Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA

In vitro transcription of double-stranded DNA (dsDNA) induces a formation of two types of G-quadruplexes, intramolecular DNA G-quadruplexes or DNA:RNA hybrid G-quadruplexes, in clusters of guanine tracts. The formation of G-quadruplexes can be characterized by native PEG polyacrylamide gel electrophoresis, DMS footprinting, and ligand-induced photocleavage footprinting. The type of G-quadruplexes can be distinguished by transcription with 7-deaza-GTP (dzGTP) or 4-thio-uridine-5'-triphosphate (4^SU) to detect the participation of RNA transcript.