Formation of knots in partially replicated DNA molecules

Bacterial plasmids with two origins of replication in convergent orientatio n are frequently knotted in vivo. The knots formed are localised within the newly replicated DNA regions. Here, we analyse DNA knots tied within repli cation bubbles of such plasmids, and observe that the knots formed show pre dominantly positive signs of crossings. We propose that helical winding of replication bubbles in vivo leads to topoisomerase-mediated formation of kn ots on partially replicated DNA molecules. (C) 1999 Academic Press.