Thieme chemistry journal awardees - where are they now? Synthesis and optical properties of nile red modified 2'-deoxyuridine and 7-deaza-2'-deoxyadenosine: highly emissive solvatochromic nucleosides

Abstract

A general synthetic strategy for the attachment of Nile red through a rigid acetylene linker to 2'-deoxyuridine and 7-deaza-2'-deoxyadenosine using Sonogashira coupling is demonstrated. Protection of either 5'-OH or N-7 of the nucleosides increased the yields of the cross-couplings significantly. Both Nile red modified 2'-deoxyuridine and 7-deaza-2'-deoxyadenosine as well as their derivatives exhibit excellent fluorescence quantum efficiencies and positive solvatochromism. The incorporation of the Nile red modified 2'-deoxyuridine into oligonucleotides yields bright fluorescent probes with maintained canonical base pairing in DNA.