Shrinkable Nanotubes for Duplex Formation of Short Nucleotides

Molecular monolayer nanotubes produced by self-assembly of an amphiphile modified with a 2-nitrobenzyl group as a photoresponsive unit are able to encapsulate dinucleotides via electrostatic attraction. Upon photoirradiation, the 18 nm inner diameter of the nanotubes shrinks to less than 2 nm as a result of photochemical cleavage of the 2-nitrobenzyl group in the amphiphile. This shrinking of the nanotube channels leads to a propulsive release of the dinucleotides into the bulk solution and simultaneously accelerates formation of the dinucleotide duplexes. The larger nanotube channels without photoirradiation merely release each dinucleotide into the bulk solution, indicating that the squeezing via transportation in the narrow nanotube channels is necessary for duplex formation. In addition to the size effect, water with a lower polarity confined within the narrow nanotube channels helps to stabilize the energetically unfavorable hydrogen-bonded base pair between the dinucleotides. This system should enable researchers to perform biological reactions that occur only in specific environments and conditions in living organisms.