A Guanine Ribonucleotide Atypically Adaptive to the Syn Glycosidic Conformation in a Human Telomeric DNA–TERRA RNA Hybrid G-Quadruplex with (3 + 1) Mixed Strand Orientations Studied by NMR

The generation of RNA–DNA hybrid G-quadruplexes (RDQs) through heteromeric association between individual DNA and RNA G-rich strands has been proposed as an important mechanism in the regulation of genome transcription, replication, and telomere capping. Based on low-global-structure-resolution circular dichroism spectra, numerous RDQs have been routinely detected almost exclusively in a parallel topology because of the inherent preference of riboguanosine (rG) to adopt an anti glycosidic torsion angle. However, high atomic-resolution structures of RDQs resolved using nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or cryogenic electron microscopy (CryoEM) remain unavailable in the PDB database at present. To the best of our knowledge, this study is the first to present an NMR structure of a human telomeric RDQ (Htel-RDQ) assembled between a three-repeat human telomeric DNA strand of d(GGGTTAGGGTTAGGG) and a single-repeat TERRA RNA strand of r(UAGGGU). Interestingly, this Htel-RDQ uncommonly adopts a (3 + 1) hybrid topology featuring three parallel and one antiparallel strand orientations, with one rG atypically in the syn glycosidic torsion angle and a C2′-endo sugar pucker conformation. The findings of this study confirm that the inherent anti rG preference in RNA G-quadruplexes can be adaptively unrestricted in an RDQ assembly and disclose a latent structural complexity previously unanticipated in RDQs.