Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

Liu, Fei; Yang, Yuemeng; Wan, Xizi; Gao, Hongxiao; Wang, Yulu; Lu, Jingwei; Xu, Li-Ping; Wang, Shutao

doi:10.1021/acsnano.2c00157

Cited by 41 publications

(30 citation statements)

References 44 publications

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“…Fluorescence-based detection methods have a wide range of applications in many studies of biochemistry and biomedicine. , In our previous study, we developed a detection method using DNA-binding zinc finger proteins (ZFPs) with a size of 65 kDa, smaller than 120 kDa TALEs that provided a limit of detection of 1 nM . Considering that the height of QD-labeled TALEs was approximately 20 nm (Figure C), traveling even a short distance from the GO surface would easily extend the distance between TALEs and GO to be greater than 30 nm, resulting in more restoration of the signal and increased sensitivity.…”

Section: Resultsmentioning

confidence: 99%

Rapid and Sensitive Detection of Antibiotic Resistance Genes by Utilizing TALEs as a Diagnostic Probe with 2D-Nanosheet Graphene Oxide

2023

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As antibiotic resistance has risen as one of the major health concerns associated with infectious diseases due to the reduced efficacy of antibiotics, rapid and sensitive detection of antibiotic resistance genes is critical for more effective and faster treatment of infectious diseases. A class of programmable DNA-binding domains called transcriptional activator-like effectors (TALEs) provides a novel scaffold for designing versatile DNA-binding proteins due to their modularity and predictability. Here, we developed a simple, rapid, and sensitive system for detecting antibiotic resistance genes by exploring the potential of TALE proteins for the creation of a sequence-specific DNA diagnostic along with 2D-nanosheet graphene oxide (GO). TALEs were engineered to directly recognize the specific double-stranded (ds) DNA sequences present in the tetracycline resistance gene (tetM), avoiding the need for dsDNA denaturation and renaturation. We take advantage of the GO as an effective signal quencher to quantum dot (QD)-labeled TALEs for creating a turn-on strategy. QD-labeled TALEs are adsorbed on the GO surface, which will bring QDs in close proximity to GO. Due to the fluorescence quenching ability of GO, QDs are expected to be quenched by GO via fluorescence resonance energy transfer (FRET). QDlabeled TALE binding to the target dsDNA would lead to the conformational change, which would result in dissociation from the GO surface, thereby restoring the fluorescence signal. Our sensing system was able to detect low concentrations of dsDNA sequences in the tetM gene after only 10-minute incubation with the DNA, providing a limit of detection as low as 1 fM of Staphylococcus aureus genomic DNA. This study demonstrated that our approach of utilizing TALEs as a new diagnostic probe along with GO as a sensing platform can provide a highly sensitive and rapid method for direct detection of the antibiotic resistance gene without requiring DNA amplification or labeling.

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Section: Resultsmentioning

confidence: 99%

Rapid and Sensitive Detection of Antibiotic Resistance Genes by Utilizing TALEs as a Diagnostic Probe with 2D-Nanosheet Graphene Oxide

2023

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“…The innovation of medical techniques for diagnosis and treatment has posed a considerable challenge: developing advanced biomaterials to enable stable fixation and high-efficient interfacing with soft tissues. Traditional fixation methods in physiological environments using sutures and staples entail experienced surgical operations and are time-consuming. − Meanwhile, these metal-based materials are mechanically mismatched with soft tissues and inevitably bring damage and discomfort to patients. − In light of these drawbacks, hydrogel-based bioadhesives have been introduced and explored for decades attributed to their unique features of minimal invasion and simplified surgical procedures. Previous research has focused on the design of interfacial interactions between hydrogel adhesives and target substrates via two major mechanisms, specifically modulating marine mussel-derived catechol chemistry − and engineering topological connections , at contact interfaces.…”

Section: Introductionmentioning

confidence: 99%

Orchestrating Asymmetric Surface Functionalities on Hydrogel Stamps where Adhesion Meets Lubrication

Pan

Shui

et al. 2023

Chem. Mater.

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Bioadhesives applied on human organs are promising soft implants for interventional diagnostics and therapeutics. However, the conventional bioadhesive interfaces on organs typically lack apical−basal polarity to resemble the surface functions of original organ epithelia. To overcome the bioadhesive-induced dysfunction on treated organs, we have developed an innovative strategy via engineering asymmetric surface functionalities on a tough yet biodegradable polysaccharide-peptide-derived hydrogel platform, mimicking the functions of a ciliated columnar epithelium enabled by its adhesive basal surface and defensive apical ciliated surface. The resulting hydrogel bioadhesive serves as a "stamp" with a polyacrylic acid-functionalized adhesive side, facilitating instant and robust adhesion on wet tissues within 1 min via body liquid-removing mechanisms and Ca 2+ -assisted complexation. The back side is functionalized with hyaluronic acid, demonstrating an outstanding biolubrication performance (coefficient of friction of ∼0.038 in the synovial fluid). The hydrogel stamp can also be integrated with biosensing and drug encapsulation/release functions for diagnostics and therapeutics. Our strategy devises a new path to simultaneously enable reliable wet tissue adhesion and reproduce the characteristics of original tissues, with useful insights into designing bioactive interfaces for broad biomedical applications.

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“…Pathological examination, sometimes known as the “gold standard” for breast cancer diagnosis, can diagnose the disease scientifically and accurately. , However, it has the disadvantages of being time-consuming and invasive, which is not conducive to early cancer diagnosis. As a noninvasive detection tool, liquid biopsy has a promising future in the early diagnosis of cancers. − Exosomes are extracellular vesicles with a diameter of around 30–150 nm and are ideal biomarkers for liquid biopsy, as they carry a variety of bioactive molecules from their parent cells like DNA, RNA, proteins, and so on. − The identification of tumor-related proteins on exosomes can be exploited for early tumor diagnosis, which is especially important for breast cancer detection. In particular, recent studies have proved that high expression of epithelial cell adhesion molecule (EpCAM) and human epidermal growth factor receptor 2 (HER2) proteins can accurately distinguish breast cancer patients from healthy individuals. , Therefore, the strategy of simultaneously identifying EpCAM and HER2 proteins is likely to be employed for the precise identification of breast cancer cell-derived exosomes.…”

mentioning

confidence: 99%

Dual-Aptamer-Assisted Ratiometric SERS Biosensor for Ultrasensitive and Precise Identification of Breast Cancer Exosomes

Zhang

et al. 2023

ACS Sens.

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Due to the heterogeneity of breast cancer, its early accurate diagnosis remains a challenge. Exosomes carry abundant genetic materials and proteins and are ideal biomarkers for early cancer detection. Herein, a ratiometric surface-enhanced Raman scattering (SERS) biosensor for exosome detection was constructed using a regularly arranged Au@Ag nanoparticles/graphene oxide (Au@Ag NPs/GO) substrate with 4nitrothiophenol (4-NTP) molecules as an internal standard. Aptamers of two overexpressed proteins (epithelial cell adhesion molecule and human epidermal growth factor receptor 2) were linked by a short complementary DNA with rhodamine X modified at the 3′-terminal to form V-shaped double-stranded DNA, which attached to the surface of Au@Ag NPs/GO substrate for the selective recognition of breast cancer cell-derived exosomes. In the presence of exosomes, a competitive reaction occurred, resulting in the formation of the V-shaped double-stranded DNA/exosomes complex, and the V-shaped double-stranded DNA separated from the SERS substrate. The SERS signal of rhodamine X on the V-shaped double-stranded DNA decreased with the concentration of exosomes increasing, whereas the SERS signal of 4-NTP on the substrate remained stable. The ratiometric SERS strategy provides huge electromagnetic enhancement and abundant DNA adsorbing sites on the GO layer, achieving a wide detection range of 2.7 × 10 2 to 2.7 × 10 8 particles/mL and an ultralow limit of detection down to 1.5 × 10 2 particles/mL, without the requirement of any nucleic acid amplification. Particularly, the proposed method has significant applications in early cancer diagnosis as it can accurately identify breast cancer cell-derived exosomes in clinical serum samples and can differentiate pancreatic cancer patients and healthy individuals.

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Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

Cited by 41 publications

References 44 publications

Rapid and Sensitive Detection of Antibiotic Resistance Genes by Utilizing TALEs as a Diagnostic Probe with 2D-Nanosheet Graphene Oxide

Rapid and Sensitive Detection of Antibiotic Resistance Genes by Utilizing TALEs as a Diagnostic Probe with 2D-Nanosheet Graphene Oxide

Orchestrating Asymmetric Surface Functionalities on Hydrogel Stamps where Adhesion Meets Lubrication

Dual-Aptamer-Assisted Ratiometric SERS Biosensor for Ultrasensitive and Precise Identification of Breast Cancer Exosomes

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