Aminoallyl nucleotide
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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.
[edit] Uses
The aminoallyl group in aminoallyl-modified nucleotides is reactive with dyes such as Cy3 and Cy5, 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.
A good guide is present on the Invitrogen's Molecular Probes web site.
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