The presence of non-complementary probes could prevent aggregation and the solution remains red; while complementary probes could not prevent gold nanoprobe aggregation resulting in a color change from red to blue.
After scanning and image analysis, the RNA abundance (amount of RNA molecules bound to the complementary probes on the microarray) is analysed and the relative gene expression of the treated sample can be compared to the untreated control.
The enormous advantage an mRNA diagnostic would enjoy over protein is that unlike the lengthy optimization required for each protein assay, the ability to detect newly discovered mRNA sequences is as easy as synthesizing complementary probes.
With a sandwich assay format and a rational design of the capture and tagged-signaling probes the problems posed by the strong secondary structure of the target and complementary probes were alleviated.
The SOMAmers that remain attached to beads are eluted under high pH-denaturing conditions and hybridized to sequence-specific complementary probes printed on a standard DNA microarray (Figure 7G,H).
The complementary probes were then checked for uniqueness (see below), and removed if non-unique (exemplified by the removal of 166 out of 273.414 probes from the original E. coli design).
