Figure 1.

(A) Crystal structure of 1dcw, the inverted repeat d(CCGGTACCGG)₄ (ApC) junction resolved to 2.1 Å. In the center of the junction in pink is a crystallographically resolved sodium ion. Strands I and III are linear; II and IV are crossover strands. The reported J_twist and IDA angles between the pseudoduplexes are ∼41° and ∼60°, respectively. (B) Strand sequence and numbered base layout for the ApC junction. Junction bases refer to A16pC17 and A36pC37 of strands II and IV. (C) A schematic representing the canonical stacked-X and open-X conformations of a Holliday junction, denoted STX and OPN, respectively. The STX form is characterized by either an antiparallel or parallel directionality, the former of which applies to the ApC junction. (D) Phosphate group atoms in the junction crossover site of bases A16, C17, A36, and C37, and the crystallographically resolved sodium ion in pink. Distances are shown in angstroms.