A nucleoside probe containing a 19F label serves as an efficient NMR probe to detect different G-quadruplex and i-motif topologies

Abstract

G-rich and C-rich DNA sequences capable of forming G-quadruplex (GQ) and i-motif structures are often found in the telomeric region and in the promoter region of several oncogenes. Despite extensive studies in vitro, determining their topologies in the native cellular environment is not easy. In this work, we have used one of the conservatively modified nucleoside analogs, namely 5-fluoro-2’-deoxyuridine (FdU) to study the GQ and i-motif structures of the human telomeric (H-Telo) DNA repeat sequence. The probe was found to be minimally perturbing and could distinguish different GQ topologies by providing unique signatures. Previous reports in the presence of synthetic crowding agents have indicated the formation of parallel GQ conformation. However, we found out that the H-Telo DNA ONs did not assume parallel conformation in intracellular buffer conditions using our probe. Further, with the incorporation of the probe into a C-rich H-Telo DNA ON, we were able to study the transition from i-motif to random coil structure. Besides, we were also able to validate the ipH of the C-rich sequence using CD studies. Taken together, 5-fluoro-2’-deoxyuridine is a promising probe, which can be used to determine the structure of non-canonical nucleic acid motifs in the native cellular environment.