Figure 1. Library development. (a) Ethidium bromide‐stained 1.2% agarose gel showing the size distributions of genomic Arabidopsis thaliana DNA after isolation (lane 1) and after fragmentation via ultrasound (lane 2). Lane M1 is a lambda HindIII marker; lane M2 is 100 bp DNA size ladder (Fermentas); (b) Example of an autoradiogram showing size distribution of the fragmented DNA after ligation of primer‐adaptors. Lanes 2 and 4 are control lanes showing radioactively labeled reverse (R _ran) and forward (F _ran) primers, respectively. Lanes 1 and 3 are DNA from the first and second Klenow extension reaction, respectively. Lane M is a φX174 DNA/HinfI‐labeled size marker (Promega).

Figure 2. Recovery of RNA during the selection cycles with atCyp59 as a bait. This example of a typical Genomic SELEX experiment shows the increasing recovery of selected RNAs with increasing numbers of selection cycles. The first four cycles are carried out under relaxed selection conditions, with a molar excess of RNA over protein of 3:1. These conditions allow the selection of ligands with a low affinity. Further cycles of selection are performed with an excess of RNA over protein of 10:1. In the penultimate step, a counter‐selection step is included with GST‐tag protein alone to assure the exclusion of binders to the GST‐tag from the pool.