Molecular beacon strategies for sensing purpose

The improvement of nucleic acid probes as vital molecular engineering devices will cause a noteworthy contribution to developments in bioimaging, biosensing, and disorders diagnosis. The molecular beacon (MB) which was designed by Tyagi and Kramer in 1996, are loop-stem hairpin-designed oligonucleotides armed with a quencher and a dye (also named reporter groups) at the 30 or 50 ends. This construction allows that MBs in the absence of their target complementary molecules do not fluoresce. Through hybridization with their specific targets a spontaneous configuration change on MBs occur and the dye and quencher separate from each other, resulting in emitting the fluorescence. MBs are effective probes for biosensing because of their extraordinary target-specificity, unique structure, inherent fluorescent signal transduction mechanism, low background fluorescence emission, recognition without separation, and favorable thermodynamic properties. In comparison to other probes (such as linear DNA sequences), MBs with the same number of complementary nucleotides matching their target, are multitasking probes. They have advantages of thermodynamic and photostability, flexible ability for conjugation, higher efficient intrinsic signal switching, and ultra-sensitivity. MBs not only are useful for identifying a nucleic acid target but can also be employed for recognition of various non-nucleic acid goals, including heavy metals and cations, enzymes, cells, ATP, etc. Hence, this review highlights the potential of MBs in the improvement of biosensors and their usage in detection of different analytes such as miRNA, mRNA, cocaine, methamphetamine, actin, thrombin, heavy metal and cations and so on. (C) 2020 Elsevier B.V. All rights reserved.Peer reviewe

New trends in the development of electrochemical biosensors for the quantification of microRNAs

MicroRNAs (miRNAs) are non-coding regulatory RNAs that play an important role in RNA silencing and post-transcriptional gene expression regulation. Since their dysregulation has been associated with Alzheimer disease, cardiovascular diseases and different types of cancer, among others, miRNAs can be used as biomarkers for early diagnosis and prognosis of these diseases. The methods commonly used to quantify miRNAs are, in general, complex, costly, with limited application for point-of-care devices or resource-limited facilities. Electrochemical biosensors, mainly those based on nanomaterials, have emerged as a promising alternative to the conventional miRNA detection methods and have paved the way to the development of sensitive, fast, and low-cost detection systems. This review is focused on the most relevant contributions performed in the field of electrochemical miRNAs biosensors between 2017 and the beginning of 2020. The main contribution of this article is the critical discussion of the different amplification strategies and the comparative analysis between amplified and non-amplified miRNA electrochemical biosensing and between the different amplification schemes. Particular emphasis was given to the importance of the nanostructures, enzymes, labelling molecules, and special sequences of nucleic acids or analogues on the organization of the different bioanalytical platforms, the transduction of the hybridization event and the generation the analytical signal.Fil: López Mujica, Michael Earvin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Gallay, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Perrachione, Fabrizio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Montemerlo, Antonella Evelin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Tamborelli, Luis Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Vaschetti, Virginia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Reartes, Daiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Bollo, Soledad. Facultad de Ciencias Químicas y Farmacéuticas; ChileFil: Rodríguez, Marcela C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Dalmasso, Pablo Roberto. Universidad Tecnologica Nacional. Facultad Regional Cordoba. Departamento de Ingenieria Quimica. Centro de Investigacion y Transferencia En Ingenieria Quimica.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rubianes, María Dolores. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Rivas, Gustavo Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Rolling circle amplification as an efficient analytical tool for rapid detection of contaminants in aqueous environments

Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring

Pushing Forward the DNA Walkers in Connection with Tumor-Derived Extracellular Vesicles

Qingyi Liu,1,2 Qiongdan Zhang,1,2 Zhijian Yao,1,2 Gangqiang Yi,2 Yeonseok Kang,3 Yixing Qiu,1,2 Yupei Yang,1,2 Hanwen Yuan,1,2 Ronggeng Fu,2 Wenbing Sheng,1,2 Lidong Cheng,4 Wei Wang,1,2 Huizhen Wang,1,2 Caiyun Peng1,5 1TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China; 2School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China; 3College of Korean Medicine, Wonkwang University, Jeonbuk, Korea; 4Hunan Yirentang Chinese Herbal Pieces Co., Ltd, Changde, People’s Republic of China; 5Institute of Innovation and Applied Research in Chinese Medicine Hunan University of Chinese Medicine, Changsha, People’s Republic of ChinaCorrespondence: Huizhen Wang; Caiyun Peng, Tel +86-151-1648-1295 ; +86-138-7480-7689, Email [email protected]; [email protected]: Extracellular vesicles (EVs) are microparticles released from cells in both physiological and pathological conditions and could be used to monitor the progression of various pathological states, including neoplastic diseases. In various EVs, tumor-derived extracellular vesicles (TEVs) are secreted by different tumor cells and are abundant in many molecular components, such as proteins, nucleic acids, lipids, and carbohydrates. TEVs play a crucial role in forming and advancing various cancer processes. Therefore, TEVs are regarded as promising biomarkers for the early detection of cancer in liquid biopsy. However, the currently developed TEV detection methods still face several key scientific problems that need to be solved, such as low sensitivity, poor specificity, and poor accuracy. To overcome these limitations, DNA walkers have emerged as one of the most popular nanodevices that exhibit better signal amplification capability and enable highly sensitive and specific detection of the analytes. Due to their unique properties of high directionality, flexibility, and efficiency, DNA walkers hold great potential for detecting TEVs. This paper provides an introduction to EVs and DNA walker, additionally, it summarizes recent advances in DNA walker-based detection of TEVs (2018– 2024). The review highlights the close relationship between TEVs and DNA walkers, aims to offer valuable insights into TEV detection and to inspire the development of reliable, efficient, simple, and innovative methods for detecting TEVs based on DNA walker in the future. Keywords: EVs, TEVs, DNA walker, detectio

Novel Biosensing Strategies for the <em>in Vivo</em> Detection of microRNA

As a regulatory molecule of post-transcriptional gene expression, microRNA (miRNA) is a class of endogenous, non-coding small molecule RNAs. MiRNA detection is essential for biochemical research and clinical diagnostics but challenging due to its low abundance, small size, and sequence similarities. In this chapter, traditional methods of detecting miRNA like polymerase chain reaction (PCR), DNA microarray, and northern blotting are introduced briefly. These approaches are usually used to detect miRNA in vitro. Some novel strategies for sensing miRNAs in vivo, including hybridization probe assays, strand-displacement reaction (SDR), entropy-driven DNA catalysis (EDC), catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), DNAzyme-mediated assays, and CRISPR-mediated assays are elaborated in detail. This chapter describes the principles and designs of these detection technologies and discusses their advantages as well as their shortcomings, providing guidelines for the further development of more sensitive and selective miRNA sensing strategies in vivo

DNA Walkers: Emerging Analytical Applications, Biomolecular-Nanomaterial Probes and Biomolecule Sensors

DNA walkers are a unique class of dynamic DNA devices that move nucleic acid walkers processively along designated one-, two-, or three-dimensional tracks. Because of the unique mechanical motion, dynamic interaction, and capabilities for signal amplification, programmable signal transduction, high directionality, and predictable analytical performance on the basis of Watson-Crick base paring rules, this class of dynamic DNA nanodevice has gained great attention from the analytical community in the recent years. This includes bioanalytical applications that range from nucleic acid sensing, to protein detection and to cellular imaging and analysis. The research described herein focuses on improving the understanding of biophysical processes involved in the design and operation of DNA walkers. Specifically, we developed a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the biomolecule-nanoparticle (bio-nano) interface. By monitoring dynamics of DNA walkers on spherical nucleic acid (SNA) tracks, we systematically investigated effects of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic activities at the bio-nano interface. Leveraging the newly gained knowledge at the interface, we also fabricated ultrasensitive biosensors for amplified detection of nucleic acids and antibodies. Our study revealed critical roles of interfacial factors to enzyme activities and performance of enzyme-driven nanodevices. We also demonstrate that improvement in understanding bio-nano interfaces will facilitate the design and operation of biosensors and inspire new sensing mechanisms

PNA-based microRNA detection methodologies

MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays

A concise overview of advancements in ultrasensitive biosensor development

Electrochemical biosensing has evolved as a diverse and potent method for detecting and analyzing biological entities ranging from tiny molecules to large macromolecules. Electrochemical biosensors are a desirable option in a variety of industries, including healthcare, environmental monitoring, and food safety, due to significant advancements in sensitivity, selectivity, and portability brought about by the integration of electrochemical techniques with nanomaterials, bio-recognition components, and microfluidics. In this review, we discussed the realm of electrochemical sensors, investigating and contrasting the diverse strategies that have been harnessed to push the boundaries of the limit of detection and achieve miniaturization. Furthermore, we assessed distinct electrochemical sensing methods employed in detection such as potentiometers, amperometers, conductometers, colorimeters, transistors, and electrical impedance spectroscopy to gauge their performance in various contexts. This article offers a panoramic view of strategies aimed at augmenting the limit of detection (LOD) of electrochemical sensors. The role of nanomaterials in shaping the capabilities of these sensors is examined in detail, accompanied by insights into the chemical modifications that enhance their functionality. Furthermore, our work not only offers a comprehensive strategic framework but also delineates the advanced methodologies employed in the development of electrochemical biosensors. This equips researchers with the knowledge required to develop more accurate and efficient detection technologies

Advanced Electrochemical and Opto-Electrochemical Biosensors for Quantitative Analysis of Disease Markers and Viruses

The recent global events of the SARS-CoV-2 pandemic in 2020 have alerted the world to the urgent need to develop fast, sensitive, simple, and inexpensive analytical tools that are capable of carrying out a large number of quantitative analyses, not only in centralized laboratories and core facilities but also on site and for point-of-care applications. In particular, in the case of immunological tests, the required sensitivity and specificity is often lacking when carrying out large-scale screening using decentralized methods, while a centralized laboratory with qualified personnel is required for providing quantitative and reliable responses. The advantages typical of electrochemical and optical biosensors (low cost and easy transduction) can nowadays be complemented in terms of improved sensitivity by combining electrochemistry (EC) with optical techniques such as electrochemiluminescence (ECL), EC/surface-enhanced Raman spectroscopy (SERS), and EC/surface plasmon resonance (SPR). This Special Issue addresses existing knowledge gaps and aids in exploring new approaches, solutions, and applications for opto-electrochemical biosensors in the quantitative detection of disease markers, such as cancer biomarkers proteins and allergens, and pathogenic agents such as viruses. Included are seven peer-reviewed papers that cover a range of subjects and applications related to the strategies developed for early diagnosis

A Responsive "Nano String Light" for Highly Efficient mRNA Imaging in Living Cells via Accelerated DNA Cascade Reaction

Nonenzymatic DNA catalytic amplification strategies have greatly benefited bioanalysis. However, long period incubation is usually required due to its relatively low reaction rate and efficiency, which limits its in vivo application. Here we design a responsive DNA nano string light (DNSL) by interval hybridization of modified hairpin DNA probe pairs to a DNA nanowire generated by rolling circle amplification and realize accelerated DNA cascade reaction (DCR) for fast and highly efficient mRNA imaging in living cells. Target mRNA initiates interval hybridization of two paired hairpin probes sequentially along the DNA nanowire and results in instant lighting up of the whole DNA nanowire with high signal gain due to the fast opening of all the self-quenched hairpins. The reaction time is about 6.7 times shorter compared with a regular DNA cascade reaction due to the acceleration based on domino effect. The cell delivery is achieved by modifying one of the hairpin probes with folic acid, and this intracellular imaging strategy is verified using human HeLa cells and intracellular survivin mRNA with a series of suppressed expressions as model, which provides a useful platform for fast and highly efficient detection of low-abundance nucleic acids in living cells