Cited by DNA logic circuit coupled with enzymatic amplification for signal-enhanced, AND-gated imaging of inflammation-associated mRNAs

Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues DOI

Zeyin Zhao, Mengyuan Jiang,

Chen He

et al.

ACS Nano, Journal Year: 2024, Volume and Issue: 18(14), P. 9958 - 9968

Published: March 28, 2024

Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging formalin-fixed paraffin-embedded (FFPE) specimens. Moreover, associated complex procedures can produce uncertain results poor image quality. Herein, by combining specificity split DNA probes readout ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, high-brightness smFISH technology, to quantify expression mRNA both cell lines FFPE samples breast cancer lung squamous carcinoma. Owing its signal-to-noise ratio, split-FISH is fast, inexpensive, sensitive method quantifying tumor tissues, making it suitable biomarker pathology.

Language: Английский

Citations

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections DOI

Xinbin Tang,

Jiayu Chen, Xinya Zhang

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(9), P. 652 - 660

Published: Feb. 15, 2023

Language: Английский

Citations

Enhanced single RNA imaging reveals dynamic gene expression in live animals DOI

Yucen Hu,

Jingxiu Xu,

Erqing Gao

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: March 3, 2023

Imaging endogenous mRNAs in live animals is technically challenging. Here, we describe an MS2-based signal amplification with the Suntag system that enables live-cell RNA imaging of high temporal resolution and 8xMS2 stem-loops, which overcomes obstacle inserting a 1300 nt 24xMS2 into genome for mRNAs. Using this tool, were able to image activation gene expression dynamics epidermis C. elegans .

Language: Английский

Citations

Dye disaggregation light-up aptamer for super-resolution RNA imaging DOI

Chunyu Yan,

Miao Lü, Yan Zhang

et al.

Sensors and Actuators B Chemical, Journal Year: 2023, Volume and Issue: 386, P. 133731 - 133731

Published: March 25, 2023

Language: Английский

Citations

Apicobasal RNA asymmetries regulate cell fate in the early mouse embryo DOI

Azelle Hawdon, Niall D. Geoghegan,

Monika Mohenska

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 30, 2023

Abstract The spatial sorting of RNA transcripts is fundamental for the refinement gene expression to distinct subcellular regions. Although, in non-mammalian early embryogenesis, differential localisation presages cell fate determination, mammals it remains unclear. Here, we uncover apical-to-basal asymmetries outer blastomeres 16-cell stage mouse preimplantation embryos. Basally directed transport facilitated a microtubule- and lysosome-mediated manner. Yet, despite an increased accumulation basal regions, higher translation activity occurs at more dispersed apical foci, demonstrated by heterogeneities subtypes, RNA-organelle interactions events. During transition 32-cell stage, biased inheritance transcripts, coupled with capacity, regulates allocation trophectoderm cells destined form pluripotent inner mass. Our study identifies paradigm spatiotemporal regulation post-transcriptional governing mammalian embryogenesis fate.

Language: Английский

Citations

Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction DOI

Xiaoxue Cheng,

Xiaosong Li,

Yuexi Kang

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(22), P. e111 - e111

Published: Nov. 6, 2023

RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency time-consuming operation hinder clinical application. Here, we first proposed a new strand displacement (SDR) model (Cas12a thrusting SDR, CtSDR), which Cas12a could overcome inherent limitation dramatically enhance energy replenishment by-product consumption. The target-initiated CtSDR amplification was established for analysis, order of magnitude lower limit detection (LOD) than Cas13a system. CtSDR-based strategy developed to monitor intra-cellular microRNA expression change delineate landscape oncogenic 66 clinic tissue samples, possessing clear advantage over classic hybridization (ISH) terms time (1 h versus 14 h) showing comparable sensitivity specificity. This work presents promising approach developing advanced molecular diagnostic tools.

Language: Английский

Citations

Spatial omics advances for in situ RNA biology DOI

Jingyi Ren, Shuchen Luo, Hailing Shi

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

Strategic Modulation of Polarity and Viscosity Sensitivity of Bimane Molecular Rotor-Based Fluorophores for Imaging α-Synuclein DOI

Yarra Venkatesh, Karthik Narayan, Tobias Baumgart

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Molecular rotor-based fluorophores (RBFs) that are target-selective and sensitive to both polarity viscosity valuable for diverse biological applications. Here, we have designed next-generation RBFs based on the underexplored bimane fluorophore through either changing in aryl substitution or varying π-linkages between rotatable electron donors acceptors produce red-shifted fluorescence emissions with large Stokes shifts. exhibit a twisted intramolecular charge transfer mechanism enables control of sensitivity, as well target selectivity. These features enable their application in: (1) turn-on fluorescent detection α-synuclein (αS) fibrils, hallmark Parkinson's disease (PD), including amplified fibrils from patient samples; (2) monitoring early misfolding oligomer formation during αS aggregation; (3) selective imaging condensates formed by liquid-liquid phase separation (LLPS). In all three cases, show our probes high levels selectivity versus other aggregating proteins. properties one study interplay tau amyloid aggregation mechanisms underlying neurodegenerative disorders.

Language: Английский

Citations

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture DOI

Luiz F. M. Passalacqua, Mary R. Starich, Katie A. Link

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 23, 2023

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, conditional fluorophore derived from GFP. It 70% sequence-identical to the previously characterized aptamer Corn, which one molecule of its cognate DFHO at interprotomer interface. We have now determined Beetroot-DFAME co-crystal structure 1.95 Å resolution, discovering this homodimer two molecules fluorophore, sites separated by ~30 Å. In addition overall architectural difference, local structures non-canonical, complex quadruplex cores Corn are distinctly different, underscoring how subtle sequence differences can give rise unexpected structural divergence. Through structure-guided engineering, we generated variant has 12-fold fluorescence activation selectivity switch toward DFHO. form heterodimers constitute starting point for engineered tags whose through-space inter-fluorophore interaction could be used monitor dimerization.

Language: Английский

Citations

CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis DOI

Shuo Huang, Rui Dai,

Zhiqi Zhang

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(17), P. 13447 - 13447

Published: Aug. 30, 2023

CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) Cas enzymes, scope has expanded beyond they been utilized various fields, particularly live-cell imaging bioanalysis. In this review, we summarize some fundamental working mechanisms concepts systems, describe recent advances design principles mediated techniques employed bioanalysis, highlight main biosensing a wide range molecular targets, discuss challenges prospects biosensing. By illustrating bio-sensing processes, hope review will guide best use quantifying biological clinical elements inspire new ideas for better tool

Language: Английский

Citations