Fig. 4.

Interstrand cross-linking of residues in front of Ter did not abolish arrest of helicase translocation. (A) (Top) Schematic representation of the cross-linked triplex with Ter in the blocking orientation showing the locations of the various oligos and the cross-links (red x). (Middle) Sequence of the triplex with Ter in the blocking orientation about the region of the cross-links; the phenyl selenide substituted oligo is shown in blue except for the GC6 pair that is shown in red with an asterisk; a part of the 30XL sequence is shown in green. (Bottom) Sequence of the control triplex with Ter in the nonblocking orientation; the 26-mer Φ-Se^NB oligo sequence is shown in blue except for GC6 that is shown in red with an asterisk; the oligo 20-XL is shown in green; the red X shows the location of the cross-link. (B) The reaction pathway for interstrand T-to-A cross-linking caused by oxidation of an oligonucleotide containing two phenyl-selenide-derivatized T residues. C, autoradiogram of a preparative gel showing the separation of residual noncross-linked 99*-mer from the cross-linked 99*-mer with 24Φ-Se^B (arrow). (D) Pooled data from four independent sets of experiments with standard error bars showing the protection of the substrate from melting at the reporter strand by Tus in the blocking and nonblocking orientations of Ter.