Electrostatic attraction, covalent binding, and hydrophobic absorption are spontaneous processes to assemble and disassemble the molecules of gold nanoparticles (GNP). This dynamic change can be performed in the presence of ions, such as NaCl or charged molecules. Current research encompasses the GNP in mediating non-biofouling and investigating the molecular attachment and detachment. Experiments were performed with different sizes of GNP and polymers. As a proof of concept, poly(ethylene glycol)-b-poly(acrylic acid), called PEG-PAAc, attachment and binding events between factor IX and factor IX-bp from snake venom were demonstrated, and the variations with these molecular attachment on GNP were shown. Optimal concentration of NaCl for GNP aggregation was 250 mM, and the optimal size of GNP used was 30 nm. The polymer PEG-PAAc (1 mg/ml) has a strong affinity to the GNP as indicated by the dispersed GNP. The concentration of 5800 nM of factor IX was proved to be optimal for dispersion of GNP, and at least 100 nM of factor IX-bp was needed to remove factor IX from the surface of GNP. This study delineates the usage of unmodified GNP for molecular analysis and downstream applications.