Synthesis of 2′-deoxycytidine and its triphosphate bearing tryptophan-based imidazolinone fluorophore for environment sensitive fluorescent labelling of DNA

Abstract

We synthesized 2′-deoxycytidine and the corresponding nucleoside triphosphate bearing (indol-3-yl)methylene-2-methyl-5-oxo-4,5-dihydroimidazol-1-yl group (a tryptophan-based fluorophore from cyan fluorescent protein) linked through a propargyl group at position 5. The fluorophore is weakly solvatochromic, sensitive to pH, and, as a molecular rotor, it is highly sensitive to viscosity. In low viscosity solvents, the fluorescence is very weak, whereas in more viscous environment it lights up. Primer extension or PCR using the modified dCTrpTP and KOD XL DNA polymerase was used for construction of labelled oligonucleotides and DNA. Preliminary study showed a 2-fold increase of fluorescence of labelled ON probe in presence of single strand-binding protein indicating a potential of this label for sensing of protein-DNA interactions.