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The biological sensitivity of a DNA chip depends on the molecular organization of the immobilized probe molecules, single stranded DNA (ss-DNA), on the substrate in terms of accessibility and non specific interactions between probes and substrate. In this article, Amplitude Modulation - Atomic Force Microscopy (AM-AFM) was used to characterize at a molecular scale, the morphological organization of different immobilized probes. In our system, three different ss-DNA were covalently grafted on a silicon substrate with the same deposit process. We studied the influence of probe length (25 bases, 12 bases) and sequence arrangement (two different 25 base oligoprobes) on the morphological organization. We showed that immobilized probes organize themselves in different structures depending on their sequence.

AFM characterization of ss-DNA probes immobilization: a sequence effect on surface organization