This study describes the first instance of the use of two differently sized Au nanoparticles (Au NPs), acting separately as donor and acceptor, in homogeneous photoluminescence quenching assays developed for the analysis of proteins. Introduction of a breast cancer marker protein, platelet-derived growth factor AA (PDGF AA), to a solution of 11-mercaptoundecanoic acid-protected, 2.0-nm photoluminescent Au nanodots (L(AuND)) led to the preparation of PDGF AA-L(AuND) as the donor. Thiol-derivative PDGF binding aptamers (Apt) and 13-nm spherical Au NPs were used to synthesize the Apt-Q(AuNP) acceptor. The photoluminescence of PDGF AA-L(AuND) at 520 nm decreased when photoluminescence quenching occurred between Apt-Q(AuNP) and PDGF AA-L(AuND). We used the PDGF AA-L(AuND)/Apt-Q(AuNP)-based molecular light switching system to analyze PDGFs and PDGF alpha-receptor in separate homogeneous solutions. In the presence of PDGFs, the interaction between Apt-Q(AuNP) and PDGF AA-L(AuND) decreased as a result of competitive reactions between the PDGFs and Apt-Q(AuNP). Similarly, the interaction between Apt-Q(AuNP) and PDGF AA-L(AuND) reduced as a result of competitive reactions between PDGF alpha-receptor and PDGF AA-L(AuND). The limits of detection (LODs) for PDGF AA and PDGF alpha-receptor were 80 pM and 0.25 nM, respectively, resulting from a low background photoluminescence signal. When using the Apt-Q(AuNP) as selectors for (a) the enrichment of PDGF AA and (b) the removal of matrixes possessing intense background fluorescence from cell media and urine samples, the LOD for PDGF AA decreased to 10 pM. Unlike quantum dots, the L(AuND) provide the advantages of biocompatibility, ease of bioconjugation, and minimal toxicity.