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. 2007 Apr 30;27(13):4745–4758. doi: 10.1128/MCB.00177-07

FIG. 1.

FIG. 1.

Synapsis occurs preferentially for a unique helical orientation of the RSSs. (A) The prototype substrate for the facilitated ligation assay, S89, contains 89 bp between the nonamers of the 12-RSS and 23-RSS (white and gray triangles and arrows, respectively) and 50-bp left and right flanks terminating in XbaI-compatible ends. Black arrows indicate the relative orientations of the two RSSs. (B) The RSS is depicted as a triangle with the wide side corresponding to the heptamer (hep) and the narrow side corresponding to the nonamer (non). A vertical arrow indicates the site of cleavage. (C) The other substrates differ from S89 by increments of 3 bp in the distance separating the two RSSs. The relative orientations of the two RSSs are represented by arrows on clock faces with the arrow for the 12-RSS arbitrarily set pointing up. (D) Ligation (circularization) efficiencies for each of the 10 substrates. Values for each substrate are the averages of results from three independent experiments and were normalized to the ligation efficiency seen with RAG1 (R1) and HMGB2 for that substrate (error bars indicate standard deviations).