Relative fluorescence intensity profiles of 2ap incorporated in native and mutated branch site constructs. (A) 2ap was incorporated in place of the canonical branch site residue (A24). The native ψ-modified construct (ψBP2ap), single-stranded intron (102ap) and complementary duplex (10 + 102ap) were used as standards; these standards exhibited comparable relative intensities as previously published (Newby and Greenbaum 2002a). Naming conventions are explained in the text (duplex sequences shown in Fig. 2). (B) With the exception of the ψBP2ap control against which fluorescence of all samples was normalized (2ap in the A24 position), 2ap replaced the adenosine residue 5′ to the branch site A (A23) to test for its intra- vs. extrahelical conformation.
