5-(3-aminoallyl)uridine 5’-triphosphate (AA-UTP) is a cost-effective alternative to direct incorporation of a labeled-UTP when preparing non-radioactive RNA probes by in vitro transcription. AA-UTP is a good substrate for T7, T3 and SP6 RNA polymerases to easily incorporate aminoallyl-uridine residues into RNA strand (Kotaskova et al.). The primary amine of aminoallyl-uridine residues can be easily coupled with NHS-ester derivatives of biotin, fluorescent dye(s) or other molecules of interest. Dye labeled aminoallyl modified RNAs are useful in microarray analysis (t Hoen et al., Scheler et. al.) and have been used for localization of RNA in cell (Wang et. al). Chen et. al. coupled 1,10-phenanthroline to an aminoallyl modified RNA for sequence specific cleavage of nucleic acids. Since AA-UTP (and 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 an introduction of primary amino-functionalities to RNA libraries (Schoetzau et al.).