Cell-Surface-Anchored Ratiometric DNA Tweezer for Real-Time Monitoring of Extracellular and Apoplastic pH

Zeng, Shu; Liu, Dan; Li, Chi‐Yu; Yu, Feng; Lin, Fan; Lei, Chunyang; Huang, Yan; Nie, Zhou; Yao, Shouzhuo

doi:10.1021/acs.analchem.8b03299

Cited by 77 publications

(71 citation statements)

References 52 publications

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“…The simple chemistry involved makes this method attractive for many different sensors and the use of DNA hybridization technology ensures a high versatility. 152 In addition to these simple examples, more advanced membrane-anchored sensors rely on structural changes of environmentally sensitive DNA motifs, such as the pH sensitive i-Motif 153,154 , G-quadruplexes 141,155,156 , aptamers 138 , DNAzymes 157 , nanotweezers 158,159 and nanoswitches 160 . In these, the structural changes are transformed into a fluorescent read-out by attaching fluorescence quencher or FRET pairs to the DNA, in order to detect protons, metal ions and even small solutes such as ATP.…”

Section: Rational Design Of Fluorescent Dyes To Follow Enzyme Functionmentioning

confidence: 99%

Current problems and future avenues in proteoliposome research

Amati

Graf

Deutschmann

et al. 2020

Biochemical Society Transactions

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Membrane proteins (MPs) are the gatekeepers between different biological compartments separated by lipid bilayers. Being receptors, channels, transporters, or primary pumps, they fulfill a wide variety of cellular functions and their importance is reflected in the increasing number of drugs that target MPs. Functional studies of MPs within a native cellular context, however, is difficult due to the innate complexity of the densely packed membranes. Over the past decades, detergent-based extraction and purification of MPs and their reconstitution into lipid mimetic systems has been a very powerful tool to simplify the experimental system. In this review, we focus on proteoliposomes that have become an indispensable experimental system for enzymes with a vectorial function, including many of the here described energy transducing MPs. We first address long standing questions on the difficulty of successful reconstitution and controlled orientation of MPs into liposomes. A special emphasis is given on coreconstitution of several MPs into the same bilayer. Second, we discuss recent progress in the development of fluorescent dyes that offer sensitive detection with high temporal resolution. Finally, we briefly cover the use of giant unilamellar vesicles for the investigation of complex enzymatic cascades, a very promising experimental tool considering our increasing knowledge of the interplay of different cellular components.

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Section: Rational Design Of Fluorescent Dyes To Follow Enzyme Functionmentioning

confidence: 99%

Current problems and future avenues in proteoliposome research

Amati

Graf

Deutschmann

et al. 2020

Biochemical Society Transactions

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“…DNA and RNA are attractive biomaterials for constructing self-secondary structures, such as aptamers and biosensors [1]. The i-motif (iM) structure represents an example of the structural elements used in biosensor construction [2,3,4,5]. I-tetraplexes are formed by C-rich sequences through intercalation of two parallel duplexes with the hemi-protonated base pairs.…”

Section: Introductionmentioning

confidence: 99%

Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC

Bielecka

Dembska

2019

Molecules

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The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.

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“…Thus motivated, here we designed a functional nucleic acid (FNA)-based DNA nanorobot (denoted as pH-RE) with improved accuracy for in vivo tumor imaging through bispecific recognition of extracellular pH (pH e ) and cell surface receptor (Scheme 1). Decreased pH e in the extracellular milieu of solid tumors is emerging as a new target for cancer diagnosis [31][32][33] due to its unparalleled spatial resolution [34][35][36] in cancer intervention. In our design, two FNAs, named as i-motif and sgc8c aptamer, were chosen to specifically bind H + and the protein tyrosine kinase 7 (PTK7) receptor, respectively.…”

mentioning

confidence: 99%