Structural studies of DNA and RNA containing AG base pairs by NMR

Base pairing between A and G residues has been suggested in some ribozymes and the structure derived from this non-standard base pairing could play a crucial role in enzymatic actions of the ribozymes. We have studied the structures of three DNAs and an RNA that base sequences were modeled after the ribozymes by NMR. It was found that the A and G residues can form a basepair in a very unique fashion both in the DNAs and RNA. "Side" instead of "head to head" alignment of the two bases was found, where an amino proton instead of an imino proton of the G residue is involved in the hydrogen bonding. As a result of the unique basepairing, certain bases stack over the bases of the opposite strand instead of over the ones of the same strand. It was also shown that the formation and thermal stability of this unique AG basepair depend on the neighbouring base sequences. Moreover existence of the unique AG basepairs was suggested in a real small metalloribozyme itself.