Cell Surface-Anchored DNA Nanomachine for Dynamically Tunable Sensing and Imaging of Extracellular pH

Abstract

DNA nanodevices that mimic natural biomolecular machines changing configurations in response to external inputs have enabled smart sensors to live cell imaging. We report for the first time the development of a dynamic DNA nanomachine that is anchored on a cell's surface and undergoes pH-responsive triplex-duplex conformation switching, allowing tunable sensing and imaging of extracellular pH. Results reveal that the DNA nanomachine can be stably anchored on the cell surface via multiple anchors, and the adjustment of CG-C content in the switch element confers tunability of pH response windows. The anchored DNA nanomachine also demonstrates desirable sensitivity, excellent reversibility, and quantitative ability for extracellular pH detection and imaging. This cell surface-anchored pH-responsive DNA nanomachine can provide a useful platform for pH sensing in extracellular microenvironments and diagnostics of different pH-related diseases.

Bifunctional DNA Duplexes Permit Efficient Incorporation of pH Probes into Liposomes

“…An oligonucleotide with a lipophilic moiety, in this case cholesterol, was hybridized with a second oligonucleotide labeled with a pH-sensitive fluorophore and the conjugate was incorporated into the vesicle membrane during liposome formation. In contrast to earlier work, where lipophilic DNA conjugates have been used to sense the extracellular pH of live cells [27,28] , our approach is suited for bottom-up assemblies of complex systems. In this article, we describe the sensitive detection of transmembrane proton transport by purified membrane proteins in synthetic vesicles, requiring a pH sensitive probe located within the liposomal volume.…”

DNA‐Based Architectures for in situ Target Biomolecule Analysis in Confined Nano‐space†

“…Schematic of (A) enzymatic synthesis of DNR structure assembled from RCA scaffold strand and staple strands; (B) a DNA nanomachine for reversible adjustable pH sensor; (C) a pH‐sensitive DNA tweezer for detecting pH in living cell; (D) intracellular operation of a DNAzyme motor initiated by a specific miRNA. (A—C) Adapted with permission from refs 33, 35, and 36. Copyright 2015, 2018, and 2018, respectively, American Chemical Society.…”

“…For example, to detect extracellular pH, Liu and co‐workers designed a novel DNA nanotweezer (NT) sensor with an I‐switch (containing i‐motif sequence) to control its conformational change, which corresponded to its pH change. [ 35 ] Under acid microenvironment, NT exhibited a quite close distance and produced a quenched fluorescent signal, while an activated fluorescence signal was generated in the basic environment. A cholesterol modifier at the end of DNA strand enhanced the stability of the nanomachine attached to the cell membrane (Figure 2B).…”

Recent Progress of SERS Nanoprobe for pH Detecting and its Application in Biological Imaging

“…It is also one of the important parameters for the study of related pathological processes, so the acids and bases inside and outside the cell play an important role in chemical reactions and biological processes [66,67]. Abnormal pHe values are associated with various pathological states, such as tumor, iron-deficiency stroke, infection, and inflammation [68]. Similarly, small changes in pHi can lead to major changes in metabolism that can lead to disease.…”