BACKGROUND: Globally, severe acute respiratory syndrome coronavirus (SARS-CoV) is a newly emerging virus that causes SARS with high mortality rate in infected people. The nucleocapsid (N) protein of the severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) is an important antigen for the early diagnosis of SARS and the detection of diseases. Here, a new quantum dots (QDs)-conjugated RNA aptamer with high sensitivity and rapidity is proposed for the detection of SARS-CoV N protein using an on chip system. RESULTS: A QDs-conjugated RNA aptamer can specifically hybridize on the immobilized SARS-CoV N protein on the surface of a glass chip. Detection is based on the optical signal variation of a QDs-supported RNA aptamer interacting on an immobilized protein chip. Using an optical QDs-based RNA aptamer chip, SARS N protein was detected at concentrations as low as 0.1 pg mL(-1). CONCLUSIONS: It was demonstrated that the QDs-conjugated RNA aptamer could interact on a designed chip specifically and sensitively. This device could form a QDs-conjugated biosensor prototype chip for SARS-CoV N protein diagnosis. The proposed visual SARS-CoV N protein detection technique may avoid the limitations of other reported methods because of its high sensitivity, good specificity, ease of use, and the ability to perform one-spot monitoring. (C) 2011 Society of Chemical Industry