Nucleic Acid Analysis Research Articles

CRISPR-Cas12a-based efficient electrochemiluminescence biosensor for ATP detection

CRISPR-Cas12a system exhibits tremendous potential in accurate recognition and quantitation of nucleic acids and non-nucleic-acid targets thanks to the discovery of its cleavage capability toward single-stranded DNA (ssDNA). In this study, we developed an efficient electrochemiluminescence (ECL) sensing platform based on CRISPR-Cas12a for the analysis of adenosine triphosphate (ATP). In the presence of the target, the successful release of the DNA activator is specially recognized by Cas12a-crRNA duplex and activates the cleavage of ferrocene (Fc) labeled–ssDNA (Fc-ssDNA) modified on the cathode of bipolar electrode (BPE), resulting in a decrease of ECL intensity of [Ru(bpy)3]2+/TPrA in the anodic cell of BPE. By means of the unique combination of Cas12a with ECL technique based on BPE, it can convert the recognition of target ATP into a detectable ECL signal. The detection limit of ATP was determined to be 0.48 nM under the optimal conditions. This work will expand the application of CRISPR-Cas detection system and propose a potential method for the analysis of non-nucleic-acid targets.

Hydrophobic magnetic deep eutectic solvent: Synthesis, properties, and application in DNA separation

Isolating high-purity nucleic acids from complex biological samples is critical to nucleic acid analysis. In the current work, four hydrophobic magnetic deep eutectic solvents (HMDESs) were firstly designed and prepared for the extraction of DNA. The conformations of the HMDESs were simulated and H-bonding interactions in the HMDESs were investigated by density functional theory (DFT) calculation. Characterization of HMDESs’ physical (magnetism, density, viscosity and hydrophobicity), and thermal (melting point and decomposition temperature) properties were conducted. Single stranded DNA (ssDNA), double stranded DNA (dsDNA) and DNA sodium salts (stDNA) that were extracted by HMDESs could be quickly collected by an external magnet. Three auxiliary extraction methods, including vortex auxiliary extraction, mechanical shaking auxiliary extraction and ultrasonic auxiliary extraction, were introduced to extract DNA with HMDESs and the extraction efficiencies were evaluated using NanoDrop. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, time, and pH, were systematically investigated via single-factor experimental analysis. The proposed extraction method can successfully extract DNA from complex matrices and E. coli cell lysate. The DNA extracted by using HMDESs are well suitable for PCR amplifications. The interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. The extraction mechanisms were discussed: hydrophobic interaction and electrostatic interaction are two main forces driving DNA extraction by HMDESs.

CRISPR/Cas12a Powered DNA Framework-Supported Electrochemical Biosensing Platform for Ultrasensitive Nucleic Acid Analysis.

Nucleic acid analysis using ultrasensitive and simple methods is critically important for the early-stage diagnosis and treatment of diseases. The CRISPR/Cas proteins, guided by a single-stranded RNA have shown incredible capability for sequence-specific targeting and detection. Herein, in order to improve and expand the application of CRISPR/Cas technology to the electrochemical interface-based nucleic acids analysis, the authors develop a CRISPR/Cas12a powered DNA framework-supported electrochemical biosensing platform via the cis and trans cleavage of Cas12a on the heterogeneous carbon interface (the existing publications which commonly adopted trans-cleavage). Their solid-liquid interface is first immobilized by 3D tetrahedral framework nucleic acids (FNAs) with specific DNA recognition probe. Based on the recognition of the complementary target through protospacer adjacent motif (PAM) confirmation and CRISPR-derived RNA (crRNA) matching, the easily formed Cas12a/crRNA duplex can get access to the interface, and the cis and trans cleavage of Cas12a can be easily activated. In combination with the enzyme catalyzed reaction, they achieved an ultralow limit of detection (LOD) of 100 fm in HPV-16 detection without pre-amplification. Furthermore, the platform is compatible with a spike-in human serum sample and has superior stability. Thus, their reported platform offers a practical, versatile, and amplification-free toolbox for ultrasensitive nucleic acid analysis.

Protein identification by nanopore peptide profiling

Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification.

Current Paradigm of Hepatitis E Virus Among Pediatric and Adult Patients.

Hepatitis E virus (HEV) infection is a polymorphic condition, present throughout the world and involving children and adults. Multiple studies over the last decade have contributed to a better understanding of the natural evolution of this infection in various population groups, several reservoirs and transmission routes being identified. To date, acute or chronic HEV-induced hepatitis has in some cases remained underdiagnosed due to the lower accuracy of serological tests and due to the evolutionary possibility with extrahepatic manifestations. Implementation of diagnostic tests based on nucleic acid analysis has increased the detection rate of this disease. The epidemiological and clinical features of HEV hepatitis differ depending on the geographical areas studied. HEV infection is usually a self-limiting condition in immunocompetent patients, but in certain categories of vulnerable patients it can induce a sudden evolution toward acute liver failure (pregnant women) or chronicity (immunosuppressed patients, post-transplant, hematological, or malignant diseases). In acute HEV infections in most cases supportive treatment is sufficient. In patients who develop chronic hepatitis with HEV, dose reduction of immunosuppressive medication should be the first therapeutic step, especially in patients with transplant. In case of unfavorable response, the initiation of antiviral therapy is recommended. In this review, the authors summarized the essential published data related to the epidemiological, clinical, paraclinical, and therapeutic aspects of HEV infection in adult and pediatric patients.

Research Progress and Application of Bioorthogonal Reactions in Biomolecular Analysis and Disease Diagnosis.

Bioorthogonal reactions are rapid, specific and high yield reactions that can be performed in in vivo microenvironments or simulated microenvironments. At present, the main biorthogonal reactions include Staudinger ligation, copper-catalyzed azide alkyne cycloaddition, strain-promoted [3 + 2] reaction, tetrazine ligation, metal-catalyzed coupling reaction and photo-induced biorthogonal reactions. To date, many reviews have reported that bioorthogonal reactions have been used widely as a powerful tool in the field of life sciences, such as in target recognition, drug discovery, drug activation, omics research, visualization of life processes or exogenous bacterial infection processes, signal transduction pathway research, chemical reaction dynamics analysis, disease diagnosis and treatment. In contrast, to date, few studies have investigated the application of bioorthogonal reactions in the analysis of biomacromolecules in vivo. Therefore, the application of bioorthogonal reactions in the analysis of proteins, nucleic acids, metabolites, enzyme activities and other endogenous molecules, and the determination of disease-related targets is reviewed. In addition, this review discusses the future development opportunities and challenges of biorthogonal reactions. This review presents an overview of recent advances for application in biomolecular analysis and disease diagnosis, with a focus on proteins, metabolites and RNA detection.

Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics.

Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.

Evaluation of Cytologic Sample Preparations for Compatibility With Nucleic Acid Analysis.

ObjectivesIn this study, the influence of several key elements of the cytologic sample workflow on DNA and RNA content was evaluated.MethodsThe A549 cell line, patient-derived organoids, and pleural effusions were used to investigate the effect of (1) several collection media and delayed time to processing; (2) cytology specimens; (3) cytologic staining; and (4) formalin-fixed, paraffin-embedded (FFPE) cell block processing on nucleic acid quality and quantity as determined by fragment analyzer, Qubit analysis (Thermo Fisher Scientific), and quantitative polymerase chain reaction–based analysis on the Idylla platform (Biocartis).ResultsAlcohol-based collection media (CytoRich Red [Thermo Fisher Scientific] and EtOH95%) displayed high DNA and RNA preservation capacity, while phosphate-buffered saline and, to a lesser extent, formalin were associated with high RNA quality. Cytospin and smear cytology specimens were subject to DNA and RNA loss. Cytologic staining had no further impact on sample quality, hence destaining is not necessary. Both H&E-stained and unstained FFPE sections are compatible with nucleic acid analysis, despite a strong decrease in DNA and RNA quality.ConclusionsAlthough several key elements of the cytologic sample workflow have an influence on DNA and RNA quality and quantity, the selection of these elements is also dependent on the downstream (ancillary) testing methods.

Integrating PCR-free amplification and synergistic sensing for ultrasensitive and rapid CRISPR/Cas12a-based SARS-CoV-2 antigen detection

Antigen detection provides particularly valuable information for medical diagnoses; however, the current detection methods are less sensitive and accurate than nucleic acid analysis. The combination of CRISPR/Cas12a and aptamers provides a new detection paradigm, but sensitive sensing and stable amplification in antigen detection remain challenging. Here, we present a PCR-free multiple trigger dsDNA tandem-based signal amplification strategy and a de novo designed dual aptamer synergistic sensing strategy. Integration of these two strategies endowed the CRISPR/Cas12a and aptamer-based method with ultra-sensitive, fast, and stable antigen detection. In a demonstration of this method, the limit of detection was at the single virus level (0.17 fM, approximately two copies/μL) in SARS-CoV-2 antigen nucleocapsid protein analysis of saliva or serum samples. The entire procedure required only 20 min. Given our system's simplicity and modular setup, we believe that it could be adapted reasonably easily for general applications in CRISPR/Cas12a-aptamer-based detection.

Preimplantation Genetic Testing for Monogenic Conditions: Is Cell-Free DNA Testing the Next Step?

Genetic assessment of an embryo via preimplantation genetic testing (PGT) represents an important reproductive option for couples wanting to try and improve success rates from in vitro fertilisation (IVF) cycles, as well as reduce their risk of having a child born with a genetic condition. Currently, biopsy of the developing embryo prior to transfer allows genetic assessment of an embryo for either chromosome copy number (aneuploidy [PGT-A] or segmental rearrangement [PGT-SR]) or to avoid the transmission of a single gene condition (monogenic conditions [PGT-M]). However, this technology is invasive and commands considerable resources. Non-invasive PGT (niPGT) offers a potential alternate mode of embryonic analysis. Whilst the utility of niPGT-A has been recently explored, there has been limited consideration of niPGT-M as an option for couples at risk of passing on a single gene or chromosomal condition. This review examines the historical and current clinical context of preimplantation embryonic analysis for monogenic conditions, in addition to important considerations surrounding the origin and analysis of cell-free deoxyribose nucleic acid (cfDNA), whether it is sourced via blastocentesis or spent embryonic culture medium (SCM). Future capabilities of this testing modality will almost certainly be enhanced by integration of whole genome sequencing into everyday practice. In addition, the increased utilisation of reproductive carrier screening as part of standard reproductive healthcare will likely result in the identification of a larger high-risk population. As a result, stratification of limited and highly specialised reproductive genetic resources will be required. Prospective parents should continue to be made aware of the limitations of this technology, with prenatal confirmatory testing remaining an essential part of antenatal care in these patients. However, niPGT-M poses an important alternate testing modality for high-risk couples, particularly in the setting of embryos that cannot be biopsied for traditional PGT-M and as demand for this treatment continues to grow.

Evaluation of Cytomegalovirus Infections in Liver Transplant Recipients Under Universal Prophylaxis: A Single Centre Experience

Background: Cytomegalovirus (CMV) is one of the leading viral agents that can pave the way for serious complications and organ damage in solid organ transplant (SOT) recipients after transplantation. Strategies have been developed to protect at-risk patients from CMV infection following transplantation. Since more than 90% of adults in Turkey were positive for CMV IgG, universal CMV prophylaxis was applied, and the results were evaluated. Objectives: This study aimed to evaluate the results of universal CMV prophylaxis after liver transplantation in the long term. Methods: A total of 1,090 liver transplant patients were evaluated in terms of CMV infection in the Organ Transplantation Institute of Inonu University, Malatya, Turkey, from October 2014 to December 2019. In order to identify the CMV infections, quantitative nucleic acid amplification (QNAT) was used to detect potential CMV DNA. The cut-off value of CMV DNA was determined to be 1000 copies/mL after transplantation. Results: According to the clinical and laboratory assessments, 33 (3%) patients were diagnosed with CMV infection, and 25 (2.3%) patients were evaluated as possibly having CMV syndrome. Also, eight of the 33 patients were assessed as having end-organ CMV disease and 25 as probable CMV syndrome. In the late period following prophylaxis, CMV infection was observed in 10 (0.9%) cases. The infection rate after prophylaxis (0.9%) was lower than the infection rate (2.1%) seen during prophylaxis. Conclusions: Close clinical follow-up with CMV prophylaxis and strict monitoring of CMV DNA by determining a specific cut-off point are important in the follow-up of liver transplant patients.

Diagnosis and Monitoring of Viral Infections in the Transplant Population

Viral infections are a major cause of morbidity and mortality in patients undergoing solid organ or hematopoietic stem cell transplantation. Due to their immunocompromised status, transplant recipients are at a higher risk for community-acquired and reactivated viral infections. Serologic screening prior to transplantation can assist with risk stratification of patients and guide decisions regarding the use of pre-emptive antiviral therapy. Following transplantation, molecular testing has become the most common method to detect viral infections, with histopathology of infected tissue often being required to confirm a diagnosis. Quantitative nucleic acid amplification tests have been the standard to detect and monitor viral infections in transplant patients; however, important challenges remain, including lack of standardization across many testing laboratories, limited availability of FDA-approved viral load assays, and the absence of universal viral load thresholds that can be used to diagnose disease and guide management decisions.

Alcoholic fixation over formalin fixation: A new, safer option for morphologic and molecular analysis of tissues.

Formalin is a widely used fixative but there is potential public health risks to exposure. Besides, alcoholic fixation is advantageous over formalin fixation because of faster fixation, optimal preservation and safer workplace environment. Following fixation by EMA and 10% neutral buffered formalin (NBF), we analyzed the tissue morphology, antigenic stability, DNA and RNA quantity with quality (OD value). The findings of EMA fixing on both the tissue morphology and molecular characterization, were satisfactory. Specially, EMA was faster in penetration of tissues than NBF, fixed ideally as early as 8 h of fixation whereas improper fixation was evident for NBF. In Hematoxylin and Eosin (H & E) staining, better cellular details with stronger affinity for staining were observed. In immunohistochemistry, better antigenic stability was reported for EMA-fixed tissues. The nucleic acid analysis revealed that total genomic DNA and RNA yield from EMA fixed tissues were significantly higher (P < 0.05) with superior quality than NBF fixed tissues. Our results suggest that EMA could be a potential alternative to NBF for fixation and preservation of tissues. These data provide new insights into an option for a safer working environment to support study and research.

Circulating microRNAs in Early Breast Cancer Patients and Its Association With Lymph Node Metastases.

MicroRNAs have emerged as important regulators of the metastatic process. In addition, circulating miRNAs appear to be surprisingly stable in peripheral blood making them ideal noninvasive biomarkers for disease diagnosis. Here, we performed a proof-of-principle study to investigate the expression profile of circulating miRNAs and their association with the metastatic lymph node status in early breast cancer patients. Sentinel lymph node status was detected by one-step nucleic acid (OSNA) analysis. We performed RNA-sequencing in 16 plasma samples and validated the results by qPCR. Gene Ontology term enrichment and KEGG pathway analyses were carried out using DAVID tools. We found16 differentially expressed miRNAs (q < 0.01) in patients with positive SLNs. Fourteen miRNAs were down-regulated (miR-339-5p, miR-133a-3p, miR-326, miR-331-3p, miR-369-3p, miR-328-3p, miR-26a-3p, miR-139-3p, miR-493-3p, miR-664a-5p, miR-146a-5p, miR-323b-3p, miR-1307-3p and miR-423-3p) and 2 were up-regulated (miR-101-3pand miR-144-3p). Hierarchical clustering using differentially expressed miRNAs clearly distinguished patients according to their lymph node status. Gene ontology analysis showed a significant enrichment of biological processes associated with the regulation of the epithelial mesenchymal transition, cell proliferation and transcriptional regulation. Our results suggest the potential role of several circulating miRNAs as surrogate markers of lymph node metastases in early breast cancer patients. Further validation in a larger cohort of patients will be necessary to confirm our results.

Study of danazol active agent effect on Mcf10a breast cells redox phosphorylation

Fibrocystic mastopathy is one of the most complex breast pathologies, occurring in about 60% of women. The causes and molecular mechanisms of cyst formation in fibrocystic mastopathy are not fully understood, and effective treatment methods are not widely implemented. However, there is evidence of the fibrocystic mastopathy malignization risk. We studied the molecular effect of the active agent danazol on the respiratory complex in mitochondria, which occur in various concentrations and are considered the cell energy center.&#x0D; A method of permeation with special agents was developed to improve the cell membrane permeability in the intracellular&#x0D; proteins and nucleic acids analysis. The scientists aimed to study the Mcf10a cell line mitochondrial respiratory complex using the permeabilization method.&#x0D; Purpose: To study the effect of different danazol concentrations on Mcf10a breast cells redox phosphorylation in women&#x0D; with fibrocystic mastopathy.&#x0D; Results: Monitoring the redox phosphorylation process using complex respiratory substrates affecting the Msf10A breast&#x0D; cells respiratory chain showed the danazol 30 μM effect on the respiratory complex I.&#x0D; Conclusions: According to oxygraphic records, 10 minutes’ exposure to danazol 30 μM after permeabilization with digitonin increased the Msf10A cells’ oxidative phosphorylation compared with the control. The respiratory rate decreased by 45% ten minutes after treatment with digitonin.

Synthesis of low-viscosity hydrophobic magnetic deep eutectic solvent: Selective extraction of DNA

Fast extraction of high-purity nucleic acid from complex biological sample is the key to downstream nucleic acid analysis. In this work, two low-viscosity hydrophobic magnetic deep eutectic solvents (HMDESs) were synthesized for the selective extraction of DNA. The conformation of the HMDES was simulated by density functional theory (DFT) calculation. Characterization of HMDESs’ physical (magnetism, density, viscosity, and hydrophobicity) properties and thermal (melting point and decomposition temperature) properties were conducted. Based on the HMDESs, a vortex-assisted liquid-liquid micro-extraction (VALLME) DNA method was developed. Single stranded DNA that was extracted by HMDESs could be quickly collected by an external magnet. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, extraction time, and pH were systematically investigated via single-factor experimental analysis. Under the optimized condition, the proposed extraction method has been demonstrated with the extraction of DNA from a series of complex sample matrices, including metal mixture, protein mixture and E. coli cell lysate. The DNA extracted by using HMDES-based VALLME method was well suitable for PCR amplifications. After extraction, the retained DNAs could be readily recovered by simply using Britton-Robison (BR) buffer. In addition, the interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. This work provides a new green magnetic solvent and a rapid and environmental-friendly extraction method for the enrichment of DNA and other biological macromolecules.

Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis

Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers.

Cavitation-microstreaming-based lysis and DNA extraction using a laser-machined polycarbonate microfluidic chip

We for the first time present a microfluidic cavitation-microstreaming-based cell lysis and DNA extraction method. Chemical lysis and DNA extraction have been demonstrated in a microfluidic format but the performance is limited by ineffective mass transport due to low Reynolds number. Here we propose to employ cavitation microstreaming for enhancing chemical lysis and magnetic-bead-based dynamic solid phase extraction (dSPE) of DNA. Cavitation microstreaming condition is optimized by exciting a microfluidic chip at its flexural resonance frequency (fr) measured via electrical impedance spectroscopy. Strong circulatory flows around bubbles excited at fr yields vigorous agitation, allowing fast lysis, and DNA extraction and purification. The microfluidic device is rapidly fabricated using CO2-laser machining and solvent-assisted thermal bonding of polycarbonate (∼25 min). Laser cutting conditions are experimentally determined to achieve a clean sidewall for negligible nonspecific binding and minimal burrs for unobstructed bonding. Solvent exposure and thermal bonding conditions are also experimentally determined for a leakage-free device with excellent dimensional integrity. Our method, although not fully optimized, exhibits an excellent DNA extraction performance, compared to a commercial kit and previous microfluidic methods. High extraction efficiency (76.9 %) and purity (A260/A280 = 1.85) are achieved for a relatively short assay time (∼25 min). Notably, DNA from as few as 18 cells is successfully extracted even from a highly diluted cell sample (0.18 cells/μl). PCR and electrophoresis results confirm the excellent quality of the extracted DNA. Considering these notable performances, and straightforward fabrication and operation, we anticipate our DNA extraction method will be widely used in microfluidic nucleic-acid analysis devices.

An Overview of Epidemiology and Diagnostic Techniques for Emerging and Re-emerging Viral Infections

In the past decades, the prevalence of emerging viral infections has escalated and is envisaged to continue to grow in the foreseeable future. More than 17 million people die every year from infectious diseases. The most deadly diseases known to humans so far are caused by emerging and re-emerging viruses such as Influenza, Chikungunya, Ebola, HIV, and the Coronavirus disease 19 outbreak, being the most recent. The clinical prognosis of serious illnesses depends on identification of the infectious agent at the onset. This review outlines the epidemiology and diagnostic techniques used to identify viral pathogens that received particular attention in the recent years. The modern diagnostic tools that are used for identification and confirmation of these disease causing agents such as viral antigen identification, viral culture, nucleic acid analysis, and serology are discussed. While rapid identification of infectious agents, quick diagnosis, and the production of vaccines against a specific virus is possible with advanced laboratory techniques, the limited resources delay the implementation of these techniques. The present need is to understand the importance of early and proper implementation of technological advancements for mitigation of damage caused by infective agents, and the introduction of some novel and appropriate approaches on priority basis in endemic and emerging areas.

Accurate Bulk Quantitation of Droplet Digital Polymerase Chain Reaction.

Droplet digital PCR provides superior accuracy for nucleic acid quantitation. The requirement of microfluidics to generate and analyze the emulsions, however, is a barrier to its adoption, particularly in low resource settings or clinical laboratories. Here, we report a novel method to prepare ddPCR droplets by vortexing and readout of the results by bulk analysis of recovered amplicons. We demonstrate the approach by accurately quantitating SARS-CoV-2 sequences using entirely bulk processing and no microfluidics. Our approach for quantitating reactions should extend to all digital assays that generate amplicons, including digital PCR and LAMP conducted in droplets, microchambers, or nanoliter wells. More broadly, our approach combines important attributes of ddPCR, including enhanced accuracy and robustness to inhibition, with the high-volume sample processing ability of quantitative PCR.