Engineering a robust DNA split proximity circuit with minimized circuit leakage.

摘要: DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, experimental implementation in silico designs has been hindered by problem leakage. Here, we systematically analyzed sources characteristics various types leakage split proximity was engineered to spatially probe target sites held within close proximity. Direct evidence that 3'-truncated oligonucleotides were major impurity contributing presented. More importantly, unique strategy translocating single nucleotide between domains, termed 'inter-domain bridging', introduced eliminate toehold-independent leakages while enhancing strand displacement kinetics across three-way junction. We also dynamics intermediate complexes involved computation order define working range domain lengths reporter toehold association region respectively. The final design successfully implemented on model streptavidin-biotin system demonstrated robust against both biological interferences. anticipate this simple signal transduction diverse interactions when conjunction with specific recognition moieties.