks and proceed past processing and food safety.Current detection methods are expensive, time consuming and unavailable for on-site detection leaving an unmet need for alternative methods of detection.Aptamers are single stranded oligonucleotides that can bind to specific target molecules with high selectivity and affinity. Emerging as molecular recognition agents, aptamers can be used in a number of novel detection methods for small molecule quantification and analysis. Aptamers are selected through an in vitro process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers can be adsorbed onto the surface of citrate-capped AuNPs to serve as the molecular recognition element of a rapid colourimetric biosensor assay. Based on this interaction, AuNPs could potentially serve as a novel platform for small molecule SELEX. Although molecular recognition of small molecules is of great interest, selection of aptamers for small molecules has proven to be a challenge. Furthermore, not all of these reported small molecule aptamers can be easily incorporated in the AuNP bioassay. Selecting for aptamers in a manner that will mimic established AuNP biosensor conditions provides a number of advantages compared to traditional SELEX. As a first step towards establishing a AuNP SELEX platform, we evaluated the partitioning of mycotoxin iv aptamers that remain on the AuNP surface from aptamers-target complexes in solution.Having uncovered several challenges associated with AuNPs as a SELEX partitioning strategy, we next synthesized, optimized, and characterized core-shell gold coated magnetic nanoparticles (Fe3O4-AuNPs), which were phase-transferred aqueous solution.We demonstrated that Fe3O4-AuNPs could function as an improved AuNP SELEX platform and provide a novel method to study ssDNA aptamer-AuNP non-specific interactions. Finally, our studies on the adsorption and separation of ssDNA aptamers using Fe3O4-AuNPs highlight future opportunities for novel aptamer biomedical applications and other biosensor development.v