Localized DNA Logic Circuit Equipped with Cascade Amplifiers for Precise Identification of Cancer Cells

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

Published: March 16, 2025

Precise and highly sensitive identification of cancer cells plays a pivotal role in early detection, diagnosis, effective treatment. While DNA logic circuits have shown great promise as diagnostic tools, their practical application has been hindered by inadequate sensitivity arising from limited signal amplification capabilities complex biological matrices. To address this issue, we constructed localized circuit (LDC) equipped with cascaded amplifiers introducing Y-shaped AND-gate module three hairpin amplifier modules into tetrahedron. The gate is activated only the simultaneous presence two cancer-specific biomarkers: intracellular microRNA-21 (miR-21) flap endonuclease 1 (FEN1). Upon activation, releases output strands that trigger assembly amplifiers, initiating strand displacement cascade generates significantly enhanced fluorescent signal. LDC exhibits remarkable detection limits 82.5 pM for miR-21 0.015 U/mL FEN1. Fluorescence assays demonstrate achieves 15.5-fold improvement over without 5.2-fold compared to nonlocalized circuits. enables dual biomarkers, generating amplified signals exclusively tumor expressing both FEN1, thus allowing precise discrimination between cancerous healthy cells. Furthermore, demonstrated system vivo imaging, effectively differentiating normal tissues. This work highlights potential proposed cascade-amplification strategy tumor-specific paving way diagnosis

Language: Английский

---

PAMAM-Based DNA Fluorescence Nanoprobe for Rapid Whole Cellular APE1 Detection and Imaging

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

Published: March 19, 2025

Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/ref-1, APE1), a vital protein for DNA repair and cellular redox regulation, is frequently overexpressed in tumor cells, underscoring the importance of developing sensitive detection methods early cancer diagnosis. However, rapid visualization nuclear APE1 cells are still challenging. In this study, we successfully developed novel fluorescent nanoprobe based on polyamidoamine (PAMAM) cytoplasmic APE1. The PAMAM surface was modified with arginine (Arg), named PR, its hydrophobic core encapsulated 1,6,7,12-tetrachloroperylene tetracarboxylic acid dianhydride (TA) dye to construct nanoparticles (TPR). Furthermore, an APE1-responsive dsDNA (SP) linked TPR surface, containing apurinic/apyrimidinic sites (AP sites) black hole quencher 2 (BHQ2) ensuring that fluorescence remains off absence TPR-SP exhibited range 0.125-25 U mL-1 limit as low 0.03 mL-1. Compared Arg-free nanoprobes (TP-SP), significantly accelerated endocytosis penetration, reducing time one-quarter (from 0.5 h). Notably, signal whole nucleus can also be detected. Thus, achieves enrichment amplification signals, leading highly detection. This innovative efficient method greatly expands technological means

Language: Английский

---

Highly-sensitive and logic platform based on spatially-constrained T7 transcription enhanced Cas13a for DNA repair enzyme detection and intracellular imaging

Biosensors and Bioelectronics, Journal Year: 2025, Volume and Issue: unknown, P. 117406 - 117406

Published: March 1, 2025

Language: Английский

---

Functionalization of Nucleic Acid Molecular Machines under Physiological Conditions: A Review

ACS Applied Bio Materials, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

In-situ fabrication of nucleic acid molecular machines in biological environments is desirable for smart theranostic applications. However, given the complex nature environments, integration multiple functional modules into a coordinated machine remains challenging. Recent advances nanotechnology offer solutions to these challenges. Here, we outline design principles acid–based tailored physiological conditions, drawing on recent examples. We review cutting-edge technologies that facilitate their functionalization settings, particularly presynthesis modifications using unnatural bases and postsynthesis via bioorthogonal chemistry noncovalent interactions. discuss advantages limitations suggest future directions overcome existing

Language: Английский

---

Double Self‐Amplified Programmable Allosteric DNA Nanomachine for Enzymatically Triggered Spatially Controllable Molecular Imaging

Advanced Functional Materials, Journal Year: 2025, Volume and Issue: unknown

Published: May 15, 2025

Abstract In vivo optical tumor molecular imaging encounters significant challenges in achieving adequate specificity and sensitivity, largely attributed to off‐tumor signal leakage the relatively low expression levels of target molecules. Therefore, a double self‐amplified programmable allosteric DNA nanomachine (named HPs‐tFNA) is developed through two elaborately designed hairpin structures (HP1 HP2) hybridized on tetrahedral framework (tFNA), enabling rapid, specific, sensitive using highly specific apurinic/apyrimidinic endonuclease 1 (APE1) cytoplasm as stimulus‐response target. presence APE1, HP2 modifies sites (AP sites), which can be specifically recognized cleaved by releasing number cyclic sequences (cyclic‐seq) initial APE1‐assisted amplification. Subsequently, cyclic‐seq hybridizes with HP1, inducing conformational change that converts stem‐loop structure HP1 linear form. This structural facilitates spatial separation fluorophore quencher, thereby generating fluorescence signals. Furthermore, APE1 incises AP within loop region, resulting release cyclic‐seq. The released hybridize additional continuously amplify manner, second round amplification assisted APE1. experimental results this study demonstrated HPs‐tFNA achieve rapid situ guide precise surgical excision vivo, superior specificity. particular, effectively monitor drug resistance neuroblastoma cells stratify risk via plasma analysis.

Language: Английский

---

Fluorogenic Aptamer-Based Hybridization Chain Reaction for Signal-Amplified Imaging of Apurinic/Apyrimidinic Endonuclease 1 in Living Cells

Biosensors, Journal Year: 2024, Volume and Issue: 14(6), P. 274 - 274

Published: May 27, 2024

A fluorogenic aptamer (FA)-based hybridization chain reaction (HCR) could provide a sensitive and label-free signal amplification method for imaging molecules in living cells. However, existing FA-HCR methods usually face some problems, such as complicated design significant background leakage, which greatly limit their application. Herein, we developed an FA-centered HCR (FAC-HCR) based on remote toehold-mediated strand displacement reaction. Compared to traditional HCRs mediated by four hairpin probes (HPs) two HPs, the FAC-HCR displayed significantly decreased leakage improved sensitivity. Furthermore, was used test non-nucleic acid target, apurinic/apyrimidinic endonuclease 1 (APE1), important BER-involved endonuclease. The fluorescence analysis results confirmed that can reach detection of 0.1174 U/mL. By using HPs with polyetherimide-based nanoparticles, activity APE1 cells be imaged. In summary, this study new idea FA-based improve performance live cell imaging.

Language: Английский

---

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

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

---

A two-color fluorescence sensing strategy based on functionalized tetrahedral DNAzyme nanotweezers for ochratoxin A detection

Talanta, Journal Year: 2024, Volume and Issue: 285, P. 127348 - 127348

Published: Dec. 6, 2024

Language: Английский

---

Enzyme‐Powered, Label‐Free DNA Walker for Uracil‐DNA Glycosylase Detection at Single‐Cell Level

Chemistry - An Asian Journal, Journal Year: 2024, Volume and Issue: 19(20)

Published: July 1, 2024

Abstract Uracil‐DNA glycosylase (UDG) plays a crucial role in the removal of damaged uracil bases, thereby upholding genetic stability and integrity. An enzyme‐powered, label‐free DNA walker was devised for UDG activity detection. Initially, track, incorporating gold nanoparticle (AuNP), multiple hairpin structures, various swing arms, engineered walking mechanism. The structure meticulously crafted to include G‐quadruplex sequence, enabling generation fluorescence signal. arm remained inert absence UDG, but became activated upon introduction initiating enzyme‐powered process generating significant dissociative sequences. By integrating selective fluorescent dye into design, an enhanced response achieved. proposed presented direct approach detection, demonstrating exceptional sensitivity with detection limit 0.00004 U/mL. Using inhibitor (UGI) as inhibitory model, assay conducted satisfactory precision. Furthermore, successful analysis cellular at single‐cell level accomplished. Consequently, developed serves label‐free, selective, sensitive tool assessment, showing great potential applications disease diagnosis, screening, biomedical investigations.

Language: Английский

---

Enzyme-accelerated catalytic DNA circuits enable rapid and one-pot detection of bacterial pathogens

Biosensors and Bioelectronics, Journal Year: 2024, Volume and Issue: 267, P. 116822 - 116822

Published: Oct. 1, 2024

Language: Английский

---