In the field of DNA based sensors, it is crucial to identify a suitable interfacial chemistry providing DNA chips that exhibit a high efficiency with respect to the hybridization process. In this study, we performed a systematic investigation on various chemical architectures by Surface Plasmon Resonance (SPR), which is an optical technique able to follow a molecular recognition process in-situ and in real time. We analyzed four different preparation methods that produce DNA based sensors on gold surfaces. For each one, we monitored by SPR the amount of molecules deposited on the chip when this latter is exposed to different target DNA solutions. For those solutions, we used either complementary or non-complementary target single stranded DNA in order to check either the sensitivity or the selectivity of the sensor. As shown by the results, the interfacial chemistry of the DNA based chips is relevant to the quality of the hybridization process, i.e., a high deposition rate with only a few unspecific adsorptions. Moreover, the importance of adding a protective layer on the gold surface in order to prevent non-specific physisorption of DNA strands is discussed. [DOI: 10.1380/ejssnt.2009.777]