Knotting dynamics during DNA replication

9 páginas, 7 figuras, -- PAGS nros. 699-707The topology of plasmid DNA changes continuously as replication progresses. But the dynamics of the process remains to be fully understood. Knotted bubbles form when topo IV knots the daughter duplexes behind the fork in response to their degree of intertwining. Here, we show that knotted bubbles can form during unimpaired DNA replication, but they become more evident in partially replicated intermediates containing a stalled fork. To learn more about the dynamics of knot formation as replication advances, we used two-dimensional agarose gel electrophoresis to identify knotted bubbles in partially replicated molecules in which the replication fork stalled at different stages of the process. The number and complexity of knotted bubbles rose as a function of bubble size, suggesting that knotting is affected by both precatenane density and bubble size.This work was partially financed by grants PM97-0138, PB98-048 and SAF2001-1740 from the Spanish Ministerio de Ciencia y Tecnología (MCyT), and by grant 99/0850 from the Spanish Fondo de Investigación Sanitaria (FIS).Peer reviewe