DNA hybridization onto solid surfaces forms the basis for applications of DNA microarrays. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is an excellent tool for chemical characterization of surfaces because of its molecular specificity, surface sensitivity and excellent mass resolution. Previous studies have indicated the possibility to follow hybridization based on the phosphate signal from the backbone. We have employed DNA molecules which have a C6 thiol linker at its 3' end and selfassemble onto gold surfaces. The positive spectrum has peaks from the sugar backbone as well as peaks from the individual bases [base + H](+) The negative spectrum has intense peaks from the phosphate backbone as well as peaks from the bases [base -H](-). Our hypothesis that hybridization onto these single-stranded DNA (ss DNA) should change the fragmentation pattern of these molecules in ToF-SIMS is confirmed by principal component analysis (PCA) of these ToF-SIMS spectra. Briefly, principal component 1 (PC1) of the positive ToF-SIMS spectra separates the hybridized DNA from the ss DNA. Similar results were observed for the negative spectra. These results were supported by surface plasmon resonance experiments (SPR), which indicate that hybridization does occur and is believed to be reason for the change in the fragmentation pattern of the ToF-SIMS spectra. (C) 2004 Elsevier B.V. All rights reserved.