Combination of RCA and DNAzyme for Dual-Signal Isothermal Amplification of Exosome RNA

Advancements in DNAzyme-based biosensors for the detection of hazardous substances in foodstuff: current applications and future perspectives

DNAzyme-based biosensors have emerged as a promising tool for ensuring food safety due to their high sensitivity, specificity, and potential for rapid, cost-effective detection of hazardous substances. These biosensors leverage DNAzymes-catalytically active DNA molecules-to detect a range of contaminants, including metal ions, fungal toxins, pesticides, and pathogens. While DNAzyme-based biosensors show significant advantages over conventional techniques, challenges such as nuclease degradation, interference from complex sample matrices, and the high costs associated with DNAzyme synthesis still hinder their widespread application. Recent advancements in the stability of DNAzymes, their immobilization strategies, and integration with nanomaterials are progressively addressing these limitations, enhancing the performance and reliability of DNAzyme-based sensors. This review highlights the structural and catalytic characteristics of DNAzymes, assesses their current applications in food safety, and discusses innovative strategies to overcome existing challenges. The continuous evolution of DNAzyme-based biosensors, particularly in design and device integration, holds great promise for their future role in routine, reliable food analysis.

Immunomodulatory Significance of Mast Cell Exosomes (MC-EXOs) in Immune Response Coordination

Mast cells (MCs) communicate with other cells by direct cell-to-cell interaction, secreting mediators, and releasing exosomes (EXOs). MC-exosomes (MC-EXOs) contain proteins, lipids, mRNAs, and noncoding RNAs (ncRNAs), exhibit typical EXO markers such as heat shock proteins, tetraspanins, tumor susceptibility gene 101 protein (TSG101), and ALG-2-interacting protein X (ALIX), and are released constitutively or following MC degranulation. MC-EXOs also have signature MC markers like FcεRI and KIT (CD117), which allows for their identification and comparison with other EXO populations. Following their release, MC-EXOs may interact with the recipient cell(s) directly or be internalized and then release their protein and nucleic acid content. This may contribute to the regulation of immune responses and other biological processes and reprogramming of recipient cells. MC-EXO proteins may integrate and become a functional part of the recipient cell membrane. The mRNA transferred by MC-EXOs is functional and the transfer of exosomal RNA to other MCs results in the expression of donor MC proteins in the recipient MCs. Moreover, MCs may function as the recipients of EXOs that are released by other non-immune and immune cells, altering the secretome of MCs. In this review, we focus on how MC-EXOs modulate the biology of other cells and vice versa; and we highlight the role of MC-EXOs in the pathogenesis of allergic and non-allergic diseases.

Ultrasensitive Biosensors Detecting m6A in Blood: Achieving Early Screening and Typing of Tumors

N6-methyladenosine (m6A) modification is one of the most widespread RNA modifications in eukaryotes and is involved in cancer development and progression by regulating oncogene expression. Herein, a reticulated rolling circle amplification (RCA) cascade reaction was used to construct a novel electrochemical biosensor for ultrasensitive detection of m6A, employing ferrocene-tyramine (Fc-Tyr) molecules as electroactive probes. In this strategy, the RCA cascade reaction not only amplifies specific circular DNA in the designed template to reduce the binding with similar nucleic acid sequences but also generates a long ssDNA through multiple repetitions to capture a large number of electrochemical signal probes and achieve the amplification of electrochemical biosensing signals. The developed biosensor demonstrated high selectivity and sensitivity toward m6A in the range of 0.5 pM-150 nM, with a detection limit of 14.07 fM. Meanwhile, total RNA extracted from cell samples was analyzed for m6A expression levels using the developed biosensor and a commercial colorimetric immunoassay, the biosensor and immunoassay showed consistent results. In addition, m6A levels in clinical serum samples were assessed using the developed electrochemical biosensor, which showed that m6A expression was much lower in healthy individuals than in cancer patients, therefore the biosensor is promising for cancer typing. This study provides a new method for rapid and convenient tumor marker detection in clinical practice, as well as a new idea for sensitive detection of other biomolecules.

Exosomes as Powerful Biomarkers in Cancer: Recent Advances in Isolation and Detection Techniques

Exosomes, small extracellular vesicles derived from cells, are known to carry important bioactive molecules such as proteins, nucleic acids, and lipids. These bioactive components play crucial roles in cell signaling, immune response, and tumor metastasis, making exosomes potential diagnostic biomarkers for various diseases. However, current methods for detecting tumor exosomes face scientific challenges including low sensitivity, poor specificity, complicated procedures, and high costs. It is essential to surmount these obstacles to enhance the precision and dependability of diagnostics that rely on exosomes. Merging DNA signal amplification techniques with the signal boosting capabilities of nanomaterials presents an encouraging strategy to overcome these constraints and improve exosome detection. This article highlights the use of DNA signal amplification technology and nanomaterials' signal enhancement effect to improve the detection of exosomes. This review seeks to offer valuable perspectives for the enhancement of amplification methods applied in practical cancer diagnosis and prognosis by providing an overview of how these novel technologies are utilized in exosome-based diagnostic procedures.

Multi-enzymatic systems synergize new RCA technique amplified super-long dsDNA from DNA circle

BACKGROUND

In the field of DNA amplification, there are great challenges in the effectively amplify of long-chain amplification, especially amplification up to several hundred kb level.

RESULTS

A novel technique for the unbiased whole genome amplification from a thimbleful of DNA circles, such as low as 10 ng/ 10 μL of the circular cpDNA or low as 5 ng/ 10 μL of the plasmid, is developed, which can amplify an abundance of the whole genome sequences. Specifically, the new technique that combines rolling-amplification and triple-enzyme system presents a tightly controlled process of a series of buffers/reactions and optimized procedures, that applies from the primer-template duplexes to the Elution step. The result of this technique provides a new approach for extending RCA capacity, where it can reach 200 kb from the circular cpDNA amplification and 150 kb from the plasmid DNA amplification, that demonstrates superior breadth and evenness of genome coverage, high reproducibility, small amplification bias with the amplification efficiency.

SIGNIFICANCE AND NOVELTY

This new technique will develop into one of the powerful tools for isothermal DNA amplification in vitro, genome sequencing/analysis, phylogenetic analysis, physical mapping, and other molecular biology applications.

Extracellular vesicles associated microRNAs: Their biology and clinical significance as biomarkers in gastrointestinal cancers

Gastrointestinal (GI) cancers, including colorectal, gastric, esophageal, pancreatic, and liver, are associated with high mortality and morbidity rates worldwide. One of the underlying reasons for the poor survival outcomes in patients with these malignancies is late disease detection, typically when the tumor has already advanced and potentially spread to distant organs. Increasing evidence indicates that earlier detection of these cancers is associated with improved survival outcomes and, in some cases, allows curative treatments. Consequently, there is a growing interest in the development of molecular biomarkers that offer promise for screening, diagnosis, treatment selection, response assessment, and predicting the prognosis of these cancers. Extracellular vesicles (EVs) are membranous vesicles released from cells containing a repertoire of biological molecules, including nucleic acids, proteins, lipids, and carbohydrates. MicroRNAs (miRNAs) are the most extensively studied non-coding RNAs, and the deregulation of miRNA levels is a feature of cancer cells. EVs miRNAs can serve as messengers for facilitating interactions between tumor cells and the cellular milieu, including immune cells, endothelial cells, and other tumor cells. Furthermore, recent years have witnessed considerable technological advances that have permitted in-depth sequence profiling of these small non-coding RNAs within EVs for their development as promising cancer biomarkers -particularly non-invasive, liquid biopsy markers in various cancers, including GI cancers. Herein, we summarize and discuss the roles of EV-associated miRNAs as they play a seminal role in GI cancer progression, as well as their promising translational and clinical potential as cancer biomarkers as we usher into the area of precision oncology.