DNA-Based pH Nanosensor with Adjustable FRET Responses to Track Lysosomes and pH Fluctuations

Abstract

Extensive attention has been recently focused on designing signal adjustable biosensors. However, there are limited approaches available in this field. In this work, to visually track lysosomes with high contrast, we used the i-motif structure as a pH-responsive unit and proposed a novel strategy to regulate the fluorescence resonance energy transfer (FRET) response of the pH sensor. By simply splitting the i-motif into two parts and modulating the split parameters, we can tune the pH transition midpoint (pHt) from 5.71 to 6.81 and the signal-to-noise ratio (S/N) from 1.94 to 18.11. To facilitate the lysosome tracking, we combined the i-motif split design with tetrahedral DNA (Td). The obtained pH nanosensor (pH-Td) displays appropriate pHt (6.12) to trace lysosomes with high S/N (10.3). Benefited from the improved stability, the superior cell uptake and lysosomal location of pH-Td, the visualization of the distribution of lysosomes, the lysosome–mitochondria interaction, and the pH changes of lysosomes in response to different stimuli were successfully achieved in NIH 3T3 cells. We believe that the design concept of controlling the split sequence distance will provide a novel insight into the design of i-motif-based nanosensors and even inspire the construction of smart DNA nanodevices for sensing, disease diagnosis, and controllable drug delivery.

Intracellular pH Control by Membrane Transport in Mammalian Cells. Insights Into the Selective Advantages of Functional Redundancy

“…Concerning lysosomal pH, Yue and collaborators (Yue et al, 2021) developed an interesting FRET-based approach, in which they used a split motif design with tetrahedral DNA that changes conformation with pH to build a nanosensor that has a very good signal to noise ratio around pH 6, well in the range of endo-lysosomal pH values. The large advantage is that such nanoparticular probes can be endocytosed and arrive in lysosomes and endosomes where they will be able to change their emission properties as a function of the pH.…”

DNA Logic Nanodevices for the Sequential Imaging of Cancer Markers through Localized Catalytic Hairpin Assembly Reaction

“…Some cellular ingredients, such as proteins and DNases, may disintegrate the structure of probes to produce false-positive signals. , Hence, the stability of the TDLNs in 0.5 U/mL DNase I and 10% (v/v) FBS was investigated using fluorescence spectra and agarose electrophoresis (Figures S9 and S10). There were negligible changes in electrophoresis band and fluorescence intensity of the TDLNs regardless of whether incubated with DNase I or FBS, revealing that the TDLNs had almost no degradation.…”

Size-Controllable DNA Origami-Stacked Gold Nanoparticles for Deep Tumor-Penetrating Therapy

“…The two components are prepared separately and conjugated easily. More importantly, the pH-sensing range of both the triplex and i-motif structure can be controlled by modulating the cytosine (C) content and positions, , so that the pH-responsive detachment of TDN from GNP could be designed in the case of heterogeneous pH in solid tumors.…”