New Strategies for Evaluation and Analysis of SELEX Experiments

Figure 6

The result of mapping the found motif TGGTCCGG onto different predicted secondary structures of aptamers frequently occurring within the final SELEX round is shown. This is done using two examples. In both cases, based on the output of the VARNA [27] online tool, the optimally predicted secondary structure is schematically drawn with the following coloring. Light gray circles are nucleotides of the primer sequences, whereas dark gray and yellow circles are nucleotides of the actual aptamer. The latter are containing the searched motif. The area containing the motif is shaded in a light green tone and additionally presented in a separated detail view besides. In (a), the motif is exactly matching a hairpin loop. In (b) the motif is distributed over paired and unpaired nucleotides. A second detailed view (b′) shows the same part based on a suboptimal structure instead providing a larger loop as an only difference, which holds the motif.