Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.A rapid and multiplex approach to prepare engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing.相似文献
The lack of an efficient, low-cost sequencing method has long been a significant bottleneck in protein research and applications. In recent years, the nanopore platform has emerged as a fast and inexpensive method for single-molecule nucleic acid sequencing, but attempts to apply it to protein/peptide sequencing have resulted in limited success. Here we report a strategy to control peptide translocation through the MspA nanopore, which could serve as the first step toward strand peptide sequencing. By conjugating the target peptide to a helicase-regulated handle-ssDNA, we achieved a read length of up to 17 amino acids (aa) and demonstrated the feasibility of distinguishing between amino acid residues of different charges or between different phosphorylation sites. Further improvement of resolution may require engineering MspA-M2 to reduce its constriction zone''s size and stretch the target peptide inside the nanopore to minimize random thermal motion. We believe that our method in this study can significantly accelerate the development and commercialization of nanopore-based peptide sequencing technologies.A new technique for single molecular peptide sequencing is demonstrated by translocation of ssDNA-conjugated-peptide through MspA nanopore which is regulated by a DNA helicase motor.相似文献
The review (with 95 refs.) starts with an introduction that addresses the need for magnetic actuation in microfluidics. A second section describes the equations governing magnetic micromixing, with subsections on magnetic equations, fluid flow equations, and on convection–diffusion equations. The next section specifically covers magnetically actuated micromixers, with subsections on those actuated by external permanent magnets, by electromagnets, by microstirrers, and on micromixers with integrated electrodes. The conclusion summarizes the state of the art and addresses current challenges and trends.
Graphical abstract In this review, micromixers are classified into four types according to drive mode including external permanent magnet, electromagnet, microstirrer and the integrated electrode. The basic governing equations and operating rules of magnetic micromixers are given. The review is supposed to provide a helpful reference for those intending to study this field.
This review (with 340 refs) focuses on methods for specific and sensitive detection of metabolites for diagnostic purposes, with particular emphasis on electrochemical nanomaterial-based sensors. It also covers novel candidate metabolites as potential biomarkers for diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis. Following an introduction into the field of metabolic biomarkers, a first major section classifies electrochemical biosensors according to the bioreceptor type (enzymatic, immuno, apta and peptide based sensors). A next section covers applications of nanomaterials in electrochemical biosensing (with subsections on the classification of nanomaterials, electrochemical approaches for signal generation and amplification using nanomaterials, and on nanomaterials as tags). A next large sections treats candidate metabolic biomarkers for diagnosis of diseases (in the context with metabolomics), with subsections on biomarkers for neurodegenerative diseases, autism spectrum disorder and hepatitis. The Conclusion addresses current challenges and future perspectives.
Graphical abstract This review focuses on the recent developments in electrochemical biosensors based on the use of nanomaterials for the detection of metabolic biomarkers. It covers the critical metabolites for some diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis.
Electrochemical DNA sensors represent a simple, accurate and economical platform for DNA detection. Gold nanoparticles are known to be efficient labels in electrochemical sensors and to be viable materials to modify the surface of electrodes thereby to enhance the detection limit of the sensor. For surface modification, gold nanoparticles are used in combination with nanomaterials like graphene, graphene oxide, or carbon nanotubes to improve electrochemical performance in general. This review (with 116 refs.) mainly covers the advances made in recent years in the use of gold nanoparticles in DNA sensing. It is divided into the following main sections: (a) An introduction covers aspects of electrochemical sensing of DNA and of appropriate nanomaterials in general. (b) The use of gold nanoparticles in DNA is specifically addressed next, with subsections on AuNPs acting as electrochemical labels, electron transfer mediators, signal amplifiers, carriers of electroactive molecules, catalysts, immobilization platforms, on silver enhancement strategies, on AuNPs modified with carbonaceous materials (such as graphenes and nanotubes), and on multiple amplification schemes. The review concludes with a discussion of current challenges and trends in terms of highly sensitive DNA based sensing using AuNPs.
Graphical abstract The review describes the state of the art in the use of gold nanoparticles in the electrochemical DNA sensors and contains sections on the use of AuNPs as labels, signal amplifiers, carriers of electroactive molecules, catalyst, immobilization platform, and on silver enhancement and multiple amplification strategies.
The authors describe a colorimetric method for the determination of DNA based on the deaggregation of gold nanoparticles (AuNPs) induced by exonuclease III (Exo III). DNA amplification is accomplished by Exo III to generate large quantities of the residual DNA. Residual DNA tethers onto the surfaces of AuNPs which prevents their aggregation. Hence, the color of the solution is red. However, in the absence of DNA, salt-induced aggregation is not prevented, and the bluish-purple color of the aggregated AuNPs is observed. The ratio of absorbances at 525 and 625 nm increases up to 150 nM DNA concentrations, and the LOD is as low as 3.0 nM. It is shown that the presence of 300 nM concentrations of random DNA (with a mass up to 10-fold that of target DNA) does not interfere. The method was successfully applied to the analysis of DNA in spiked serum samples. The method is simple, reliable, and does not require complicated amplification steps and expensive instrumentation.
Graphical abstract Schematic of a sensing strategy for DNA detection by exonuclease III-induced deaggregation of gold nanoparticles. DNA concentrations as low as 3 nM can be detected via colorimetric monitoring of the color change from red to purple-blue.
The authors describe a fluorescence based aptasensor for adenosine (AD), a conceivable biomarker for cancer. The assay is based on the immobilization of capture DNA on newly synthesized quaternary CuInZnS quantum dots (QDs) and the conjugation of probe DNA on gold nanoparticles (AuNPs). The capture DNA is an adenosine-specific aptamer that is partly complementary to the probe DNA. Once the capture aptamer hybridizes probe DNA, the fluorescence of the QDs (measured at excitation/emission wavelengths of 522/650 nm) is quenched by the AuNPs. However, when AD is added, it will bind to the aptamer and restrain the hybridization between capture DNA and probe DNA. Therefore, the fluorescence of the QDs will increase with increasing AD concentration. Under optimal conditions, fluorescence is linearly related to the AD concentration in the range from 50 to 400 μM, the detection limit being 1.1 μM. This assay is sensitive, selective, reproducible and acceptably stable. It was applied to the determination of AD in spiked human serum samples where it gave satisfactory results.
Intercalating fluorescent probes are widely used to visualize DNA in studies on DNA-protein interactions. Some require the presence of adenosine triphosphate (ATP). We have investigated the mechanical properties of DNA stained with the fluorescent intercalating dyes YOYO-1 and YOYO-3 as a function of ATP concentrations (up to 2 mM) by stretching single molecules in nanofluidic channels with a channel cross-section as small as roughly 100?×?100 nm2. The presence of ATP reduces the length of the DNA by up to 11 %. On the other hand, negligible effects are found if DNA is visualized with the minor groove-binding probe 4′,6-diamidino-2-phenylindole. The apparent drop in extension under nanoconfinement is attributed to an interaction of the dye and ATP, and the resulting expulsion of YOYO-1 from the double helix.
Graphical Abstract Nanochannel-stretched DNA (48.5 kbp) stained with YOYO-1 is sensitive to ATP concentration in buffer. Nanochannels with a cross-section of 80?×?80 nm2 were used to stretch DNA.
A toehold-aided DNA recycling amplification technology was developed based on the combination of toehold-aided DNA recycling and the hemin/G-quadruplex label. The dsDNA formed between aptamer and DNA1 was first immobilized on magnetic beads. On addition of target analyte (exemplified here for riboflavin), the aptamer-riboflavin complex is formed and DNA1 is released by the beads. After magnetic separation, the supernatant containing the released DNA1 is added to a solution containing the hairpin capture DNA on magnetic beads. DNA1 will hybridize with the hairpin capture DNA via toehold binding and branch migration. This process will open the hairpin structure, and an external toehold is formed in the newly formed dsDNA. On addition of reporter DNA containing the G-quadruplex, it will interact with the formed dsDNA via toehold binding and branch migration, resulting in the releasing of DNA1 and capturing of reporter DNA on the magnetic beads. The released DNA1 will bind to another hairpin capture DNA which can start another round of DNA1 recycling. Chemiluminescence (CL) is generated by the G-quadruplex-hemin-luminol CL reaction system. Under optimal conditions, the calibration plot is linear in the 0.1 to 700 nM riboflavin concentration range, with a 30 pM detection limit (at a signal-to-noise ratio of 3). The method was successfully applied to the quantitation of riboflavin in spiked urine samples.
Anabolic androgenic steroids (AAS) are frequently abused in human and animal sports as performance-enhancing drugs, and consequently their use is controlled by international sports authorities. Testosterone is one of the most frequently used AAS, and therefore the accurate determination of its levels in biological fluids is very important. The authors describe the selection of testosterone-binding aptamers performed using a classic SELEX approach with the target immobilized on magnetic beads. Counter selections with structurally similar steroids were implemented at different stages. Pools from different selection rounds were sequenced with Next Generation Sequencing and ten aptamer candidates were selected for further characterization. Low nanomolar range dissociation constants were calculated by a bead-based PCR assay and verified by microscale thermophoresis. Future work will focus on the development of aptamer-based platforms for the sensitive detection of testosterone in biological samples and the validation of these assays for the rapid screening of suspicious samples.
Graphical abstract The selection of testosterone-binding aptamers is described via classic SELEX using the target immobilized on magnetic beads combined with Next Generation Sequencing. The process let to the identification of several unique aptamer candidates which were characterized and their binding to testosterone was evaluated.
The authors describe a novel assay for the detection of methylated DNA site. Rolling circle amplification and CdSe/ZnS quantum dots with high fluorescence efficiency are applied in this method. The CdSe/ZnS quantum dots act as electron donors, and hemin and oxygen (derived from hydrogen peroxide act as acceptors in photoinduced electron transfer. The assay, best performed at excitation/emission peaks of 450/620 nm, is sensitive and specific. Fluorometric response is linear in the 1 pM to 100 nM DNA concentration range, and the lowest detectable concentration of methylated DNA is 142 fM (S/N =?3). The method is capable of recognizing 0.01% methylated DNA in a mixture of methylated/unmethylated DNA.
Graphical abstract A novel method for methylated sites detection in DNA is established. Rolling circle amplification and photoinduced electron transfer. CdSe/ZnS quantum dots with high fluorescence efficiency act as the electron donor, while G-quadruplex/hemin and hydrogen peroxide derived oxygen act as electron acceptor. It presents a linear response towards 1 pM to 100 nM methylated DNA with a correlation coefficient of 0.9968, and the lowest detectable concentration of methylated DNA was 142 fM, with selectivity significantly superior to other methods.
The authors describe an impedimetric method for the quantitation of the DNA of the human papilloma virus (HPV) type 16. A glassy carbon electrode (GCE) was modified with gold nanosheets and is shown to be superior to a common gold disk electrode. A single-stranded 25mer oligonucleotide (ssDNA) acting as the probe DNA was immobilized via its thiolated 5′ end on both electrodes. After hybridization with target (analyte) DNA, electrochemical impedance spectra were acquired in the presence of hexacyanoferrate as a redox marker. The sensor can distinguish between complementary, non-complementary and single base pair mismatches of HPV ssDNA. At a 1 mM hexacyanoferrate concentration, the biosensors respond to target DNA in the 1 μM to 1 pM concentration range, and the detection limit is 0.15 pM. The results illustrate that the use of gold nanosheets on a GCE distinctly improves the detection and differentiation of HPV compared to using bare gold.
Graphical abstract Schematic of exploiting gold nanosheets as a platform for HPV detection. The method works in the 1 μM to 1 pM HPV concentration range and has a 0.15 pM detection limit..
A DNAzyme-embedded hyperbranched DNA dendrimer is used as a colorimetric signal amplifier in an ultrasensitive detection scheme for nucleic acids. The hyperbranched DNA dendrimers were constructed by single-step autonomous self-assembly of three structure-free DNA monomers. A cascade of self-assembly reactions between the first and second strands leads to the formation of linear DNA concatemers containing overhang flank fragments. The third strand, which bears a peroxidase-mimicking DNAzyme domain, serves as a bridge to trigger self-assembly between the first and second strands across the side chain direction. This results in a chain branching growth of the DNAzyme-embedded DNA dendrimer. This signal amplifier was incorporated into the streptavidin-biotin detection system which comprises an adaptor oligonucleotide and a biotinylated capture probe. The resulting platform is capable of detecting a nucleic acid target with an LOD as low as 0.8 fM. Such sensitivity is comparable if not superior to most of the reported enzyme-free (and even enzyme-assisted) signal amplification strategies. The DNA dendrimer based method is expected to provide a universal platform for extraordinary signal enhancement in detecting other nucleic acid biomarkers by altering the respective sequences of adaptor and capture probe.
Graphical abstract Schematic of an assembly of a DNAzyme-embedded hyperbranched DNA dendrimer which operates as a signal amplifier for nucleic acids detection. The nanostructure is constructed by autonomous self-assembly of three DNA monomers. Colored letters represent each domain, and complementary domains are marked by asterisk. Domain d represents the DNAzyme sequence.
Removal of ceftriaxone sodium antibiotic from water using cellulose acetate (CA) mixed matrix nanofiltration membranes was investigated in this work. Silica nanoparticles were functionalized with (3-aminopropyl)triethoxysilane (APTES). Then, the hydrophilic and negatively charged 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) monomer was grafted from the surface of the amino-functionalized silica nanoparticles via surface-initiated redox polymerization. Finally, CA/silica and CA/modified silica nanocomposite membranes were prepared via phase inversion method, and the rejection of ceftriaxone sodium was studied. Rejection ratios were about 90 and 96% for CA/silica and CA/modified silica membranes at pH 8, respectively, wherein both were higher compared to the neat CA membrane. In fact, in case of nanocomposite membranes, size exclusion and charge repulsion between negatively charged functional groups of the membrane and anionic groups of drug operated synergistically at alkaline pH values, and the pharmaceutical rejection was improved.
The authors have investigated (a) the self-assembly of single-stranded DNA (ssDNA) on glass surfaces, and (b) the interaction of DNA with liquid crystals (LCs) on solid surfaces. The results suggest that ssDNA (compared to dsDNA) on the solid interface causes particularly different orientations in LCs. The LC molecules assume a uniform homeotropic orientation on the surface with a typical surface ssDNA coverage of ~2.4 × 1012 molecules per square cm. Once complementary DNA is hybridized on the surface, the homotropic orientation of the LCs becomes disrupted. This orientation transition can be visually observed by using a crossed polarizer. The findings were exploiting to design an assay for target DNA (= analyte DNA) that has an ~0.1 nM detection limit. The assay is highly selective and can easily differentiate target DNA from single-base mismatch and non-complementary DNA. In our perception, it represents a powerful, label-free and portable DNA detection scheme.
Graphical abstract Schematic illustration of the mechanism for orientation behavior of a liquid crystal film supported on different surfaces. The homeotropic orientation of LC molecules was induced by ssDNA with appropriate surface coverage and was disrupted by ssDNA with lower or higher surface coverage or P1/T1 complex. 5CB: 4-Cyano-4′-pentylbiphenyl. TEA: Triethoxysilylbutyraldehyde.
The authors describe a method for the detection of DNA by using immobilized molecular beacons (MBs) on the surface of silicon, with a view on possible application in biosensing. MB hybridization and protein recognition were interrogated on silicon-on-insulator (SOI) surfaces by using fluorescently tagged probes. In order to better understand the conformational changes that occur to MBs upon hybridization, the process was studied by using dual polarization interferometry (DPI). A model system was developed that matches thickness, mass, and density parameters. The results experimentally demonstrate that hybridization promotes the displacement of a protein away from the surface. This finding may be further exploited in techniques such as photonic sensors, thereby paving the way to the design of more sensitive biosensors based on the use of MBs.
Graphical abstract Schematic of a new DNA/RNA detection scheme by using immobilized molecular beacons (MBs) on silicon, with a view on possible application in biosensing. A study was performed on the conformational changes that occur to MBs upon hybridization by Dual Polarization Interferometry (DPI).
The authors introduce a method for spatially arranged DNA immobilization on 10-nm gold nanoparticles (GNP) deposited on a silicon substrate carrying nanogapped interdigitated electrodes. The GNPs are covalently bound to the surface via silane chemistry, and the single steps of fabrication are monitored by FTIR spectroscopy and atomic force microscopy. This GNP deposition technique is shown to reduce the size of the nanogaps to 130 nm. FTIR also was used to monitor the immobilization of DNA on the surface of the interdigitated electrodes. This method allows DNA to be immobilized in a uniform and homogenous way. The utility of the method is demonstrated by immobilizing probe DNA on the surface and detecting target DNA specific for the human papilloma virus via fluorescence with a detection limit as low as 1 pM. In our perception, this method for GNP-mediated DNA immobilization enables high-performance sensing of a wide range of target (analyte) DNA.
Graphical abstract Schematic presentation of gold nanoparticle-mediated and spatially resolved deposition of DNA on nano-gapped interdigitated electrodes. The method was applied to the chemiluminescent determination of the human papillomavirus
The paper describes a voltammetric method for the quantitation of the activity of telomerase extracted from cancer cells. A thiolated single-stranded telomerase substrate primer was firstly immobilized on a gold electrode. In the presence of a mixture of telomerase and deoxynucleotide triphosphates, the primer becomes elongated and contains repetitive nucleotide sequences (TTAGGG)n. After hybridization with blocker DNA, gold nanoparticles are added and captured by the elongated single-stranded DNA. This reduces the charge transfer resistance of the gold electrode. The telomerase activity is then quantified via differential pulse voltammetry, typically at 0.12 V (vs. SCE). The method is PCR-free, rapid, and convenient. It was applied to the detection of HeLa cells via the telomerase activity of lysed cells. The detection range was from 500 to 50,000 cells/mL and the detection limit was as low as 500 cells/mL.
Graphical abstract A telomerase substrate (TS) primer is immobilized on a gold electrode as the sensing interface to detect the activity of telomerase extracted from cancer cells. Unmodified gold nanoparticles (AuNPs) are utilized which change the electrochemical responses.
MicroRNAs are endogenous noncoding RNAs that play critical roles in biological processes and can be considered as molecular markers for early diagnosis and pathogenesis of diseases. The authors describe a highly sensitive electrochemical biosensor for microRNA that is based on the use of tetrahedral DNA nanostructure probes and guanine nanowire amplification. The DNA tetrahedral probe is self-assembled on a gold electrode and enhances reactivity, accessibility, and molecular recognition efficiency. Combined with the tetrahedral probe, the guanine nanowire amplifies the signal and improves the analytical performance of the biosensor. Operated best at a voltage of typically 150 mV (vs. Ag/AgCl), the sensor has a linear response to the logarithmic microRNA concentration in the 500 f. to 10 nM range, with a 176 f. detection limit. It is highly selective and can be applied to real samples. It is concluded that this strategy has a good potential with respect to the determination of microRNA in clinical diagnosis and in biological research.
Graphical abstract Schematic of a tetrahedral DNA nanostructure-based amperometric biosensor coupled to guanine nanowire amplification for analysis of microRNA-21. This strategy is highly selective and also performs well for the detection of microRNA levels of breast cancer patients.
This review (with (318) refs) describes progress made in the design and synthesis of morphologically different metal oxide nanoparticles made from iron, manganese, titanium, copper, zinc, zirconium, cobalt, nickel, tungsten, silver, and vanadium. It also covers respective composites and their function and application in the field of electrochemical and photoelectrochemical sensing of chemical and biochemical species. The proper incorporation of chemical functionalities into these nanomaterials warrants effective detection of target molecules including DNA hybridization and sensing of DNA or the formation of antigen/antibody complexes. Significant data are summarized in tables. The review concludes with a discussion or current challenge and future perspectives.
