Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Visual Detection of Cucumber Green Mottle Mosaic Virus Based on Terminal Deoxynucleotidyl Transferase Coupled with DNAzymes Amplification

A simple, rapid, and sensitive visual detection method for observing cucumber green mottle mosaic virus was reported based on the template-independent polymerization activity of terminal deoxynucleotidyl transferase (TdT), coupled with the cascade amplification of Mg²⁺-dependent DNAzyme and hemin/G-quadruplex DNAzyme. Briefly, the hybridized dsDNA of T1/P1 was cut into two parts at its position of 5′-AA↓CG↑TT-3′ by the restricted enzyme AcII. The longer, newborn fragment originating from P1 was tailed at its 3’-end by oligo dG, and an intact enzymatic sequence of Mg²⁺-dependent DNAzyme was generated. The substrate sequence in the loop segment of the hairpin probe (HP) hybridized with the newborn enzymatic sequence and was cleaved into two parts in the presence of Mg²⁺. The locked G-quadruplex sequence in the stem segment of the HP was released, which catalyzed the oxidation of ABTS^2- in the presence of H₂O₂, and the resulting solution turned green. A correlation between the absorbance and concentration of T1 was obtained in a range from 0.1 pM to 2 nM, with a detection limit of 0.1 pM. In addition to promoting a lower detection limit and shorter monitoring time, this method also demonstrated an excellent selectivity to single or double nucleotide changes. Therefore, the designed strategy provided a rapid and efficient platform for viral inspection and plant protection.

Determination of the activity of uracil-DNA glycosylase by using two-tailed reverse transcription PCR and gold nanoparticle-mediated silver nanocluster fluorescence: a new method for gene therapy-related enzyme detection

The authors present a fluorometric method for ultrasensitive determination of the activity of uracil-DNA glycosylase (UDG). It is based on the use of two-tailed reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and an entropy-driven reaction. The assay involves the following steps: (1) UDG-driven uracil excision repair, (2) two-tailed RT-qPCR-mediated amplification, (3) RNA polymerase-aided amplification, and (4) DNA-modified silver nanoclusters (AgNCs) as a transducer to produce a fluorescent signal. UDG enables uracil to be removed from U·A pairs in DNA1 and produces a depurinated/depyrimidinated site that is readily cleaved by endonuclease IV (Endo IV). The cleaved DNA contains the T7 RNA polymerase primer for the T7 RNA polymerase amplification which produces a large number of microRNA sequences. Subsequent two-tailed RT-qPCR leads to the formation of a prolonged DNA termed DNA3. The prolonged part of DNA3 is then hybridized with an added DNA4/DNA5 duplex, where DNA5 is labeled with gold nanoparticles (AuNPs), and DNA 4 is labeled with AgNCs. The AuNPs quench the fluorescence of the AgNCs. The duplex has a toehold to hybridize the prolong part of DNA3. This results in the formation of a DNA5/DNA3 duplex due to strand displacement (by replacing the DNA4 in the DNA4/DNA5 duplex). DNA4 is released and moves away from the AuNPs. This results in restored AgNC fluorescence, best measured at excitation/emission wavelengths of 575/635 nm. The method has a detection limit as low as 0.1 mU mL^-1 of UDG activity (3σ criterion) with a range of 0.001-0.01 U mL^-1. It was used to measure UDG activity in cell lysates. Conceivably, it may be used to screen for UDG inhibitors such as Ugi. Graphical abstract Schematic presentation of the two-tailed RT-qPCR assay platform for ultrasensitive detection of uracil-DNA glycosylase (UDG). Two-tailed RT-qPCR-mediated amplification and RNA polymerase-aided amplification are utilized for signal amplification. DNA-modified silver nanoclusters (AgNCs) are used as a transducer to produce a fluorescent signal.

Sensitively distinguishing intracellular precursor and mature microRNA abundance

Mature microRNAs (miRNAs) produced from precursor microRNAs (pre-miRNAs) by the RNase Dicer have showed significant potential for cancer diagnosis and prognosis due to their key regulatory roles in various pathological processes. However, discriminatory detection of low-abundance miRNAs and pre-miRNAs remains a key challenge since the mature sequence is also present in the pre-miRNA forms. Herein, we report a novel cascade reaction to sensitively distinguish miRNAs versus pre-miRNAs in living cells based on two pairs of programmable hairpin oligonucleotide probes with a simple sequence design. The programmable hairpin probes can metastably coexist until the introduction of miRNAs or pre-miRNAs, which can trigger a specific hybridization chain reaction (HCR), respectively, leading to the self-assembly of nicked DNA duplex structures and a remarkable specific fluorescence intensity increase. The system can readily and sensitively assess the miRNA or pre-miRNA abundance in a homogeneous solution. The intracellular miRNA and pre-miRNA expression level assessment in different living cells is realized. Thus, we provide a novel investigation tool for discriminatorily and accurately assessing miRNA and pre-miRNA abundance, which could be useful for the biomedical application of miRNAs.

A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine for nucleic acid detection

A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine was proposed for one-step, isothermal and dual-level amplified detection of nucleic acids.

Anion induced supramolecular polymerization: a novel approach for the ultrasensitive detection and separation of F−

A novel approach for the ultrasensitive detection and separation of F⁻ has been developed. F⁻ could induce a tripodal naphthalimide sensor (TNA) to carry out reversible supramolecular polymerization and lead to strong AIEE.

BSA stabilized tetraphenylethylene nanocrystals as aggregation-induced enhanced electrochemiluminescence emitters for ultrasensitive microRNA assay

An ultrasensitive ECL biosensing platform was constructed based on BSA stabilized tetraphenylethylene nanocrystals to achieve microRNA detection in cancer cells.

Trifunctional integrated DNA-based universal sensing platform for detection of diverse biomolecules in one-pot isothermal exponential amplification mode

Template constructed with only a short single-stranded DNA is necessary; it is first recognized by the target enzyme, then multiple amplification cycles are initiated, achieving ultra-high sensitivity by a one-pot isothermal reaction.

Aptamer Conformation Switching-Induced Two-Stage Amplification for Fluorescent Detection of Proteins

Basing on the conformation change of aptamer caused by proteins, a simple and sensitive protein fluorescent assay strategy is proposed, which is assisted by the isothermal amplification reaction of polymerase and nicking endonuclease. In the presence of platelet-derived growth factor (PDGF-BB), the natural conformation of a DNA aptamer would change into a Y-shaped complex, which could hybridize with a molecular beacon (MB) and form a DNA duplex, leading to the open state of the MB and generating a fluorescence signal. Subsequently, with further assistance of isothermal recycling amplification strategies, the designed aptamer sensing platform showed an increment of fluorescence. As a benefit of this amplified strategy, the limit of detection (LOD) was lowered to 0.74 ng/mL, which is much lower than previous reports. This strategy not only offers a new simple, specific, and efficient platform to quantify the target protein in low concentrations, but also shows a powerful approach without multiple washing steps, as well as a precious implementation that has the potential to be integrated into portable, low-cost, and simplified devices for diagnostic applications.

Ultrasensitive Photoelectrochemical Assay with PTB7-Th/CdTe Quantum Dots Sensitized Structure as Signal Tag and Benzo-4-chlorohexadienone Precipitate as Efficient Quencher

Herein, an ultrasensitive photoelectrochemical (PEC) assay was developed for the monitoring of microRNA-141 (miRNA-141) based on poly{4,8-bis[5-(2-ethylhexyl)thiophen-2-yl]benzo[1,2- b:4,5- b']dithiophene-2,6-diyl- alt-3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4- b]thiophene-4,6-diyl}/CdTe quantum dots ( PTB7-Th/CdTe QDs) sensitized structure as signal tag and the benzo-4-chlorohexadienone (4-CD) precipitate as efficient quencher. PTB7-Th and CdTe QDs were successively modified on the electrode surface to form a novel sensitized structure with eminent photovoltaic performances and surpassing film-forming ability. The PTB7-Th/CdTe QDs sensitized structure served as signal tag for achieving a strong initial PEC signal. Besides, a tiny amount of target (miRNA-141) could be transformed into numerous DNA products via enzyme-assisted target cycling procedure, which further triggered the formation of a DNA supersandwich structure on the electrode surface for loading abundant manganese porphyrin (MnPP). Thereafter, MnPP as mimetic enzyme could catalyze 4-chloro-1-naphthol (4-CN) to generate 4-CD precipitate on the sensing interface in the presence of H₂O₂, which could efficiently block electron transfer, leading to a significantly quenched PEC signal for determination of miRNA-141. The designed PEC biosensor performed a wide detection range from 0.1 fM to 1 nM with a low detection limit of 33 aM for miRNA-141, which paved a new avenue for highly accurate and ultrasensitive monitoring of multifarious analytes in bioanalysis and clinical diagnosis.

Lighting Up MicroRNA in Living Cells by the Disassembly of Lock-Like DNA-Programmed UCNPs-AuNPs through the Target Cycling Amplification Strategy

Intracellular microRNAs imaging based on upconversion nanoprobes has great potential in cancer diagnostics and treatments. However, the relatively low detection sensitivity limits their application. Herein, a lock-like DNA (LLD) generated by a hairpin DNA (H1) hybridizing with a bolt DNA (bDNA) sequence is designed, which is used to program upconversion nanoparticles (UCNPs, NaYF₄ @NaYF₄ :Yb, Er@NaYF₄ ) and gold nanoparticles (AuNPs). The upconversion emission is quenched through luminescence resonance energy transfer (LRET). The multiple LLD can be repeatedly opened by one copy of target microRNA under the aid of fuel hairpin DNA strands (H2) to trigger disassembly of AuNPs from the UCNP, resulting in the lighting up of UCNPs with a high detection signal gain. This strategy is verified using microRNA-21 as model. The expression level of microRNA-21 in various cells lines can be sensitively measured in vitro, meanwhile cancer cells and normal cells can be easily and accurately distinguished by intracellular microRNA-21 imaging via the nanoprobes. The detection limit is about 1000 times lower than that of the previously reported upconversion nanoprobes without signal amplification. This is the first time a nonenzymatic signal amplification method has been combined with UCNPs for imaging intracellular microRNAs, which has great potential for cancer diagnosis.

Platinum Nanozyme-Catalyzed Gas Generation for Pressure-Based Bioassay Using Polyaniline Nanowires-Functionalized Graphene Oxide Framework

Pressure-based bioassays incorporating biomolecular recognition with a catalyzed gas-generation reaction have been developed for gas biosensors, but most involve poor sensitivity and are unsuitable for routine use. Herein we design an innovative gas pressure-based biosensing platform for the detection of Kanamycin (Kana) on polyaniline nanowires-functionalized reduced graphene oxide (PANI/rGO) framework by using platinum nanozyme-catalyzed gas generation. The signal was amplified by coupling with catalytic hairpin assembly (CHA) and strand-displacement amplification (SDA). Upon target Kana introduction, the analyte initially triggered a SDA reaction between hairpin DNA1 and hairpin DNA2, and then induced CHA conjugation between magnetic bead-labeled hairpin DNA3 (MB-H3) and platinum nanoparticle-labeled hairpin DNA4 (Pt-H4) to form a three-dimensional network. Numerous platinum nanoparticles (peroxidase-like nanozymes) were carried over with magnetic beads to reduce hydrogen peroxide into oxygen. The as-produced gas compressed PANI/rGO frameworks (modified to polyurethane sponge, used as the piezoelectric materials) in a homemade pressure-tight device, thus causing the increasing current of PANI/rGO sponge thanks to its deformation. The change in the current caused by the as-generated gas pressure was determined on an electrochemical workstation. Under optimum conditions, PANI/rGO sponge exhibited outstanding compressibility, stable signal-waveform output, fast response and recovery time (≈109 ms), and the current increased with the increasing Kana concentration within a dynamic working range of 0.2-50 pM at a detection limit of 0.063 pM. Good reproducibility, specificity, and acceptable precision were acquired for Kana analysis. In addition, the accuracy of this method was monitored to evaluate real milk samples with the well-matched results obtained by using the referenced Kana ELISA kit.

Structure-Switching Electrochemical Aptasensor for Single-Step and Specific Detection of Trace Mercury in Dairy Products

A reagentless and single-step electrochemical aptasensor with separation-free fashion and rapid response is developed for the Hg²⁺ assay in dairy products. Herein, the sensing strategy is established on Hg²⁺-induced structural transition of the methylene-blue-tagged single-stranded DNA (ssDNA) from a flexible manner to rigid hairpin-shaped double-stranded DNA (dsDNA), generating an improved peak current for the Hg²⁺ assay with a detection limit of 0.62 fM. Importantly, the best signal-to-noise ratio value can be obtained by exploiting Au flowers as sensing material and the optimal ssDNA concentration. The proposed sensor also exhibits high selectivity as a result of the specific thymine-Hg²⁺-thymine (T-Hg²⁺-T) coordination chemistry and can be applied to detect Hg²⁺ in dairy products. With the use of the electric "signal-on" switch, the electrochemical aptasensor has the advantages of simplicity, ease of operation, and high sensitivity and specificity, offering a promising method to assess the safety of dairy products polluted with Hg²⁺.

Gold Nanobipyramids as Dual-Functional Substrates for in Situ "Turn On" Analyzing Intracellular Telomerase Activity Based on Target-Triggered Plasmon-Enhanced Fluorescence

Herein, we developed a novel plasmon-enhanced fluorescence (PEF)-based telomerase-responsive nanoprobe for in situ fluorescence "turn on" visualization of telomerase activity in live cells. The as-prepared nanoprobe was composed of a nicked molecular beacon (which contains Cy5.5-labeled hairpin-DNA sequences hybridized with telomerase primers)-functionalized gold nanobipyramids (Au NBPs). Au NBPs were selected as both fluorescence resonance energy-transfer and PEF dual-functional substrates, while DNA was selected to be the precise spacer to manage the interval between the Au NBPs and Cy5.5. On the basis of this target-triggered PEF probe, optimal fluorescence enhancement can be obtained with 49 DNA bases, which was higher than gold nanorods. The proposed method accomplishes sensitive telomerase activity detection down to 23 HeLa cells with a dynamic range of 40-1200 HeLa cells. On the basis of this, in situ fluorescence imaging of telomerase activity in live cells and real-time analysis of the variation in intracellular telomerase activity can be achieved. Moreover, cancer cells and normal cells can also be successfully discriminated even in their co-cultured mixtures, indicating promising potential in clinical diagnoses.

Electrochemiluminescence biosensing based on different modes of switching signals

Electrochemiluminescence (ECL) has attracted much attention in various fields of analysis owing to low background signals, high sensitivity, and excellent controllability.