A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes.
After denaturing labelled targets were hybridized onto the microarray surface and covered with a glass coverslip (24 × 9 × 60 mm, Menzel-Glazer, Germany).
Furthermore, these approaches do not take into consideration probe interaction with microarray surface, in particular the impact of mismatches position between the target and probes, as shown by Hughes et al [ 15].
In the experiment, the microarray surface was first equilibrated with the buffer solution, followed by the injection of HA protein solution (marked by a downward arrow) and, after some time, the injection of washing buffer to remove the unbound HA (upward arrow).
200 pmoles of purified Cy3- and Cy5-labelled aRNAs were combined in a buffer containing 2× SSC, 0.08% SDS and Liquid Blocking Reagent (GE Healtcare), and were dispensed over the microarray surface, and incubated at 55°C overnight with agitation.
PCR-amplified yeast control sequences and the corresponding high-quality yeast control oligonucleotides were used on the microarray surface to assess whether a bias with respect to oligonucleotide position within the transcript had occurred.
The chamber was then removed, and the microarray surface was washed twice (approximately 30 s each) with water at 37°C and air-dried.
In addition, the St-2-1 aptamer forms a double-stranded structure with two loops, which may further increase molecular crowding at the microarray surface.
Comparison of the secondary structure with the microarray results led to the hypothesis that binding of probes on the microarray surface may induce structural rearrangement of RNRspBs.
