Excision of Tn6283 from the E. coli chromosome.

(A) Design for PCR detection of recombination products. The diagrams show the hypothetical scenario in which Tn6283 excises itself as a circular molecule and forms a heteroduplex joint, while the Tn6283 donor site also forms a heteroduplex joint. The PCR-amplified heteroduplex joints should contain two types of sequences in the spacer between terminal repeat sequences. (B) PCR detection of joint formation on the recombination products. Lane 1: long PCR designed to detect the occupied Tn6283 donor site (primer set 2599572R-2599370F). Lane 2: detection of unoccupied Tn6283 donor sites (primer set 2599572R-2599370F). Lane 3: detection of circularized Tn6283 (primer set 3F-3R). (C) Sequences of PCR-amplified joints on the circularized Tn6283. The observed frequency is indicated next to each sequence. (D) Sequences of PCR-amplified joints on the unoccupied Tn6283 donor sites. In the upper panel, two types of expected joint sequences are shown. The lower panel shows the unexpectedly observed sequence, designated Scar.