Catalytic Formation of Luminescent Complex Clusters Based on Autonomous Strand Exchange Reaction of DNA

DNAs can act as flexible interfaces for arranging particular reactant partners such as biomolecules and other functional molecules modified on DNAs in close proximity to increase their effective concentrations. Here, we focused on dynamic programmability of the DNA structure based on sequence-specific autonomous strand exchange reactions triggered by an initiator DNA, i.e., DNA circuits, to achieve a catalytic reaction providing physical and chemical signals. For analytical applications, DNA-templated formation of luminescent lanthanide (Ln) complexes was combined with the described amplification system. An appropriate microenvironment for the accommodation of a lanthanide ion [Ln(III)] was constitutively generated by ethylenediaminetetraacetic acid (a chelator) and 1,10-phenanthroline (a sensitizer) tethered to the ends of assembled DNAs to form a luminescent complex. For DNA circuits, we used hybridization chain reaction and catalytic hairpin assembly to construct linear and cruciform DNA structures, respectively, as scaffolds of Ln cluster formation. Both systems were designed for complex formation at every site where the ends of constituent DNAs faced each other on the DNA scaffolds by addition of an initiator. After optimization of the reaction conditions, amplified luminescence of a Tb(III) complex was obtained, which implies formation of a large number of complexes after addition of the initiator DNA. The formation of lanthanide complex clusters can be simply governed by the thermodynamics of duplex hybridization, which can be rationally controlled by well-established parameters such as the DNA length and sequence, concentration, temperature, and ionic strength. The emission color of the Ln cluster can be easily changed by choosing Ln ions with the desired color. The principle behind this technique is simple; therefore, it can be applied to various catalytic DNA-templated reactions by replacing lanthanide complex ligands by other functional molecules and materials.