The structure of aminoallyluridine

Aminoallyl nucleotides are used in post-labeling of nucleic acids to be used in microarrays. These nucleotides are formally known as 5-(3-aminoallyl)-nucleotides since the aminoallyl group is usually attached to carbon 5 of the pyrimidine ring of uracil and cytosine. They are usually abbreviated as aa-, such as aa-dUTP. The amine group in the aminoallyl moiety is aliphatic and thus more reactive compared to the amine groups that are directly attached to the rings (aromatic) of the bases.

Uses

The aminoallyl group in aminoallyl-modified nucleotides is reactive with dyes such as the cyanine series, HiLyte Fluor, or Alexa Fluor dyes that also been modified to be amine-reactive. A problem with this method is that the dyes react with the buffering agent usually used for storage of nucleotides. Instead a carbonate buffer is used. The DNA or RNA from a sample is copied in vitro by T7 polymerase, RT polymerase or some other polymerase (except of eukaryotic origin) in a mix of nucleotides in which one, typically uracil (RNA and also DNA), is a mix aminoallyl-NTP and normal UTP. An alternative method is using thiol reactive dyes.