Harnessing Demethylase-Regulated Catalytic DNA Circuit for In-Situ Investigation of the Regulatory Connection with MicroRNA DOI
Guangqin Liu, Yifei Wang,

Yuqiu He

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(51), P. 20304 - 20311

Published: Dec. 12, 2024

Insight into the epigenetic modulation-correlated molecule interactions has significant implications for in-depth understanding of intracellular intricate biological networks. However, there is currently a lack reliable tools elucidating potential correlation between regulators and relevant genes, e.g., microRNAs (miRNAs). Herein, an alkB homologue 5 (ALKBH5, key regulator)-modulated catalytic DNA circuit (ACD) was constructed by grafting N6-methyladenosine (m6A)-caged I-R3 DNAzyme circuitry components achieving on-site miRNA imaging in living cells. Specifically, activity could be effectively suppressed m6A modification situated at its highly sequence-conserved core region then selectively restored through ALKBH5-mediated demethylation pathway. And ALKBH5-activated allowed efficient cleaving reaction presence cofactors, resulting liberation hairpin assembly (CHA) reactants. Subsequently, target triggered CHA to produce duplex product while releasing analyte. The liberated autonomously trigger next round cycle generating amplified fluorescence readout. By virtue stimuli-responsive activation amplification circuit, ACD system achieved specific sensitive tumor Moreover, this efficiently reliably demonstrated reveal underlying relationship activator ALKBH5 miRNA. Overall, developed provides promising tool robust profiling epigenetic-involved signal pathways, thus displaying great bioanalytical applications.

Language: Английский

A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals DOI

Yuxuan Zhu,

Ruomeng Li, Yifei Wang

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(23), P. 9666 - 9675

Published: May 30, 2024

Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) live cells and mice by eliminating undesired off-site signal leakage. The simple robust DSC composed primary cell-specific regulation (CR) module ultimate signal-transducing amplifier (SA) module. After the modularly designed was delivered into target cells, DNAzyme CR site-specifically activated endogenous demethylase produce fuel strands subsequent miRNA-targeting SA Through on-site multiply guaranteed recognitions, lucid efficient realized reliably amplified vivo miRNA sensing enabled in-depth exploration demethylase-involved pathway with cells. Our bioorthogonally on-site-activated represents universal versatile biomolecular platform via various regulations shows more prospects different personalized theragnostics.

Language: Английский

Citations

10
An Enzymatically Activated and Catalytic Hairpin Assembly-Driven Intelligent AND-Gated DNA Network for Tumor Molecular Imaging DOI
Mengxin Zhang, Yingyu Zhang, Xianwei Zhang

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(24), P. 10084 - 10091

Published: June 5, 2024

Due to the potential off-tumor signal leakage and limited biomarker content, there is an urgent need for stimulus-responsive amplification-based tumor molecular imaging strategies. Therefore, two tetrahedral framework DNA (tFNA-Hs), tFNA-H1AP, tFNA-H2, were rationally engineered form a polymeric tFNA network, termed intelligent in AND-gated manner. The network was designed tumor-specific by leveraging elevated expression of apurinic/apyrimidinic endonuclease 1 (APE1) cytoplasm instead normal cells high miRNA-21 cytoplasm. activation tFNA-H1AP can be achieved through specific recognition cleavage APE1, targeting site (AP site) modified within stem region hairpin (H1AP). Subsequently, facilitates hybridization activated H1AP on with 2 (H2) triggering catalytic assembly (CHA) reaction that opens at vertices bind H2 tFNA-H2 generate fluorescence signals. Upon completion hybridization, released, initiating subsequent cycle CHA reaction. achieve vivo also enables risk stratification neuroblastoma patients.

Language: Английский

Citations

9
All-In-One Entropy-Driven DNA Nanomachine for Tumor Cell-Selective Fluorescence/SERS Dual-Mode Imaging of MicroRNA DOI
Shuzhen Yue, Xuan Xu, Liping Jiang

et al.

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

An entropy-driven catalysis (EDC) strategy is appealing for amplified bioimaging of microRNAs in living cells; yet, complex operation procedures, lacking cell selectivity, and insufficient accuracy hamper its further applications. Here, we introduce an ingenious all-in-one DNA nanomachine (termed as AIO-EDN), which can be triggered by endogenous apurinic/apyrimidinic endonuclease 1 (APE1) to achieve tumor cell-selective dual-mode imaging microRNA. Compared with the traditional EDC strategy, integrated design AIO-EDN achieves autocatalytic signal amplification without extra fuel strands. Moreover, leverages APE1 overexpressed cancer cells activate reaction, which, however, exerts no target sensing activity normal cells. Combining fluorescence- surface-enhanced Raman scattering (FL/SERS) techniques, this exhibits significantly improved selectivity microRNA This study provides a new paradigm develop EDC-based platform shows great potential in-depth diagnosis high precision.

Language: Английский

Citations

1
Endogenous Glutathione-Activated Nucleic Acid Molecular Circuitry for Cell-Specific MicroRNA Imaging DOI
Hui Wang, Yingying Chen, Yuqian Jiang

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(31), P. 12854 - 12861

Published: July 23, 2024

Sensitive and reliable microRNA imaging in living cells has significant implications for clinical diagnosis monitoring. Catalytic DNA circuits have emerged as potent tools tracking these intracellular biomarkers probing the corresponding biochemical processes. However, their utility is hindered by low resistance to external interference, leading undesired off-site activation consequent signal leakage. Therefore, achieving endogenous control of circuit's preferable target analysis cells. In this study, we attempted address challenge engineering a simple yet effective glutathione (GSH)-regulated hybridization chain reaction (HCR) circuit acquiring high-contrast miRNA imaging. Initially, HCR hairpin reactants were blocked engineered disulfide-integrated duplex, thus effectively passivating sensing function. And precaged was liberated cell-specific GSH molecule, initiating system selectively amplified detection microRNA-21 (miR-21). This approach prevented unwanted leakage before exposure into cells, ensuring robust miR-21 with high accuracy reliability specific tumor Moreover, endogenously responsive established link between small regulatory factors miRNA, thereby enhancing gain. summary, activatable represents versatile toolbox bioanalysis exploration potential signaling pathways

Language: Английский

Citations

5
Leveraging Demethylase Activation in DNA Circuits to Overcome Signal Leakage for Reliable MicroRNA Bioimaging DOI
Yuchen Gao,

Mengdi Yu,

Jinhua Shang

et al.

Small, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Abstract DNA circuits show great potential in monitoring intracellular biomarkers based on their high programmability, predictability, and unique signal amplification capabilities, yet face challenges from uncontrollable leakage caused by the complex environment. Herein, a demethylase‐activated DNA‐assembly (DAD) circuit is designed for reliable robust imaging of cellular microRNA, incorporating sequential activation hybridization chain reaction (HCR) amplifier system. The DAD consists DNAzyme module microRNA‐recognizing HCR signal‐amplifying module. m 6 A‐modified sequence module, initially possessing temporally caged substrate‐cleavage activity, integrated into probe effectively blocking its miRNA‐sensing capacity. In presence ALKBH5 demethylase, methyl‐modifying unit removed, thus restoring catalytic substrate‐cleaving activity. This process exposed previously toehold region probe, thereby activating sensing miRNA. By leveraging activation, this can substantially enhance signal‐to‐background ratio, enabling highly sensitive miRNA detection efficient differentiation cancerous normal cells. Furthermore, established relationship between demethylase enzyme miRNA, paving way investigating more complicate biological processes intricate signaling pathways within

Language: Английский

Citations

0
Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications DOI
Hong Wang,

Hanyan Zou,

Fuan Wang

et al.

ChemBioChem, Journal Year: 2024, Volume and Issue: 25(15)

Published: May 27, 2024

Abstract Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability addressability DNA probes enable their precise, on‐demand accurate execution hybridization, significantly enhancing target detection capabilities. Decades research in nanotechnology have led to advances structural design functional probes, resulting increasingly sensitive robust sensors. Moreover, increasing attention has been devoted accuracy sensitivity DNA‐based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at These involve guarantee procedures, utilizing dual signal output mechanisms, implementing sequential regulation methods. Our goal is provide new insights into development more sensors, ultimately facilitating widespread application clinical diagnostics assessment.

Language: Английский

Citations

2
On‐Site Multiply Stimulated Self‐Confinement of an Integrated DNA Cascade Circuit for Highly Reliable Intracellular Imaging of miRNA and In Situ Interrogation of the Relevant Regulatory Pathway DOI
Yuqian Jiang, Yingying Chen,

Jinhua Shang

et al.

Small, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 16, 2024

Abstract Artificial DNA circuits represent a versatile yet promising toolbox for in situ monitoring and concomitant regulation of diverse biological events within live cells. Nonetheless, their performance is significantly impeded by the diffusion‐dominated slow reaction kinetics uncontrollable off‐target activation. Herein, self‐localized cascade (SLC) circuit reported robust efficient microRNA (miRNA) analysis living The SLC consists cell‐specific localization module analyte‐specific signal amplification module. By integrating probes these two modules, complexity system reduced to realize responsive co‐localization circuitry simultaneous amplification. Taking advantage specifically activated, self‐localized, design, successfully achieves miRNA‐21 (miR‐21) imaging accurate cells differentiation. Moreover, reverse mechanism explored between messenger RNA (mRNA) miRNA through engineered further elucidates underlying signaling pathways them. Therefore, provides powerful tool sensitive detection intracellular biomolecules study corresponding cell regulatory mechanisms.

Language: Английский

Citations

2
Redox-Stimulated Catalytic DNA Circuit for High-fidelity Imaging of MicroRNA and in situ Interpretation of the Relevant Regulatory Pathway DOI

Yujing Liang,

Yifei Wang,

Mengdi Yu

et al.

Biosensors and Bioelectronics, Journal Year: 2024, Volume and Issue: 272, P. 117109 - 117109

Published: Dec. 28, 2024

Language: Английский

Citations

2
Acidic Extracellular pH-Activated Allosteric DNA Nanodevice for Fluorescence Imaging of APE1 Activity in Tumor Cells DOI
Hui He, Yuchen Wu, Mingjian Chen

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(45), P. 18079 - 18085

Published: Oct. 30, 2024

Allostery is a phenomenon where the binding of ligand at one allosteric site influences affinity for another an active site. Different from orthosteric regulation, it allows more precise control biomolecular activity and enhances stability molecules. Inspired by regulation natural molecules, we present Y-shaped DNA nanodevice, termed YssAP, that was pH-responsive functionalized with AS1411 aptamer accurate fluorescence imaging human apurinic/apyrimidinic endonuclease (APE1) in tumor cells. With rational design, YssAP could not be cut APE1, Cy5 proximity BHQ2, leading to suppressed signal emission. In contrast, since acidic pH acted as effector, underwent conformational change into activated probe (YdsAP) extracellular pH. After entering cell via specific recognition aptamer, overexpressed APE1 AP on YdsAP. moved far away resulting strong output. Compared direct construction substrate, nanodevices have effects, which can precisely adjusted changing switching state. We anticipate this strategy will applied screening inhibitors diagnosis.

Language: Английский

Citations

1
Sequentially amplified integration of catalytic DNA circuits for high-performance intracellular imaging of miRNA and interpretation of mRNA-miRNA signalling pathway DOI

Mengdi Yu,

Yushi Wang,

Jinhua Shang

et al.

Nano Today, Journal Year: 2024, Volume and Issue: 61, P. 102563 - 102563

Published: Dec. 1, 2024

Language: Английский

Citations

1