Small molecules play a significant role in a variety of applications. Current detection methods present limitations leaving an unmet need for alternative methods of detection. Selected through an in vitro process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX), aptamers are single stranded oligonucleotides that can bind to specific target molecules with high selectivity and affinity. Aptamers can be used as the molecular recognition agent of various biosensors. Based on a non-covalent interaction, AuNPs could potentially serve as a novel platform for small molecule SELEX. Selecting for aptamers in a manner that will mimic established AuNP biosensor conditions provides a number of advantages. As a first step towards establishing a AuNP SELEX platform, we evaluated SELEX partitioning. Having uncovered several challenges, we next synthesized, optimized, and characterized Fe3O4-AuNPs. We demonstrated that Fe3O4-AuNPs could function as a novel method to study ssDNA aptamer-AuNP non-specific interactions.