Unwanted initial and asymptotic leakages are vital to fabricating integrated circuitries. This paper presents a novel strategy that combines simulations and experiments to extend the circuitries of spherical nucleic acid (SNA) to three layers. The results indicate that SNA-based circuits are insensitive to initial leakage but are significantly influenced by asymptotic leakage, particularly for the two-layer circuit. The dynamic behaviors of and the effects of leakage on the performance of the integrated system can be regulated by fine tuning of toehold domains and the molar ratio of the species. Small upstream layers and a large downstream layer are experimentally adopted to balance the stability and operation efficiency of the integrated three-layer circuitry. This work soundly demonstrates the capability of fabricating modular cascaded circuitry for driving SNA assembly in sophisticated systems, and modulating or programming the molecular machinery for developing an autonomous system.