C-DNS: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences

Abstract

With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized C-DNS, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. C-DNS undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing C-DNS are dependent on the nature of the flanking and neighboring bases. Notably, C-DNS exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of C-DNS can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.