Analysis of RNA–DNA Triplex Structures In Vitro and In Vivo

RNA can bind within the major groove of purine-rich DNA via Hoogsteen base pairing and form a triple helical RNA–DNA structure that anchors the RNA to specific DNA sequences, thereby targeting RNA-associated regulatory proteins to distinct genomic sites. Here we present methods to analyze the potential of a given RNA to form triplexes in vitro and to validate these structures in vivo.