Figure 1.

Nucleic acid recognition by peptides, proteins, and synthetic ligands. (A) Two codes for sequence-specific recognition of DNA have been established: pyrrole-imidazole (Py-Im) polyamides bind DNA in the minor groove (PDB code 3omj) while zinc-finger proteins recognize the DNA major groove (PDB code 1mey). RNA recognition by protein secondary structures is illustrated by the Rev α-helix peptide (PDB code 1etf) and Tat β-hairpin mimetic (PDB code 2kdq). (B) Specific nucleic acid recognition by protein and peptides requires nucleobase - side chain contacts; two canonical examples of Hoogsteen surface recognition by guanidine and amide protein side chain functionality are shown.