Self-assembly of polydeoxyadenylic acid studied at the single-molecule level

The investigation on the self-assembly of polydeoxyadenylic acid (poly(dA)) is highly important to fully understand its biological function and for its application in the field of nanotechnology. Using the fluorescence resonance energy transfer (FRET) technique, we report investigations for the self-assembly of adenine oligomers induced by pH and coralyne binding at the single-molecule level and in the bulk phase. Results presented here show that A-motif 1 (Alexa488-5'-(dA)(20)-3'-Cy5-5'-(dA)(20)-3'-Alexa488) forms the wire-type duplex at acidic pH, whereas the same conformation of A-motif 2 (Alexa488-5'-(dA)(20)-3'-Cy5-3'-(dA)(20)-5'-Alexa488) is induced by coralyne binding at neutral pH. These results indicate that poly(dA) at acidic pH forms a right-handed helical duplex with parallel-mannered chains, whereas the coralyne-poly(dA) binding induces a stable antiparallel duplex. Furthermore, we found that the antiparallel duplex of poly(dA) formed by coralyne binding has a rather extended and less twisted structure as compared to the parallel duplex of poly(dA) formed at acidic pH. On the other hand, from dilution experiments, we found that the parallel duplex formed at acidic pH is converted to "S-form", which has the single-stranded structure with short intramolecular double-stranded regions formed by intramolecular A:A base pairing, while the A-motif-coralyne assembly is dissociated into single strands below a certain concentration. The formation of S-form with a short intramolecular double-stranded region formed at acidic pH and very low concentration is confirmed by the quantitative analysis of FCS curve to measure the hydrodynamic radius of a molecule.