Fig. 2.

Determination of the affinity distribution for UP1 binding to all possible variants of the 7-nt SL3^ESS3 apical loop. (A) Secondary structure of SL3^ESS3 showing the constant base-paired stem loop and the randomized 7-nt apical loop region (red). (B) Affinity distribution of K_A,rel values for UP1 binding to all possible sequence variants in the randomized pool of SL3^ESS3 variants. The vertical line corresponds to the value for the reference native SL3^ESS3 (lnK_A,rel = 0). Seven hundred twenty-two variants bind with higher affinities than native SL3^ESS3, of which 72% contain at least one 5′-AG-3′ dinucleotide. (C) Probability sequence logo calculated for the 50 highest affinity SL3^ESS3 variants. (D) Comparison of experimental K_A,rel values and K_A,rel values predicted using a PWM model that includes interaction coefficients (IC values) between nucleobases. (E) Comparison of the IC values derived from fitting the K_A,rel affinity distribution to Eq. S7 as described in SI Materials and Methods. The magnitude of the IC values is indicated by differences in color: red, positive interactions; blue, negative interactions.