Bioanalytical applications of isothermal nucleic acid amplification techniques

The most popular in vitro nucleic acid amplification techniques like polymerase chain reaction (PCR) including real-time PCR are costly and require thermocycling, rendering them unsuitable for uses at point-of-care. Highly efficient in vitro nucleic acid amplification techniques using simple, portable and low-cost instruments are crucial in disease diagnosis, mutation detection and biodefense. Toward this goal, isothermal amplification techniques that represent a group of attractive in vitro nucleic acid amplification techniques for bioanalysis have been developed. Unlike PCR where polymerases are easily deactivated by thermally labile constituents in a sample, some of the isothermal nucleic acid amplification techniques, such as helicase-dependent amplification and nucleic acid sequence-based amplification, enable the detection of bioanalytes with much simplified protocols and with minimal sample preparations since the entire amplification processes are performed isothermally. This review focuses on the isothermal nucleic acid amplification techniques and their applications in bioanalytical chemistry. Starting off from their amplification mechanisms and significant properties, the adoption of isothermal amplification techniques in bioanalytical chemistry and their future perspectives are discussed. Representative examples illustrating the performance and advantages of each isothermal amplification technique are discussed along with some discussion on the advantages and disadvantages of each technique.     

A general strategy for selective detection of hypochlorous acid based on triazolopyridine formation

Triazolopyridines are an important kind of fused-ring compounds. A HOCl-promoted triazolopyridine formation strategy is reported here for the first time in which hypochlorous acid (HOCl) mildly and efficiently promotes the formation of 1,2,4-triazolo[4,3-a]pyridines NT1-NT6 from various 2-pyridylhydrazones N1-N6. N6, a rhodol-pyridylhydrazone hybrid, was developed into a fluorescent probe for the selective detection of HOCl, and successfully applied to probe endogenous HOCl in living cells and zebrafish in situ and in real time. The present intramolecular cyclization reaction is selective and atom-economical, thereby not only providing an important approach for the convenient synthesis of triazolopyridines, but also offering a general strategy for sensitive, selective and biocompatible detection of endogenous HOCl in complex biosystems.     

核酸等温扩增技术在电化学生物传感器中的应用

生物分子检测在临床诊断、基因治疗、基因突变分析等方面变得日益重要,因而,建立简单、快速、灵敏的检测方法具有重要意义。近年,电化学生物传感器因其简单、便携、易操作、成本低等优势在生物分子检测的研究中备受关注。为了提高检测方法的灵敏度,不同的核酸等温扩增技术被应用于电化学生物传感器的构建中。本文简单介绍了电化学生物传感器的工作原理,着重综述了几种主要应用于电化学传感器中的核酸等温扩增技术,同时比较了各方法的优缺点。     

A general strategy for selective detection of hypochlorous acid based on triazolopyridine formation

Triazolopyridines are an important kind of fused-ring compounds. A HOCl-promoted triazolopyridine formation strategy is reported here for the first time in which hypochlorous acid (HOCl) mildly and efficiently promotes the formation of 1,2,4-triazolo[4,3-a]pyridines NT1-NT6 from various 2-pyridylhydrazones N1-N6. N6, a rhodol-pyridylhydrazone hybrid, was developed into a fluorescent probe for the selective detection of HOCl, and successfully applied to probe endogenous HOCl in living cells and zebrafish in situ and in real time. The present intramolecular cyclization reaction is selective and atom-economical, thereby not only providing an important approach for the convenient synthesis of triazolopyridines, but also offering a general strategy for sensitive, selective and biocompatible detection of endogenous HOCl in complex biosystems.     

A smartphone‐based on‐site nucleic acid testing platform at point‐of‐care settings

We developed a smartphone‐based on‐site nucleic acid testing (NAT) platform that can image and analyze lateral flow nucleic acid assays at point‐of‐care settings. An inexpensive add‐on was devised to run lateral flow assays while providing homogeneous ambient light for imaging. In addition, an Android app with a user‐friendly interface was developed for the result analysis and management. Linear color calibration is implemented inside the app to minimize the colorimetric reaction difference between smartphones. A relationship function between nucleic acid concentration and colorimetric reaction was established and evaluated by leave‐one‐out cross validation. The predicted concentration and true concentration showed a good agreement with an R‐squared value of 0.96. This smartphone‐based NAT platform can be used to diagnose infectious diseases and monitor disease progression, and assess treatment efficacy, especially for resource‐limited settings.     

Study on the interaction between nucleic acid and Eu3+-oxolinic acid and the determination of nucleic acid using the resonance light scattering technique

At pH 9.75, the resonance light scattering (RLS) intensity of OA–Eu³⁺ system is greatly enhanced by nucleic acid. Based on this phenomenon, a new quantitative method for nucleic acid in aqueous solution has been developed. Under the optimum condition, the enhanced RLS is proportional to the concentration of nucleic acid in the range of 1.0 × 10⁻⁹ to 1.0 × 10⁻⁶ g/ml for herring sperm DNA, 8.0 × 10⁻¹⁰ to 1.0 × 10⁻⁶ g/ml for calf thymus DNA and 1.0 × 10⁻⁹ to 1.0 × 10⁻⁶ g/ml for yeast RNA, and their detection limits are 0.020, 0.011 and 0.010 ng/ml, respectively. Synthetic samples and actual samples were satisfactorily determined. In addition, the interaction mechanism between nucleic acid and OA–Eu³⁺ is also investigated.     

Development of a BODIPY-based ratiometric fluorescent probe for hypochlorous acid and its application in living cells

A BODIPY-based ratiometric fluorescent probe for HOCl has been designed based on the transduction of thioether to sulfoxide function. This probe features a marked absorption and emission blue-shift upon the HOCl-promoted rapid transduction, enabling the highly selective and ratiometric detection. In addition, the probe works excellently within a wide pH range of 4–10, addressing the existing pH dependency issue. Living cells studies demonstrate that the probe is cell membrane permeable and can be employed successfully to image endogenous HOCl generation in macrophage cells.     

A ratiometric fluorescent probe for the detection of hypochlorous acid in living cells and zebra fish with along wavelength emission

A ratiometric fluorescence probe, NClO, for the rapid and selective detection of HClO had been designed and synthesized based on a 1,8-naphthalimide derivative. Probe NClO displayed a red emission(λ_(max)= 615 nm). In the presence of HClO, the solution of probe NClO gave off a strong green fluorescence(λ_(em), _(max)= 520 nm) with a rapid response(within seconds). This probe had been applied to image HClO in living cells and zebra fish.     

石墨烯材料在蛋白质和核酸分离/检测中的应用进展

石墨烯是碳材料家族新兴成员之一,因其具有化学性质稳定、良好生物兼容性、催化性、零带隙、特殊的电子能带等特点而受到科学家们广泛关注。 石墨烯特殊的六元环基底平面对很多分子、离子具有亲和性,可通过非共价键或共价键将目标物质富集于表面,大多数情况下被吸附的物质在特定条件下易解吸且不会引起其结构和性质的改变。 石墨烯因而在生物成像、生物医学、光催化、生物传感、药物载体和释放、 环境等方面应用前景广阔。 本文主要论述石墨烯和它的衍生物在生命大分子( 蛋白质和核酸) 分析化学方面的应用,并展望了其发展趋势。     

Fluorimetric determination of nucleic acid using the enhancement of terbium-gadolinium-nucleic acid-cetylpyridine bromide system

It is found that the fluorescence intensity of Tb-cetylpyridine bromide (CPB)-nucleic acid system can be enhanced by La³⁺, Gd³⁺, Lu³⁺, Sc³⁺ and Y³⁺, of which Gd³⁺ has the greatest enhancement. The experiments indicate that under the optimum condition, the fluorescence intensity of the system is in proportion to the concentration of nucleic acids in the range from 9×10⁻⁸ to 1×10⁻⁵ g ml⁻¹ for yeast RNA, from 1×10⁻⁷ to 1×10⁻⁵ g ml⁻¹ for fish sperm DNA. The detection limits are 3.2 and 4.1 ng ml⁻¹, respectively. This method has been used satisfactorily for the determination of both synthetic and actual samples. In comparison with most fluorescence method for the determination of nucleic acids, this method has higher sensitivity and stability.     

Chemiluminescent Imaging Assay of SARS-CoV-2 Protein with Target-Induced Enzyme Activity Regulation

Simple but robust testing assays are essential for screening and diagnosis of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in COVID-19 pandemic. Here, we described a chemiluminescent imaging assay (CLIA) for sensitive and convenient detection of SARS-CoV-2 nucleocapsid protein (NP) by a target-induced enzyme activity regulation (T-EAR) strategy. The T-EAR used a pair of antibody-DNA probes to recognize SARS-CoV-2 NP and proximity-induce rolling circle amplification for mass-production of pyrophosphate to coordinate with Cu²⁺, which prevented the reduction of Cu²⁺ to Cu⁺ by sodium ascorbate as well as the Cu⁺-caused inactivation of horseradish peroxidase (HRP). The activity retention of HRP produced strong CL signal for the detection of SARS-CoV-2 NP by catalyzing the oxidation of luminol by H₂O₂. The T-EAR based CLIA showed a wide detection range from 1 pg/mL to 100 ng/mL (13 fM to 1.3 nM) with the requirement of only 0.75 μL of sample. This CLIA had advantages of good sensitivity, simple wash-free operation, acceptable accuracy, and high-throughput imaging detection, displaying potential applicability in screening assay of COVID-19 infection.     

四磺化铁酞菁-阿尔新蓝8GX-对-羟基苯乙酸-H2O2催化荧光反应体系在核酸定量中的应用

阳离子荧光染料阿尔新蓝8GX与阴离子荧光染料四磺化铁酞菁发生缔合作用，使四磺化铁酞菁的荧光猝灭，当核酸存在时，削弱了离子缔合作用使四磺化铁酞菁的荧光恢复。荧光增强的程度与核酸的量成线性关系，据此实现了对核酸的定量测定。     

Modeling of nucleic acid adsorption on 3D prisms in microchannels

Understanding nucleic acid adsorption in microchannels is critical to improve the efficiency of purifying and extracting nucleic acid (NA) from sample solutions by microfluidic technologies. Using a microchannel with 3D prismatic silica elements on the wall can dramatically increase the surface area-to-volume ratio, and hence facilitate the nucleic acid adsorption on the wall. In this study a theoretical model for modeling adsorption in a microchannel with a designed 3D surface structure was developed, and five dimensionless numbers were found to be the key parameters in the adsorption process. Extensive numerical simulations were conducted. Two flow modes, the electroosmotic flow (EOF) and pressure-driven flow (PDF), were investigated for their effect on the adsorption. It was found that the EOF is more desirable than PDF. The 3D prismatic elements can increases the NA molecule adsorption not only by providing more surface areas, but also by the induced pressure resisting the central bulk electroosmotic flow. Finally, the effects of adsorption kinetic parameters (i.e., the kinetic association/dissociation constants, the diffusion coefficient, the total site density, the loading concentration, and the channel height), on the adsorption process were discussed in detail.     

Review of structural design guiding the development of lipid nanoparticles for nucleic acid delivery

Lipid nanoparticles (LNPs) are the most versatile and successful gene delivery systems, notably highlighted by their use in vaccines against COVID-19. LNPs have a well-defined core–shell structure, each region with its own distinctive compositions, suited for a wide range of in vivo delivery applications. Here, we discuss how a detailed knowledge of LNP structure can guide LNP formulation to improve the efficiency of delivery of their nucleic acid payload. Perspectives are detailed on how LNP structural design can guide more efficient nucleic acid transfection. Views on key physical characterization techniques needed for such developments are outlined including opinions on biophysical approaches both correlating structure with functionality in biological fluids and improving their ability to escape the endosome and deliver they payload.     

Reaction of hypochlorous acid with imidazole: formation of 2-chloro- and 2-oxoimidazoles

Reaction of hypochlorous acid (HOCl) with imidazole (Im) taken as a model for the 5-membered ring of guanine, leading to the products 2-chloro- and 2-oxo-imidazoles was investigated at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels of density functional theory. For all cases, single point energy calculations were performed at the MP2/AUG-cc-pVDZ level of theory using the geometries optimised at the B3LYP/AUG-cc-pVDZ level. Intrinsic reaction coordinate calculations were performed to ensure genuineness of all the calculated transition states. Effect of aqueous media was investigated by solvating all the species involved in the reactions using the polarizable continuum model. It is found that 2-chloroimidazole (2-ClIm) can be formed following three different reaction schemes while 2-oxoimidazole (2-oxoIm) can be formed following two different reaction schemes. The calculated barrier energies show that formation of 2-oxoIm would be less favored than that of 2-ClIm, which explains the experimental observations on relative yields of 8-chlorodeoxyguanosine and 8-oxodeoxyguanosine.     

First improvements in the detection and quantification of label-free nucleic acids by laser-induced breakdown spectroscopy: Application to the deoxyribonucleic acid micro-array technology

The accurate quantification of nucleic acids is essential in many fields of modern biology and industry, and in some cases requires the use of fluorescence labeling. Yet, in addition to standardization problems and quantification reproducibility, labeling can modify the physicochemical properties of molecules or affect their stability. To address these limitations, we have developed a novel method to detect and quantify label-free nucleic acids. This method is based on stoichiometric proportioning of phosphorus in the nucleic acid skeleton, using laser-induced breakdown spectroscopy, and a specific statistical analysis, which indicates the error probability for each measurement. The results obtained appear to be quantitative, with a limit of detection of 10⁵ nucleotides/µm² (i.e. 2 × 10¹³ phosphorus atoms/cm²). Initial micro-array analysis has given very encouraging results, which point to new ways of quantifying hybridized nucleic acids. This is essential when comparing molecules of different sequences, which is presently very difficult with fluorescence labeling.     

Effect of nucleic acid contamination on partitioning of proteins in two-phase PEG-Dextran system

Downstream processing of bioproducts results in considerable losses of compounds of interest in a large number of cases. For the intracellular enzyme tartrate dehydrogenase, an analysis of the laboratory process for enzyme recovery revealed that maximum losses occur in the initial stages of purification when the enzyme is separated from nucleic acids and other undesirable enzymes. Hence, aqueous twophase extraction was studied to investigate the separation of several enzymes from nucleic acids. Single-component and binary equilibria for three commercially available enzymes (bovine serum albumin, trypsin, chymotrypsin) and yeast RNA were studied in a two-phase system consisting of dextran and polyethylene glycol (PEG). The effects of pH and concentrations of the components and salts (NaC1) were investigated.     

New N1-(4-aryloxybenzyl)uracils containing N3-positioned 4-(trimethyleneoxy)benzoic acid moiety,and study of their antiviral activity against SARS-CoV-2 and influenza virus

New title uracil derivatives, 4-{3-[2,6-dioxo-3-(4-aryl-oxybenzyl)-3,6-dihydropyrimidin-1(2H)-yl]propoxy}benzoic acids and their butoxy homologues, were obtained in three steps using 2,4-bis(trimethylsilyloxy)pyrimidine, 4-aryloxy-benzyl bromides and methyl 4-(ω-bromoalkoxy)benzoates as the key reactants. The compounds were studied as inhibitors of H1N1 influenza virus and SARS-CoV-2 R replication in MDCK and Vero E6 cell cultures, respectively, which revealed that the tested compounds had high levels of anti-SARS-CoV-2 activity.     

Development and evaluation of a novel nucleic acid sequence-based amplification method using one specific primer and one degenerate primer for simultaneous detection of Salmonella Enteritidis and Salmonella Typhimurium

Salmonella Enteritidis and Salmonella Typhimurium are the most widespread causes of salmonellosis and gastrointestinal diseases worldwide. Thus, their simple and sensitive detection is significantly important in biosafety and point-of-care diagnostics. In that regard, although present nucleic acid-based attempts are mainly focused on the detection methods encompassing all Salmonella enterica members in a single reaction, serotypes other than S. Enteritidis and S. Typhimurium are clinically and epidemiologically rare to humans. Therefore, regarding high ribosomal RNA (rRNA) copy numbers in a cell, isothermal nucleic acid sequence-based amplification (NASBA) technique was employed for simple, sensitive and simultaneous detection of the bacteria. However, due to high sequence homology among 16S rRNA genes and consequently, very few specific regions, we developed a novel NASBA method called “single specific primer-NASBA or SSP-NASBA” in which the specificity of the antisense primer is sufficient to perform a specific NASBA reaction. Accordingly, we designed highly specific NASBA antisense and degenerate sense primers for a segment of 16S rRNA variable region by universal sequence alignment to simultaneously detect S. Enteritidis and S. Typhimurium. Meanwhile, the approach was successfully evaluated for various Salmonella as well as closely related non-Salmonella serovars. Specific and simultaneous detection of both bacteria was achieved with the designed primer set in a single reaction environment with a detection limit of less than 10 CFUs mL⁻¹. The developed NASBA assay should facilitate the overall process and provide a simple, fast, specific and sensitive approach for molecular diagnostics of pathogens under various circumstances, e.g. outbreaks.