Screening peptoid microarrays with labeled RNA. (A) RNAs used to probe the arrays. A fluorescent dye, Dy547, was appended to the 5′ end of each RNA for microarray screening. The adenosines in large bold type were replaced with 2-ap in subsequent experiments to determine dissociation constants by fluorescence. RNA I (miR-21 hp) corresponds to the apical loop from the primary transcript of miR-21. RNA II (control) was used as a control to counter-screen for specificity. The secondary structures shown for RNAs I and II are predicted by the Mfold program (Zuker 2003). (B,C) Fluorescence scans of a region of an array (Sublibrary B) that contains the feature (indicated by the arrows) corresponding to 12 after treatment with (B) labeled RNA I or (C) labeled RNA II. A grid of circles is overlaid on each scan to indicate the pattern of spotting. Each circle corresponds to an area with a diameter of 150 µm.
