Formation of DNA:RNA Hybrid G‐Quadruplexes of Two G‐Quartet Layers in Transcription: Expansion of the Prevalence and Diversity of G‐Quadruplexes in Genomes

Abstract

AbstractG‐quadruplexes are implicated in important cellular processes. Previous studies mostly focused on intramolecular G‐quadruplexes of three or more G‐quartets. Those composed of two G‐quartets were only shown to form in single‐stranded oligonucleotides. On the basis of electrophoresis, DMS footprinting, fluorescence labeling, and photo‐cross‐linking, we detected the formation of DNA:RNA hybrid G‐quadruplexes (HQs) of two G‐quartets during the transcription of DNA duplexes. These HQs have a lifetime on the minute scale and are stabilized by a stabilizing ligand. They are far shorter‐lived than the HQs of three G‐quartets, which last for hours. The occurrence of putative formation motifs of such HQs shows a transcription‐dependent strand‐biased selection, thus supporting their formation and function in genomes. They are present in almost all human genes in large amounts. We speculate that the two‐G‐quartet HQs may be a distinct type of G‐quadruplexes that may play a role in timely responsive processes and for purposes of fine‐tuning.