5-(Acridin-9-ylamino)uracil - A hydrolytically labile nucleobase modification in peptide nucleic acid

5-Aminouracil (5-AU) is a readily available yet underutilized starting material for the synthesis of labelled nucleobase analogues. We have prepared the derivative of 5-AU with the amine-reactive chromophore 9-chloroacridine for the purpose of investigating its potential as a base-discriminating fluorophore. 9-Chloroacridine readily undergoes substitution by reaction with 5-AU to yield a fluorescent nucleobase that after standard manipulations produced a monomer suitable for incorporation into peptide nucleic acid (PNA) by fluorenylmethyloxycarbonyl (Fmoc)-based oligomerization chemistry. Although the monomer was stable in organic solvents, once incorporated into an oligomer the 5-substitution was found to be thermally labile and hydrolyzed to a small degree in neutral aqueous solution during study of its hybridization to cDNA. We have determined that 5-(acridin-9-ylamino)uracil and related derivatives produce the highly fluorescent acridone and 5-AU by hydrolysis in water.