5-Fluoro-2′-deoxyuridine as an efficient 19F NMR reporter for G-quadruplex and i-motif structures

Abstract

DNA sequences that are composed of multiple G- and C-tracts can potentially form non-canonical structures called G-quadruplex (GQ) or i-motif (iM), respectively. Such sequences are found at the ends of chromosomes (telomeric repeats) and in the promoter region of several genes that cause cancer. Despite extensive studies, distinguishing different GQ and iM topologies is not easy. In this work, we have used one of the conservatively modified nucleoside analogs, namely 5-fluoro-2′-deoxyuridine (FdU) to study different GQ and iM structures of the human telomeric (H-Telo) DNA repeat sequence using ¹⁹F NMR technique. The probe is minimally perturbing and distinguishes different GQ topologies by providing unique ¹⁹F signatures. Our findings suggest that the telomeric repeat assumes hybrid-type GQ structures in intracellular ionic conditions as opposed to a parallel form predicted by using synthetic cellular crowding mimics. Further, with the incorporation of the probe into a C-rich H-Telo DNA ON, we were able to study the transition from iM structure to a random coil structure. Taken together, FdU is a promising probe, which could be used to determine the structure of non-canonical nucleic acid motifs in vitro and potentially in the native cellular environment.