Figure 2.

N/N 2D gel analyses of replication intermediates from the predicted replication origin region of P. abyssi. Replication intermediates were prepared from asynchronous P. abyssi cultures by an agarose plug method. A–D correspond to the analysis of restriction fragments A to D with the use of probe 1 (Fig. 1). (E) The expected pattern for fragments containing either one replication fork (Y arc) or two replication forks with an internal initiation site (bubble arc). The filled arrows indicate the bubble arcs observed for fragments B and C by probe 1 (similar results for fragments B and C were obtained when probe 2 was used). In addition to a well-defined Y arc, fragments A and D show weak signals (small arrows) detected by probe 1. These signals are consistent with an asymmetrically located replication origin within the central third of the fragments B and C. The mobilities of the dark spots on the line traced by linear fragments are consistent with impartial digests. (F) Structure of the oriC region with the identification of the two duplex unwinding elements (DUE) (19) and conserved nucleotide repeats (indicated by arrows) (12). Longer arrows indicate 34-bp repeats earlier unnoticed.