Catalytic hairpin assembly-programmed formation of clickable nucleic acids for electrochemical detection of liver cancer related short gene

A Novel Liver Cancer POC Diagnostic Detection Technique by a Gate-engineered Source-extended TFET Device

This work reports a novel POC diagnostic technique to identify the cancerous liver cell lines by designing a Source-Extended (SE) Tunnel Field Effect Transistor (TFET) having a Single-Gate (SG) with Single-Metal (SM) and Dual-Metal (DM) structure. The proposed structures have been equipped with nanocavities by trenching the gate oxide layer where the needle biopsy obtained liver sample has been immobilized. The detection is based on the difference in drain current and the ratio of the proposed device's ON and OFF state currents, which has been evaluated by obtaining the sensitivities. The cancerous and non-cancerous liver cell lines possess different dielectric properties in high frequencies ranging from 100 MHz to 5 GHz, affecting the cavity region's effective capacitances. The change in the dielectric constant of the specimen at 900 MHz has been considered which results in the change in device drain current and device performance. Various parameters of the device, like the adhesive layer in the cavity region, the material of the gate, the length of the cavities, and the orientation of the cavities, have been modified to observe the performance. The total work has been done in the simulation environment, which includes the study considering the different proportions of cancerous and non-cancerous cells in a particular specimen. A comparative analysis has been made between the performance of the proposed SM and DM gate structure. The proposed detection method has been compared with the existing methods reported in the literature. The proposed method can be considered a novel technique and can be implemented as a point of care (POC) diagnostic to detect whether the specimen liver cell line is cancerous.

Molecular Characterization of Exosomes for Subtype-Based Diagnosis of Breast Cancer

Breast cancer is very heterogeneous and the most frequently diagnosed cancer worldwide, and precise therapy targeting specific subtypes may improve the survival rates of breast cancer patients. In this study, we designed a biomimetic vesicle by camouflaging catalytic DNA machinery with a breast cancer cell membrane, which enabled the molecular classification of circulating exosomes for subtype-based diagnosis through homotypic recognition. In addition, the vesicles specifically targeted and fused with breast cancer exosomes with phenotypic homology and manipulated the DNA machinery to amplify electrochemical signaling using exosomal RNA as an endogenous trigger. The biomimetic vesicles prepared with MCF-7 cancer cell-derived membranes were shown to recognize estrogen receptor-positive breast cancer exosomes and exhibited a low detection limit of 557 particles mL^-1 with microRNA-375 used as the endogenous biomarker. Furthermore, the biomimetic vesicles prepared with MDA-MB-231 cancer cell-derived membranes displayed satisfactory performance in a homotypic analysis of triple-negative breast cancer exosomes with a potential therapeutic target, PD-L1 mRNA, used as the endogenous biomarker. Most importantly, cross-validation experiments confirmed the high accuracy and selectivity of this homotypic recognition-driven analysis for molecular subtyping of breast cancer. When applied to clinical samples of breast cancer patients, the vesicles demonstrated feasibility and reliability for evaluating the molecular features of cancer cell-derived exosomes and enabled stage-specific monitoring of breast cancer patients because the electrochemical signals showed a positive correlation with disease progression. Therefore, this work may provide new ideas for the precise diagnosis and personalized treatment of breast cancer patients throughout the whole disease process.

Silica nanoparticle assists determining liver cancer gene sequence on interdigitated electrode surface

A high-performance interdigitated electrode (IDE) biosensing surface was reported here by utilizing self-assembled silica nanoparticle (SiNP). The modified surface was used to evaluate the complementation of hairpin forming region from Mitoxantrone resistance gene 7 (MXR7; liver cancer-related short gene). The conjugated SiNPs on 3-aminopropyl triethoxysilane functionalization were captured with probe sequence on IDE biosensing surface. The physical and chemically modified surface was used to quantify MXR7 and an increment in the current response upon complementation was noticed. Limit of target DNA detection was calculated (1-10 fM) and this label-free detection is at the comparable level to the fluorescent-based sensing. A linear regression was calculated [y = 0.243x - 0.0773; R² = 0.9336] and the sensitivity was 1 fM on the linear range of 1 fM to 10 pM. With the strong attachment of capture DNA on IDE through SiNP, the surface clearly discriminates the specificity (complementary) versus nonspecificity (complete-, single-, and triple-mismatched sequences). This detection strategy helps to determine liver cancer progression and the similar strategy can be followed for other gene sequence complementation.

Binding-Induced 3D-Bipedal DNA Walker for Cascade Signal Amplification Detection of Thrombin Combined with Catalytic Hairpin Assembly Strategy

As an important biomarker, thrombin (TB) is a major player in thrombosis and hemostasis and has attracted increasing attention involving its determination. Herein a universal and ultrasensitive fluorescence biosensor based on a binding-induced 3D-bipedal DNA walker and catalytic hairpin assembly (CHA) strategy has been proposed for cascade signal amplification detection of thrombin. In this study, we designed two proximity probes (foot 1 and foot 2) which include a specific affinity ligand for TB binding and a Pb²⁺-dependent DNAzyme tail sequence. In the presence of TB, the simultaneous binding of TB to foot 1 (F1) and foot 2 (F2) via TB aptamer (TBA) brings the tail sequences into close proximity and the melting temperature for tail sequences and track DNA is increased, allowing the Pb²⁺-dependent DNAzyme to cleave the track DNA into two short fragments which have lower affinities for the DNAzyme and, finally, leading to the release of trigger DNA (T-DNA) for subsequent CHA reaction. In the meantime, the dissociated DNA walkers (F1 and F2) explore adjacent unwound track DNA, and the walking procedure is conducted. Unlike the conventional unipedal DNA walkers that anchor foot DNA and track DNA on the same sensing surface, the proposed 3D-bipedal DNA walking machine can not only increase the local concentration of track DNA but can also improve the walking efficiency and expand the range of the walkers to some extent due to the two free feet. Moreover, with the advantages of superior sensitivity and excellent specificity, this biosensing platform exhibits a huge potential in practical application in biomedical research and clinical diagnosis.

A catalytic molecule machine-driven biosensing method for amplified electrochemical detection of exosomes

Nowadays, exosomes that carry abundant information have attracted increasing attention as potent biomarkers of liquid biopsy and ideal candidates for early diagnosis and treatment of cancers. In this work, we propose a "principle-of-proof" biosensing method for amplified electrochemical detection of exosomes by using HepG2-derived exosomes as models. Specifically, target exosomes are enriched on anti-CD63-functionalized immunobeads and then recognized by a DNA chain containing CD63 aptamer region, which subsequently initiates a catalytic molecule machine that relies on cascade toehold-mediated strand displacement reaction. Benefiting from high efficiency of the molecule machine, the method shows a linear range from 1 × 10⁵ to 5 × 10⁷ particles/mL and a detection limit of 1.72 × 10⁴ particles/mL toward target exosomes, better than most existing detection methods. Moreover, the method demonstrates a high specificity even in serum samples and suggests a potential use in clinic, which may provide sufficient information for disease diagnosis, especially early detection and prognosis monitoring of tumors.

Recent Advances in Biosensors for Nucleic Acid and Exosome Detection

Biosensors are analytical devices for biomolecule detection that compromise three essential components: recognition moiety, transducer, and signal processor. The sensor converts biomolecule recognition to detectable signals, which has been applied in diverse fields such as clinical monitoring, in vitro diagnostics, food industry etc. Based on signal transduction mechanisms, biosensors can be categorized into three major types: optical biosensors, electrochemical biosensors, and mass-based biosensors. Recently, the need for faster, more sensitive detection of biomolecules has compeled researchers to develop various sensing techniques. In this review, the basic structure and sensing principles of biosensors are introduced. Additionally, the review discusses multiple recent works about nucleic acid and exosome sensing.

A smart fluorescent biosensor for the highly sensitive detection of BRCA1 based on a 3D DNA walker and ESDR cascade amplification

Nucleic acid analysis plays an important role in the diagnosis of diseases. There is a continuous demand to develop rapid and sensitive methods for the specific detection of nucleic acids. Herein, we constructed a highly sensitive and rapid fluorescent biosensor for the detection of BRCA1 by coupling a 3D DNA walker machine with spontaneous entropy-driven strand displacement reactions (ESDRs). In this study, the 3D DNA walker machine was well activated by the target DNA; this resulted in the cyclic utilization of the target DNA and the release of intermediate DNAs. Subsequently, the free intermediate DNAs triggered the circulation process of ESDRs with the help of the assistant probe A, leading to a significant enhancement of the fluorescence intensity. Due to the robust execution of the 3D DNA walker machine and highly efficient amplification capability of ESDRs, the developed biosensing method shows a wide linear range from 0.1 pM to 10 nM with the detection limit as low as 41.44 fM (S/N = 3). Moreover, the constructed biosensor displays superior specificity and has been applied to monitor BRCA1 in complex matrices. Thus, this elaborated cascade amplification biosensing strategy provides a potential platform for the bioassays of nucleic acids and the clinical diagnosis of diseases.

Nucleic acid analysis plays an important role in the diagnosis of diseases.