Aminoallyl-UTP can be enzymatically incorporated into RNA with T7, T3 and SP6 RNA polymerases. The resulting amine-containing RNA can be subsequently labelled with any amine-reactive fluorescent dye, biotin, or hapten. Dye labelled aminoallyl modified RNAs are used in microarray analysis and for localization of RNA in the cell. Also, 1,10-phenanthroline can be coupled to an aminoallyl modified RNA for sequence specific cleavage of nucleic acids.

Since AA-UTP (as well as AA-CTP) maintains a strict Watson-Crick base pairing recognition, it is suited for the systematic evolution of ligands by exponential enrichment (SELEX) process thus allowing introduction of primary amino-functionalities to RNA libraries.

Molecular formula: C₁₂H₂₀N₃O₁₅P₃  (Acid Form)