Bridge DNA guided assembly of nanoparticles to program chemical reaction networks

Bridge DNA is an essential structure for programming chemical reaction networks. In this work, a bridge DNA guided assembly of nanoparticles has been constructed to program one-step and multi-step reactions via toehold-mediated strand displacement reaction for higher structural complexity and dynamic regulation behaviors. The structures of the bridge DNA linker and the length of the toeholds have an essential effect on successful construction of a molecular machine and achievement of multi-step reactions. A six-base toehold is enough to achieve the toehold-mediated strand displacement reaction in bridge DNA. When the difference between toehold length-2 and toehold length-1 is equal to or larger than one, the multi-step reaction can be triggered and performed by the driving of bridge DNA. For application, both simultaneous detection of two target DNA strands as well as the construction of logic gates can be achieved by changing the four single-stranded tails on the bridge DNA. In principle, this approach of the bridge DNA guiding the assembly of AuNPs can implement any behavior that can be expressed mathematically.