Gold nanoparticles (AuNPs) have a unique optical phenomena termed localized surface plasmon resonance that is determined by particle shape, size, interparticle distance (or aggregation status), and local refractive index. AuNPs can also modulate fluorescence emission of proximal fluorophores under the Förster resonance energy transfer and/or nanoparticle surface energy transfer mechanisms. In this study, we use AuNPs (13 and 100 nm in diameter) as sensing elements to study sequence-dependent protein-DNA interactions by exploring all possible principles, namely (1) particle aggregation based colorimetric sensing, (2) refractive index sensing, and (3) fluorescence quenching/enhancement based fluorimetric sensing, exemplified by transcription factors, i.e., FoxA1 and AP2γ, and their respective DNAs. We conclude that the first principle, i.e., particle aggregation-based colorimetric assay that measures preformed complex by exploring complex protection of AuNPs from salt-induced aggregation, is simple to use. However, its performance is protein specific. For second and third principles that measure on-particle complex formation, we prove that the fluorescence quenching/enhancement assays supported by AuNPs are more sensitive than assays exploiting analyte-binding induced refractive index principle. This study provides a comprehensive assessment of the versatility of AuNPs as sensing probes for studying bioaffinity interactions especially protein-DNA complexes. The discovery of the DNA binding properties of FoxA1 and AP-2γ is important in revealing their roles in gene regulation. © 2014 Springer Science+Business Media New York.