Biotin-11-UTP serves as the label in the MessageAmp II-Biotin Enhanced Kit. Only a single biotinylated NTP is used because studies at Ambion and elsewhere  showed that in previous dual labeling experiments using biotin-UTP and biotin-CTP, the signal contributed by biotin-CTP was minimal, and relative signal intensity between genes was not altered with the use of a single biotin UTP label.
While various linker arm sizes (e.g., Biotin-11-UTP, Biotin-16-UTP) did not affect modified UTP incorporation into aRNA during IVT, the longer linker arms slightly impeded subsequent purification of the aRNA. Biotin-11-UTP provided the highest yields of aRNA.
The ratio of biotin UTP to unlabeled UTP was optimized
to provide the highest yield of aRNA and the highest signal:noise on Affymetrix
GeneChip Arrays. A fairly wide range of concentrations of Biotin-UTP (25 60%) can be used for acceptable detection,
whereas at lower concentrations the signal drops dramatically, and at