Engineered DNA bonsai system for ultrasensitive wide-field determination and intracellular dynamic imaging of protein with tunable dynamic range and sensitivity

Abstract

Herein, an engineered DNA bonsai system was assembled using DNA nanocube (DNC) as pot and a group of DNA recognition hairpins (RHpn, n = 1–5) as plants for ultrasensitive wide-field detection and dynamic intracellular imaging of matrix metalloproteinase-2 (MMP-2) with tunable dynamic range and sensitivity. Impressively, by changing the stem length of the RHpn (n = 1–5), the thermodynamic parameter free energy (△G) of RHpn was regulated to control the binding reaction between RHpn and output target (OT) (like changing the plants species of bonsai, Bonsai 4-RHpn, n = 1–5). When the △G of RHpn was low, the target detection in high concentration range could be achieved. Conversely, the target detection within the low concentration range also could be realized with the high △G of RHpn. Therefore, the developed biosensing platform based on the engineered DNA bonsai system could achieve the ultrasensitive wide-field determination of MMP-2 with 150000-fold tuned detection sensitivity. Meanwhile, by virtue of the spatial restriction effect of DNC to vary the loaded number and the local concentration of RHp1 (like changing the plants density of bonsai, Bonsai n-RHp1, n = 1–4), the kinetic property of the binding process between RHp1 and OT could be manipulated, in which a low substrate concentration leaded to a low reaction efficiency and a high local concentration resulted in a quick reaction rate with high collision probability. Moreover, the designed DNA bonsai system with the highest local concentration (Bonsai 4-RHp1) could achieve rapid detection of the target MMP-2, which easily conquered the main predicaments of dynamic detection methods: limited dynamic range and low detection efficiency. Most importantly, the programmable DNA bonsai system had been successfully applied in ultrasensitive and high-efficient dynamic visualization of protein MMP-2 in living cells, which could not only make it possible to quickly and precisely monitor disease related proteins with tiny changes at different concentration ranges, but also possess tremendous potential to provide high-precision disease information at different stages in disease diagnosis and prognosis monitoring.