Triplex hairpin oligosensor for ultrasensitive determination of miRNA-155 as a cancer marker using Si quantum dots and Au nanoparticles

In this study, a new triplex hairpin oligosensor was developed for the determination of a breast cancer biomarker using silicon quantum dots (Si QD) (λex = 370 nm, λem = 482 nm) as donor and gold nanoparticles (GNP) as an acceptor in a FRET (fluorescence resonance energy transfer) mechanism. In the triplex hairpin oligosensor, a triplex-forming oligonucleotide (TFO) labeled with Si QD and a single-strand DNA labeled with GNP form a hairpin shape with a triplex structure at the hairpin stem. In a turn-on mechanism, the triplex hairpin stem is opened in the presence of sequence-specific miRNA-155 which leads to the release of the Si QD-labeled TFO probe and recovery of the fluorescence signal. About 80 % of the fluorescence intensity of the Si QD-TFO is quenched in the triplex hairpin structure of the oligosensor and in the presence of 800 pM miRNA-155, the fluorescence signal recovered to 57.7 % of its initial value. The LOD of about 10 pM was obtained. The designed triplex-based biosensor can discriminate concentrations of breast cancer biomarkers with high selectivity.

Triple-helix molecular-switch-actuated rolling circle amplification and catalytic hairpin assembly multistage signal amplified fluorescent aptasensor for detection of aflatoxin B1

BACKGROUND

Mycotoxins, a class of secondary metabolites produced by molds, are widely distributed in nature and are very common in food contamination. Aflatoxin B1 (AFB1) is a highly stable natural mycotoxin, and many agricultural products are easily contaminated by AFB1, it is important to establish a sensitive and efficient AFB1 detection method for food safety. The fluorescence aptamer sensor has shown satisfactory performance in AFB1 detection, but most of the fluorescence aptasensors are not sensitive enough, so improving the sensitivity of the aptasensor becomes the focus of this work.

RESULTS

Herein, an innovative fluorescent aptasensor for AFB1 detection which is based on catalytic hairpin assembly (CHA) and rolling circle amplification (RCA) driven by triple helix molecular switch (THMS) is proposed. A functional single-strand with an AFB1 aptamer, here called an APF, is first designed to lock onto the signal transduction probe (STP), which separates from THMS when target AFB1 is present. Subsequently, STP initiates the RCA reaction along the circular probe, syntheses macro-molecular mass products through repeated triggering sequences, triggers the CHA reaction to produce a large number of H1-H2 structures, which causes FAM to move away from BHQ-1 and recover its fluorescence signal. The fluorescence signal from FAM at 520 nm was collected as the signal output of aptasensor in this work. With high amplification efficiency of RCA and CHA of the fluorescence sensor, resulting in a low LOD value of 2.95 pg mL-1(S/N = 3).

SIGNIFICANCE

The successful establishment of the sensor designed in this work shows that the cascade amplification reaction is perfectly applied in the fluorescent aptamer sensor, and the signal amplification through the reaction between DNA strands is a simple and efficient method. In addition, it's also important to remember that the aptasensor can detect other targets only by changing the sequence of the aptamer, without redesigning other DNA sequences in the reaction system.

A Nanopore Sensor for Multiplexed Detection of Short Polynucleotides Based on Length-Variable, Poly-Arginine-Conjugated Peptide Nucleic Acids

Real-time and easy-to-use detection of nucleic acids is crucial for many applications, including medical diagnostics, genetic screening, forensic science, or monitoring the onset and progression of various diseases. Herein, an exploratory single-molecule approach for multiplexed discrimination among similar-sized single-stranded DNAs (ssDNA) is presented. The underlying strategy combined (i) a method based on length-variable, short arginine (poly-Arg) tags appended to peptide nucleic acid (PNA) probes, designed to hybridize with selected regions from complementary ssDNA targets (cDNA) in solution and (ii) formation and subsequent detection with the α-hemolysin nanopore of (poly-Arg)-PNA-cDNA duplexes containing two overhangs associated with the poly-Arg tail and the non-hybridized segment from ssDNA. We discovered that the length-variable poly-Arg tail marked distinctly the molecular processes associated with the nanopore-mediated duplexes capture, trapping and unzipping. This enabled the detection of ssDNA targets via the signatures of (poly-Arg)-PNA-cDNA blockade events, rendered most efficient from the β-barrel entrance of the nanopore, and scaled proportional in efficacy with a larger poly-Arg moiety. We illustrate the approach by sensing synthetic ssDNAs designed to emulate fragments from two regions of SARS-CoV-2 nucleocapsid phosphoprotein N-gene.

Current Simultaneous Discrimination of Mismatched MicroRNAs Using Base-Flipping within the α-Hemolysin Latch

The simultaneous discrimination of let-7 microRNAs (miRNAs) would greatly facilitate the early diagnosis and prognosis monitoring of diseases. In this work, a molecular beacon DNA probe was designed to be able to flip out its mismatched cytosine base within the α-hemolysin (α-HL) latch and generate completely separated blocking currents to identify the single-base difference. As a result, the characteristic blocking current of fully matched MB/let-7a and single-base mismatched MB/let-7f was 84.30 ± 0.92 and 87.05 ± 0.86% (confidence level P 95%), respectively. Let-7 miRNA family let-7a and let-7f were completely simultaneously discriminated, which could be attributed to the following strengths. (1) The statistic distribution of blocking current is extremely concentrated with a small relative standard deviation (RSD) of less than 1% and a narrow distribution range. (2) Complete separation is achieved with a high separation resolution of 1.54. (3) The cytosine base flipping out within the α-HL latch provides a universal labeling-free strategy to simultaneously discriminate the single-base mismatch. Overall, the target let-7f sequences were detected with a linear range from 0.001 to 10 pM in human serum samples containing 200 nM let-7a. Great potential has been demonstrated for precise detection, early diagnosis, and prognosis monitoring of diseases related to single-base difference.

The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing

Hairpin structures play an essential role in DNA replication, transcription, and recombination. Single-molecule studies enable the real-time measurement and observation of the energetics and dynamics of hairpin structures, including folding and DNA-protein interactions. Nanopore sensing is emerging as a powerful tool for DNA sensing and sequencing, and previous research into hairpins using an α-hemolysin (α-HL) nanopore suggested that hairpin DNA enters from its stem side. In this work, the translocation and interaction of hairpin and dumbbell DNA samples with varying stems, loops, and toeholds were investigated systematically using a Mycobacterium smegmatis porin A (MspA) nanopore. It was found that these DNA constructs could translocate through the pore under a bias voltage above +80 mV, and blockage events with two conductance states could be observed. The events of the lower blockage were correlated with the loop size of the hairpin or dumbbell DNA (7 nt to 25 nt), which could be attributed to non-specific collisions with the pore, whereas the dwell time of events with the higher blockage were correlated with the stem length, thus indicating effective translocation. Furthermore, dumbbell DNA with and without a stem opening generated different dwell times when driven through the MspA nanopore. Finally, a new strategy based on the dwell time difference was developed to detect single nucleotide polymorphisms (SNPs). These results demonstrated that the unzipping behaviors and DNA-protein interactions of hairpin and dumbbell DNA could be revealed using nanopore technology, and this could be further developed to create sensors for the secondary structures of nucleic acids.

Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores

DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.

Cucurbiturils in nucleic acids research

During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.

A bifunctional DNA probe for sensing pH and microRNA using a nanopore

We have developed a bifunctional probe based on triplex molecular beacons for the measurement of environmental pH and quantification of microRNA-10b using a nanopore. The probe responds sharply to solution pH changes in the range of 6.0-7.5. The limit of detection for microRNA-10b is as low as 5.0 pM.

Early Monitoring Drug Resistant Mutation T790M with a Two-Dimensional Simultaneous Discrimination Nanopore Strategy

With the aim of detecting low frequency of drug resistant mutation T790M against wild-type sequences, we reported a two-dimensional signal analysis strategy by combining a three locked nucleic acids (LNAs)-modified probe (LP15-3t) and an α-HL nanopore. The specific hybridization of the LP15-3t probe with the T790M generated unique long two-level signals, including characteristic blocking current and characteristic dwell time. Due to the significant dwell time difference (114.2-fold) and the blocking current difference ranging from 81% to 96%, this two-dimensional signal analysis strategy can simultaneously distinguish T790M sequences with a sensitivity of 0.0001% against wild-type sequences. The LOD of T790M was 0.1 pM. This high discrimination capability would have great potential in the detection of rare mutation sequences and the early monitoring of clinical outcome of NSCLC patients with TKI drug resistance.

Unzipping Mechanism of Free and Polyarginine-Conjugated DNA-PNA Duplexes, Preconfined Inside the α-Hemolysin Nanopore

In this work, comparative studies on DNA-PNA and polyarginine-conjugated DNA-PNA duplexes unzipping inside the α-hemolysin nanopore (α-HL) are presented. We identified significant differences in the blockade currents, as the applied voltage across the nanopore facilitated the duplex capture inside the nanopore's vestibule against the constriction region, subsequent cDNA strand insertion inside the nanopore's β-barrel past the constriction site, its complete unzip from the duplex, and translocation. We observed that inside the voltage-biased nanopore, polyarginine-conjugated DNA-PNA duplexes dehybridize faster than their DNA-PNA counterparts and proposed a model to describe the duplex unzipping. This study identifies key particularities of DNA-PNA duplex unzipping as it takes place inside the nanopore and being preceded by entrapment in the vestibule domain of the α-HL. Our results are a crucial step toward understanding the nucleic acids duplexes unzipping kinetics variability, in confined, variable geometries.

Nonfunctionalized PNAs as Beacons for Nucleic Acid Detection in a Nanopore System

In this work, single-channel current recordings were used to selectively detect individual ssDNA strands in the vestibule of the α-hemolysin (α-HL) protein nanopore. The sensing mechanism was based on the detection of the intrinsic topological change of target ssDNA molecules after the hybridization with complementary PNA fragments. The readily distinguishable current signatures of PNA-DNA duplexes reversible association with the α-HL's vestibule, in terms of blockade amplitudes and kinetic features, allows specific detection of nucleic acid hybridization.

Nanopore-Assisted, Sequence-Specific Detection, and Single-Molecule Hybridization Analysis of Short, Single-Stranded DNAs

We report here on the ability of the α-hemolysin (α-HL) nanopore to achieve label-free, selective, and real-time detection of 15 nt long ssDNA fragments in solution, by exploiting their hybridization with freely added, polycationic peptides-functionalized PNAs. At the core of our work lies the paradigm that when PNAs and ssDNA are mixed together, the bulk concentration of free PNA decreases, depending upon the (mis)match degree between complementary strands and their relative concentrations. We demonstrate that the ssDNA sensing principle and throughput of the method are determined by the rate at which nonhybridized, polycationic peptides-functionalized PNA molecules arrive at the α-HL's vestibule entrance and thread into the nanopore. We found that with the application of a 30-fold salt gradient across the nanopore, the method enhances single-molecule detection sensitivity in the nanomolar range of ssDNA concentrations. This study demonstrates that the transmembrane potential-dependent unzip of single PNA-DNA duplexes at the α-HL's β-barrel entry permits discrimination between sequences that differ by one base pair.

Triple-helix molecular-switch-actuated exponential rolling circular amplification for ultrasensitive fluorescence detection of miRNAs

We have developed a rapid and high-efficiency fluorescent biosensing platform based on triple-helix molecular-switch (THMS)-actuated exponential rolling circular amplification (RCA) strategy for the ultrasensitive detection of miR-21.

Sensitive discrimination of single nucleotide variants using a PDA microtube waveguide platform with heterogeneous CHA amplification and competitive inhibition strategy

The CHA system preferentially amplifies the target signal while the competitive system preferentially inhibits the SNV signal using PDA microtubes.

A novel thermometer-type hydrogel senor for glutathione detection

A thermometer-type visual sensor for glutathione (GSH) sensing was developed with stimulus-responsive fluorescent hydrogel which was obtained by using 5, 6-bicarboxylic fluorescein crossli`nked partly ammoniated polyacrylamide. Various experimental parameters such as the particle size of hydrogel, buffer solution and swelling time were optimized. It is accessible to measure the volume change of hydrogel with the sensor by reading the graduation on a pipette like thermometer with naked eye. The concentration of the GSH depended on the volume in a certain range as the signal. Satisfactory agreements between the sensor and HPLC results for atuomolan tablet assays indicated the capability of the thermometer-type sensors for the analysis of real samples. These findings proved the utility of stimulus-responsive, intelligent hydrogel and the suitability of thermometer-style visual sensor design for quantitative assays.

Ultrasensitive electrochemical detection of miRNA based on DNA strand displacement polymerization and Ca2+-dependent DNAzyme cleavage

An ultrasensitive electrochemical sensing strategy for the detection of miRNA is developed combining strand displacement polymerization and a DNAzyme-catalyzed cleavage reaction.