The encoding mechanism of DNA display. A DNA “gene” (left) is chemically “translated” in three cycles into a small molecule (DAlanine-DLeucine-Norleucine) that remains covalently attached by a linker (purple) to the gene that encoded its synthesis. The system is simplified for illustrative purposes, with only three coding positions (codons) drawn. Each codon is defined by a unique 20-mer DNA sequence. Firstly, the DNA is passed through columns that, together, have oligos complementary to all possible first codon sequences, with the DNA hybridizing to the single column that has a perfect complementary sequence. A different monomer is then reacted with the DNA on each column. This cycle is then repeated for the second and third coding positions. Another example using the nine columns shown is that a DNA with codons B-D-G encodes DLeu-DAla-DAla. In contrast to biological translation, the same codon cannot be repeated in a different codon position. Note that the number of small molecules encoded by a random DNA library increases exponentially as the number of columns increases linearly (e.g., 3³ = 27 small molecules are encoded by 3 × 3 = 9 columns). Once the library is “translated,” it is then subjected to a binding selection, PCR amplification, and potentially DNA shuffling (not shown). All of these steps are then reiterated until DNA sequencing reveals consensus sequences for encoded small molecule binders.