File:Nicholson1997Fig1.PNG

Figure 1 from Zhang and Nicholson, PNAS 1997.

(A) Substrate alignment analysis. Ten substrates were aligned whose cleavage sites were accurately determined, either by direct RNA sequence analysis or by primer extension of RNA cleaved in vitro by purified RNase III. (B) The “disfavored” bp, displayed in a dsRNA structure. The proximal box (PB) and distal box (DB) are included within an 11-bp helix. S = C or G, with S′ complementary to S. N, N′ indicate complementary nucleotides; while n, n′ indicate less strict complementarity. Arrowheads indicate the (blocked) cleavage sites. (C) Absence of conservation (degeneracy) of RNase III substrate sequence. H = A, G, U, with D′ (A, C, U) complementary to H; B = C, G, U, with V′ (G, C, U) complementary to B; W, W′ = A, U. (D) Secondary structure of the T7 R1.1 RNase III substrate, showing the proximal and distal boxes and the single cleavage site (arrowhead).