A generic sandwich-type biosensor with nanomolar detection limits

A quantitative and highly sensitive, yet simple and rapid, biosensor system was developed for the detection of nucleic acid sequences that can also be adapted to the detection of antigens. A dipstick-type biosensor with liposome amplification, based on a sandwich assay format with optical detection, was combined with a simple coupling reaction that allows the transformation of the generic biosensor components to target specific ones by a mere incubation step. This biosensor platform system was developed and optimized, and its principle was proven using DNA oligonucleotides that provided a nucleic acid biosensor for the specific detection of RNA and DNA sequences. However, the coupling reaction principle chosen can also be used for the immobilization of antibodies or receptor molecules, and therefore for the development of immunosensors and receptor-based biosensors. The generic biosensor consists of liposomes entrapping sulforhodamine B that are coated with streptavidin on the outside, and polyethersulfone membranes with anti-fluorescein antibodies immobilized in the detection zone. In order to transform the generic biosensor into a specific DNA/RNA biosensor, two oligonucleotides that are able to hybridize to the target sequence were labeled with a biotin and a fluorescein molecule, respectively. By simultaneously incubating the liposomes, both oligonucleotides, and the target sequence in a hybridization buffer for 20–30 min at 42 ^°C, a sandwich complex was formed. The mixture was applied to the polyethersulfone membrane. The complex was captured in the detection zone and quantified using a handheld reflectometer. The system was tested using RNA sequences from B. anthracis, C. parvum and E. coli. Quantitation of concentrations between 10 fmol and 1000 fmol (10–1000 nM) was possible without altering any biosensor assay conditions. In addition, no changes to hybridization conditions were required when using authentic nucleic acid sequence-based amplified RNA sequences, and the generic biosensor compared favorably with those previously developed specifically for the RNA sequences. Therefore, the universal biosensor described is an excellent tool, for use in laboratories or at test sites, for rapidly investigating and quantifying any nucleic acid sequence of interest, as well as potentially any antigen of interest that can be bound by two antibodies simultaneously.     

Carbon nano-strings as reporters in lateral flow devices for DNA sensing by hybridization

Presently, there is a growing interest in the development of lateral flow devices for nucleic acid analysis that enable visual detection of the target sequence (analyte) while eliminating several steps required for pipetting, incubation, and washing out the excess of reactants. In this paper, we present, for the first time, lateral flow tests exploiting oligonucleotide-functionalized and antibody-functionalized carbon nanoparticles (carbon nano-strings, CBNS) as reporters that enable confirmation of the target DNA sequence by hybridization. The CBNS reporters were applied to (a) the detection of PCR products and (b) visual genotyping of single nucleotide polymorphisms in human genomic DNA. Biotinylated PCR product was hybridized with a dA-tailed probe. In one assay configuration, the hybrid is captured at the test zone of the strip by immobilized streptavidin and detected by (dT) ₃₀ -CBNS. In a second configuration, the hybrids are captured from immobilized (dA) strands and detected by antibiotin-CBNS. As low as 2.5 fmol of amplified DNA can be detected. For visual genotyping, allele-specific primers with a 5′ oligo(dA) segment are extended by DNA polymerase with a concomitant incorporation of biotin moieties. Extension products are detected either by (dT) ₃₀ -CBNS or by antibiotin-CBNS. Only three cycles of extension reaction are sufficient for detection. No purification of the PCR products or the extension product is required.     

Nucleic acid biosensors for environmental pollution monitoring

Nucleic acid-based biosensors are finding increasing use for the detection of environmental pollution and toxicity. A biosensor is defined as a compact analytical device incorporating a biological or biologically-derived sensing element either integrated within or intimately associated with a physicochemical transducer. A nucleic acid-based biosensor employs as the sensing element an oligonucleotide, with a known sequence of bases, or a complex structure of DNA or RNA. Nucleic acid biosensors can be used to detect DNA/RNA fragments or either biological or chemical species. In the first application, DNA/RNA is the analyte and it is detected through the hybridization reaction (this kind of biosensor is also called a genosensor). In the second application, DNA/RNA plays the role of the receptor of specific biological and/or chemical species, such as target proteins, pollutants or drugs. Recent advances in the development and applications of nucleic acid-based biosensors for environmental application are reviewed in this article with special emphasis on functional nucleic acid elements (aptamers, DNAzymes, aptazymes) and lab-on-a-chip technology.     

Application and analysis of structure-switching aptamers for small molecule quantification

Modern tools for the analysis of cellular function aim for the quantitative measurement of all members of a given class of biological molecules. Of the analyte classes, nucleic acid measurements are typically the most tractable, both on an individual analyte basis and in parallel. Thus, tools are being sought to enable measurement of other cellular molecules using nucleic acid biosensors. Of the variety of potential nucleic acid biosensor strategies, structure-switching aptamers (SSAs) present a unique opportunity to couple sensing and readout of the target molecule. However, little has been characterized about the parameters that determine the fidelity of the signal from SSA biosensors. In this study, a small molecule biosensor based on a SSA was engineered to detect the model small molecule, theophylline, in solution. Quantitative theophylline detection over nearly three orders-of-magnitude was achieved by scintillation counting and quantitative PCR. Further analysis showed that the biosensor fidelity is primarily controlled by the relative stability of the two conformations of the SSA.     

电化学DNA生物传感器*

对特异DNA序列的检测在基因相关疾病的诊断、军事反恐和环境监测等方面均具有非常重要的意义,DNA传感器的研究就是为了满足对特异DNA序列的快速、便捷、高灵敏度和高选择性检测的需要。近年来涌现出了多种传感策略,根据检测方法的不同可以大致分为光学传感器、电化学传感器、声学传感器等。由于电化学检测方法本身所具有的灵敏、快速、低成本和低能耗等特点,电化学DNA传感器已成为一个非常活跃的研究领域并在近几年中得到了快速发展。本文概括了近年来在DNA传感器的重要分支——电化学DNA传感器领域内的一些重要进展,主要包括DNA探针在传感界面上的固定方法和各种电化学DNA杂交信号的检测方法。     

Accurate detection of on-state quantum dot and biomolecules in a microfluidic flow with single-molecule two-color coincidence detection

Due to their unique optical and electronic properties, quantum dots (QDs) have been widely used in a variety of biosensors for sensitive detection of biomarkers and small molecules. However, single QD exhibits dynamic fluctuation of fluorescence intensity (i.e., blinking) with the transition between on and off states, which adversely influences the development of QD-based optical biosensors. Therefore, the methods for efficient evaluation of on-state QD are especially important and highly desirable. In this paper, a novel and unique approach based on single-molecule two-color coincidence detection is developed to simply and accurately evaluate the on-state QDs in a microfluidic flow. Our results demonstrate that improved QDs in the on state are detected in a microfluidic flow in comparison with that in the Brownian motion state, thus paving the way to the development of single QD-based biosensors for sensitive detection of low-abundance biomolecules. This single-molecule two-color coincidence detection has been applied for the homegeneous detection of nucleic acids in a microfluidic flow with the detection sensitivity of 5.0 fM.     

基于氧化石墨烯和DNA量子点组装体的DNA二元逻辑检测及循环可逆设计

制备了水溶性的氧化石墨烯(GO)和以DNA为模板的Cd Te量子点(P1),通过GO与P1的π-π堆积作用组装构建了纳米生物传感器,将其用于双目标DNA分子的逻辑检测,实现了较高的选择性;通过改进DNA序列,实现了该传感器对双目标分子的可逆循环检测及重复利用.利用原子力显微镜(AFM)、透射电子显微镜、电泳和荧光光谱等方法对传感器的构建和检测过程进行了表征.该P1-GO纳米生物传感器在核酸检测等领域具有较大的应用前景.     

玻璃载体表面脱氧核糖核酸的固定及其化学发光检测

用硅烷化偶联剂把ＤＮＡ直接共价固定在载玻片表面，将辣根过氧化物酶标记的探针与之进行核酸杂交，杂交后用增强的化学发光检测。方法的检出限为７５ｐｇ。研究了ＤＮＡ分子固定在玻璃载体表面的各种条件，并建立了在玻璃载体表面进行核酸杂交的体系，为研究光纤ＤＮＡ生物传感器打下了基础。     

A fluorometric lateral flow assay for visual detection of nucleic acids using a digital camera readout

A fluorometric lateral flow assay has been developed for the detection of nucleic acids. The fluorophores phycoerythrin (PE) and fluorescein isothiocyanate (FITC) were used as labels, while a common digital camera and a colored vinyl-sheet, acting as a cut-off optical filter, are used for fluorescence imaging. After DNA amplification by polymerase chain reaction (PCR), the biotinylated PCR product is hybridized to its complementary probe that carries a poly(dA) tail at 3? edge and then applied to the lateral flow strip. The hybrids are captured to the test zone of the strip by immobilized poly(dT) sequences and detected by streptavidin-fluorescein and streptavidin-phycoerythrin conjugates, through streptavidin-biotin interaction. The assay is widely applicable, simple, cost-effective, and offers a large multiplexing potential. Its performance is comparable to assays based on the use of streptavidin-gold nanoparticles conjugates. As low as 7.8 fmol of a ssDNA and 12.5 fmol of an amplified dsDNA target were detectable.

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Graphical abstract Schematic presentation of a fluorometric lateral flow assay based on fluorescein and phycoerythrin fluorescent labels for the detection of single-stranded (ssDNA) and double-stranded DNA (dsDNA) sequences and using a digital camera readout. SA: streptavidin, BSA: Bovine Serum Albumin, B: biotin, FITC: fluorescein isothiocyanate, PE: phycoerythrin, TZ: test zone, CZ: control zone.

     

Electrocatalytic assay of mercury(II) ions using a bifunctional oligonucleotide signal probe

Engineered nucleic acid probes containing recognition and signaling functions find growing interest in biosensor design. In this paper, we developed a novel electrochemical biosensor for sensitive and selective detecting of Hg²⁺ based on a bifunctional oligonucleotide signal probe combining a mercury-specific sequence and a G-quadruplex (G4) sequence. For constructing the electrochemical Hg²⁺ biosensor, a thiolated, mercury-specific oligonucleotide capture probe was first immobilized on gold electrode surface. In the presence of Hg²⁺, a bifunctional oligonucleotide signal probe was hybridized with the immobilized capture probe through thymine–mercury(II)–thymine interaction-mediated surface hybridization. The further interaction between G4 sequence of the signal probe and hemin generated a G4–hemin complex, which catalyzed the electrochemical reduction of hydrogen peroxide, producing amplified readout signals for Hg²⁺ interaction events. This electrochemical Hg²⁺ biosensor was highly sensitive and selective to Hg²⁺ in the concentration of 1.0 nM to 1 μM with a detection limit of 0.5 nM. The new design of bifunctional oligonucleotide signal probes also provides a potential alternative for developing simple and effective electrochemical biosensors capable of detecting other metal ions specific to natural or artificial bases.     

Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids

In the present study, a highly sensitive and specific bio-sensing platform for enzyme-free and colorimetric detection of nucleic acids has been developed. The biosensor is composed of two DNA nanostructures and two fuel strands that construct the foundation of a feed-forward catalytic DNA circuit. Upon binding the target strand to a specific DNA nanostructure, the circuit is run in order that at the end a hemin-binding aptamer, with the ability to convert a colorless substrate into a colored substance is released. Based on this strategy, 4 pM of the target DNA can be easily detected in serum samples by naked eyes after only a two-hour incubation with the circuit; meanwhile, if the incubation time is extended to 3 h, the biosensor can detect 1 pM of the target DNA. Besides the elevated sensitivity, the circuit can truly discriminate a spurious target containing one nucleotide mismatch with high specificity. Overall, the enzyme-free catalytic DNA circuit can be used as a sensitive alternative method to enzyme-based biosensors for the specific and cost-effective detection of nucleic acids.     

Multi-analyte single-membrane biosensor for the serotype-specific detection of Dengue virus

A multi-analyte biosensor based on nucleic acid hybridization and liposome signal amplification was developed for the rapid serotype-specific detection of Dengue virus. After RNA amplification, detection of Dengue virus specific serotypes can be accomplished using a single analysis within 25 min. The multi-analyte biosensor is based on single-analyte assays (see Baeumner et al (2002) Anal Chem 74:1442–1448) developed earlier in which four analyses were required for specific serotype identification of Dengue virus samples. The multi-analyte biosensor employs generic and serotype-specific DNA probes, which hybridize with Dengue RNA that is amplified by the isothermal nucleic acid sequence based amplification (NASBA) reaction. The generic probe (reporter probe) is coupled to dye-entrapping liposomes and can hybridize to all four Dengue serotypes, while the serotype-specific probes (capture probes) are immobilized through biotin–streptavidin interaction on the surface of a polyethersulfone membrane strip in separate locations. A mixture of amplified Dengue virus RNA sequences and liposomes is applied to the membrane and allowed to migrate up along the test strip. After the liposome-target sequence complexes hybridize to the specific probes immobilized in the capture zones of the membrane strip, the Dengue serotype present in the sample can be determined. The amount of liposomes immobilized in the various capture zones directly correlates to the amount of viral RNA in the sample and can be quantified by a portable reflectometer. The specific arrangement of the capture zones and the use of unlabeled oligonucleotides (cold probes) enabled us to dramatically reduce the cross-reactivity of Dengue virus serotypes. Therefore, a single biosensor can be used to detect the exact Dengue serotype present in the sample. In addition, the biosensor can simultaneously detect two serotypes and so it is useful for the identification of possible concurrent infections found in clinical samples. The various biosensor components have been optimized with respect to specificity and sensitivity, and the system has been ultimately tested using blind coded samples. The biosensor demonstrated 92% reliability in Dengue serotype determination. Following isothermal amplification of the target sequences, the biosensor had a detection limit of 50 RNA molecules for serotype 2, 500 RNA molecules for serotypes 3 and 4, and 50,000 molecules for serotype 1. The multi-analyte biosensor is portable, inexpensive, and very easy to use and represents an alternative to current detection methods coupled with nucleic acid amplification reactions such as electrochemiluminescence, or those based on more expensive and time consuming methods such as ELISA or tissue culture.     

Immobilization of Bovine Serum Albumin on Polytetrafluoroethylene for Application as a Potential Solid Support for Biosensor Development with Visual Detection

Immobilization of biomolecules on polymers is attractive for developing new biosensors and analytical methods. Polytetrafluoroethylene, PTFE (Teflon), is a low-cost polymer that has unique chemical and physicochemical properties. In this work, PTFE was investigated as a solid support for biosensor development. Bovine serum albumin (BSA) was immobilized directly on PTFE thin films without pretreatment. BSA was biotinylated, while the immobilization was controlled by the formation of visual spots using either streptavidin–fluorescein or streptavidin–gold nanoparticle conjugates. The visualization of the spots was accomplished by the naked eye (red spots) or a digital camera that captures the emitted fluorescence (green spots). The signal-to-background ratio was determined for both detection systems and was equal to 24.4 and 58.4 for streptavidin–fluorescein and streptavidin–gold nanoparticles, respectively.     

Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection

G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H₂O₂-mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.     

Colloid Au-enhanced DNA immobilization for the electrochemical detection of sequence-specific DNA

We use colloidal Au to enhance the DNA immobilization amount on a gold electrode and ultimately lower the detection limit of our electrochemical DNA biosensor. Self-assembly of approximately 16-nm diameter colloidal Au onto a cysteamine modified gold electrode resulted in an easier attachment of an oligonucleotide with a mercaptohexyl group at the 5′-phosphate end, and therefore an increased capacity for nucleic acid detection. Quantitative results showed that the surface densities of oligonucleotides on the Au colloid modified gold electrode were approximately (1–4)×10¹⁴ molecules cm⁻². Hybridization was induced by exposure of the ssDNA-containing gold electrode to ferrocenecarboxaldehyde labeled complementary ssDNA in solution. The detection limit is 5×10⁻¹⁰ mol l⁻¹ of complementary ssDNA, which is much lower than our previous electrochemical DNA biosensors. The Au nanoparticle films on the Au electrode provide a novel means for ssDNA immobilization and sequence-specific DNA detection.     

Recent advances in nucleic acid amplification-based optical biosensors for disease diagnosisEI北大核心CSCD

Optical biosensors have been widely used in the detection of biomarkers due to their advantages of simple operationquick responsehigh sensitivity and visualization. When constructing optical biosensors nucleic acid amplification technology can be used to improve the analytical performance of optical biosensor which can further realize the highly sensitive detection of biomarkers and provide more accurate information for disease diagnosis. In this reviewrecent advances in nucleic acid amplification-based optical biosensors for disease diagnosis were reviewed the possible problems may exist in practical applications and future development trends were proposed. © 2022, Youke Publishing Co.,Ltd. All rights reserved.     

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 DNA biosensor based on the electrocatalytic oxidation of amine by a threading intercalator

An electrochemical biosensor for the detection of DNA based a peptide nucleic acid (PNA) capture probe (CP) modified indium tin oxide electrode (ITO) is described in this report. After hybridization, a threading intercalator, N,N′-bis[(3-propyl)-imidazole]-1,4,5,8-naphthalene diimide (PIND) imidazole complexed with Ru(bpy)₂Cl (PIND-Ru, bpy = 2,2′-bipyridine), was introduced to the biosensor. PIND-Ru selectively intercalated to double-stranded DNA (ds-DNA) and became immobilized on the biosensor surface. Voltammetric tests showed highly stable and reversible electrochemical oxidation/reduction processes and the peak currents can directly be utilized for DNA quantification. When the tests were conducted in an amine-containing medium, Tris-HCl buffer for example, a remarkable improvement in the voltammetric response and noticeable enhancements of voltammetric and amperometric sensitivities were observed due to the electrocatalytic activity of the [Ru(bpy)₂Cl] redox moieties. Electrocatalytic current was observed when as little as 3.0 attomoles of DNA was present in the sample solution.     

Selective Electrochemical Detection of Pirarubicin by Means of DNA‐modified Graphite Biosensor

Pirarubicin (THP) is an anthracycline drug, which is mainly used in the anticancer treatment. Utilization of THP may be associated with many dangerous side effects, therefore monitoring of drug level in patients’ organism is an important aspect of chemotherapy. In our research we focused on designing of an electrochemical DNA‐based biosensor for selective detection of pirarubicin (THP). Our biosensor utilizes the ability of pirarubicin to interact with DNA double helix and the fact that THP is an electrochemically active compound. Graphite electrodes modified with DNA enable to obtain nearly three thousand times higher sensitivity (41.8⋅10³ A/M) than non‐modified sensors. Furthermore, in the case of THP detection by means of bare graphite electrodes, LOD was 43.6⋅10⁻⁹ M, whereas for developed DNA biosensors ‐112⋅10^‐12 M. A study of selectivity of DNA–modified biosensors was carried out in aqueous solutions containing interferents: acetaminophen (PCT) and ascorbic acid (AA) as well as in samples of fetal bovine serum (FBS) spiked with PCT and AA. In established measurement conditions one peak corresponding to THP reduction was observed, whereas no redox peaks assigned to interferents (PCT, AA) were present. These results indicate that developed biosensors are selective to pirarubicin.     

Biosensor for the specific detection of a single viable B. anthracis spore

A simple membrane strip-based biosensor for the detection of viable B. anthracis spores was developed and combined with a spore germination procedure as well as a nucleic acid amplification reaction to identify as little as one viable B. anthracis spore in less than 12 h. The biosensor is based on identification of a unique mRNA sequence from the anthrax toxin activator (atxA) gene encoded on the toxin plasmid, pXO1. Preliminary work relied on plasmid vectors in both E. coli and B. thuringiensis expressing the atxA gene. Once the principle was firmly established, the vaccine strain of B. anthracis was used. After inducing germination and outgrowth of spores of B. anthracis (Sterne strain), RNA was extracted from lysed cells, amplified using nucleic acid sequence-based amplification (NASBA), and rapidly identified by the biosensor. While the biosensor assay requires only 15-min assay time, the overall process takes 12 h for the detection of as little as one viable B. anthracis spore, and is shortened significantly, if larger amounts of spores are present. The biosensor is based on an oligonucleotide sandwich-hybridization assay format. It uses a membrane flow-through system with an immobilized oligonucleotide probe that hybridizes with the target sequence. Signal amplification is provided when the target sequence hybridizes to a second oligonucleotide probe that has been coupled to dye-encapsulating liposomes. The dye in the liposomes then provides a signal that can be read visually or quantified with a hand-held reflectometer. The biosensor can detect as little as 1.5 fmol of target mRNA. Specificity analysis revealed no crossreactivity with closely related species such as B. cereus, B. megaterium, B. subtilis, B. thuringiensis etc.