Practice question

Behind elongating RNA polymerase, DNA becomes transiently underwound creating negative supercoiling that favors strand separation and R-loop formation where nascent RNA anneals to template strand displacing non-template strand. Type IA topoisomerase I encoded by topA in E. coli cleaves single strand of duplex without ATP, allows passage of other strand through break, then religates, incrementally relaxing negative supercoils. Activity restores normal superhelical density behind complex, preventing excessive unwinding that would promote genome instability. DNA gyrase acts ahead removing positive supercoils; distinct substrate preferences ensure topological homeostasis balanced during active transcription and replication.