STRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AN AMP-DNA APTAMERCOMPLEX - DISTINCT ARCHITECTURES BUT COMMON RECOGNITION MOTIFS FOR DNA AND RNA APTAMERS COMPLEXED TO AMP

Background: Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection an d amplification have provided a wealth of information on RNA and DNA t ertiary structure and molecular recognition in solution, The RNA and D NA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report b elow on the tertiary structure of the AMP-DNA aptamer complex in solut ion and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. Results: The solution structu re of the AMP-DNA aptamer complex shows, surprisingly, that two AMP mo lecules are intercalated at adjacent sites within a rectangular widene d minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a p air of adjacent three-base platforms. The AMP molecules pair through t heir Watson-Crick edges with the minor groove edges of guanine residue s, These recognition G.A mismatches are flanked by sheared G.A and rev ersed Hoogsteen G.G mismatch pairs.Conclusions: The AMP-DNA aptamer an d AMP-RNA aptamer complexes have distinct tertiary structures and bind ing stoichiometries. Nevertheless, both complexes have similar structu ral features and recognition alignments in their binding pockets, Spec ifically, AMP targets both DNA and RNA aptamers by intercalating betwe en purine bases and through identical G.A mismatch formation, The reco gnition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes, It is striking that DNA and RNA aptamers selected independe ntly from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinit y within binding-site pockets containing common structural elements.