We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid-nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids x 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid-nucleotide interactions facilitates understanding the specificity of protein-nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.

It has been suggested that in vitro selection experiments can provide information not only on what might have occurred during the evolution of the RNA world, but can in fact yield insights into particular features of the RNA world. In particular, it has been suggested that the sequences of anti-amino acid aptamers can provide clues to the origin of the genetic code, and that there is a statistically significant association between motifs found in aptamers and codons. We argue that the suggested connections between modern motifs and ancient sequences are logically tenuous, and show that there is no statistically meaningful association between motifs found in aptamers and codons.