Stability of G/C DNA Tetraplexes at Physiological pH Formed at the Promoter-UTR Intersection of the RAP2C Gene: Structural Multitude of a G/C Rich Genomic Segment.

Genomic guanine-rich segments are prone to adopting self-associated noncanonical structures termed G-quadruplex structures. An overabundance of reports reveals their existence prevalently at important genomic locations, including oncogenic promoters, exonic regions, immunoglobulin switch regions, telomeres, etc. Undeniably, these structures have been the subject of curiosity for many decades, leading to mounting evidence suggestive of their involvement in key cellular processes. Herein, we identified a 45-mer G-rich segment containing G5 tracts, present at the intersection of the promoter and 5'-UTR region of the RAP2C gene of the ras oncogene family, found to fold into a G-quadruplex structure. We employed biochemical and biophysical techniques for structural characterization of the G-rich segment (RAP2C45) and its C-rich counterpart (RAP2C45C). RAP2C45 adopts a bimolecular and unimolecular G-quadruplex structure in Na+, whereas the presence of K+ favors predominantly the unimolecular G-quadruplex. The counterpart C-rich segment RAP2C45C adopts an i-motif (C-tetraplex) at physiological and acidic pH. Bioinformatics analysis identified the presence of Sp1 and Rap1 transcription factors in the vicinity and overlapping throughout the studied sequence, indicating the role of these noncanonical structures in gene regulation. As noncanonical structures are promising targets for developing new drugs, the present study may add to the understanding of designing novel molecules with promising therapeutic applications.