Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis

DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection

We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Engineered Biosensors for Diagnosing Multidrug Resistance in Microbial and Malignant Cells

To curtail pathogens or tumors, antimicrobial or antineoplastic drugs have been developed. These drugs target microbial/cancer growth and survival, thereby improving the host's health. In attempts to evade the detrimental effects of such drugs, these cells have evolved several mechanisms over time. Some variants of the cells have developed resistances against multiple drugs or antimicrobial agents. Such microorganisms or cancer cells are said to exhibit multidrug resistance (MDR). The drug resistance status of a cell can be determined by analyzing several genotypic and phenotypic changes, which are brought about by significant physiological and biochemical alterations. Owing to their resilient nature, treatment and management of MDR cases in clinics is arduous and requires a meticulous approach. Currently, techniques such as plating and culturing, biopsy, gene sequencing, and magnetic resonance imaging are prevalent in clinical practices for determining drug resistance status. However, the major drawbacks of using these methods lie in their time-consuming nature and the problem of translating them into point-of-care or mass-detection tools. To overcome the shortcomings of conventional techniques, biosensors with a low detection limit have been engineered to provide quick and reliable results conveniently. These devices are highly versatile in terms of analyte range and quantities that can be detected to report drug resistance in a given sample. A brief introduction to MDR, along with a detailed insight into recent biosensor design trends and use for identifying multidrug-resistant microorganisms and tumors, is presented in this review.

Toward a Home Test for COVID-19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples

Nucleic acid-based detection of RNA viruses requires an annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structures of folded viral RNA. In this study, we designed a protein-enzyme-free nano-construction, named four-armed DNA machine (4DNM), that requires neither an amplification stage nor a high-temperature annealing step for SARS-CoV-2 detection. It uses a binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with a total of four RNA-binding arms. Additional arms were found to improve the limit of detection at least 10-fold. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for the detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.

Diagnostic assay and technology advancement for detecting SARS-CoV-2 infections causing the COVID-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic has transmitted to humans in practically all parts of the world, producing socio-economic turmoil. There is an urgent need for precise, fast, and affordable diagnostic testing to be widely available for detecting SARS-CoV-2 and its mutations in various phases of the disease. Early diagnosis with great precision has been achieved using real-time polymerase chain reaction (RT-PCR) and similar other molecular methods, but theseapproaches are costly and involve rigorous processes that are not easily obtainable. Conversely, immunoassays that detect a small number of antibodies have been employed for quick, low-cost tests, but their efficiency in diagnosing infected people has been restricted. The use of biosensors in the detection of SARS-CoV-2 is vital for the COVID-19 pandemic’s control. This review gives an overview of COVID-19 diagnostic approaches that are currently being developed as well as nanomaterial-based biosensor technologies, to aid future technological advancement and innovation. These approaches can be integrated into point-of-care (POC) devices to quickly identify a large number of infected patients and asymptomatic carriers. The ongoing research endeavors and developments in complementary technologies will play a significant role in curbing the spread of the COVID-19 pandemic and fill the knowledge gaps in current diagnostic accuracy and capacity.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Point-of-Care Pathogen Detection with CRISPR-based Programmable Nucleic Acid Binding Proteins

The contemporary discovery of extremely versatile engineered nucleic acid-binding proteins has transformed a brave new world in the genome-editing scientific area. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated programmable nucleic acid-binding proteins have brought about a revolution in diagnostic platforms. The groundbreaking finding that bacteria and archaea that harbored prokaryotes have transmitted adaptive immunity through CRISPR and CRISPR-associated (Cas) proteins has driven revolutionary advances in molecular biology. Importantly, advances in gene editing focus how expanding visions in CRISPR-Cas biology are revolutionizing the area of molecular diagnostics for identifying DNA and RNA in emerging microbiological pathogens, for single nucleotide polymorphism (SNP) identifications, and for cell-free mutation. Recent advances, such as improvements in multiplexing and quantitative capabilities as well as instrument-free detection of nucleic acids, will potentially leverage the introduction of these novel technologies to detecting bacteria and viruses at the point of care (POC). In this review, we highlight the fundamental features of CRISPR/Cas-based molecular diagnostic technologies and summarize a vision of the next applications for identifying pathogens in POC settings.

Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing

Light-up DNA aptamers are promising label-free signal-transducers for biosensing applications due to their high chemical stability and low synthetic cost. Herein, we demonstrate that a dapoxyl DNA aptamer DAP-10-42 can be converted into a sensor generating a fluorescence signal at different wavelengths in the range of 500-660 nm depending on the dye that is present. This results from the discovered promiscuity of DAP-10-42 in binding fluorogenic dyes including arylmethane dyes. We have designed a split DAP-10-42 aptasensor for the detection of a katG gene fragment from Mycobacterium tuberculosis with a point mutation causing isoniazid resistance. Efficient interrogation of the gene fragment after nucleic acid sequence-based amplification (NASBA) is achieved directly in a protein-containing NASBA sample. This report lays a foundation for the application of the DAP-10-42 aptamer as a versatile sensing platform.

Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics

Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.