Nucleic acid detection using carbon nanoparticles as a fluorescent sensing platform

In this communication, we demonstrate for the first time the proof of concept that carbon nanoparticles (CNPs) can be used as an effective fluorescent sensing platform for nucleic acid detection with selectivity down to single-base mismatch. The dye-labeled single-stranded DNA (ssDNA) probe is adsorbed onto the surface of the CNP via π-π interaction, quenching the dye. In the target assay, a double-stranded DNA (dsDNA) hybrid forms, recovering dye fluorescence.     

基于银纳米粒子构建荧光传感平台用于核酸检测

报道了基于银纳米粒子构建的荧光传感平台,并用于核酸检测.此荧光传感平台对核酸检测基于以下策略:首先,荧光团标记的单链DNA探针被吸附到银纳米粒子的表面,荧光团与银纳米粒子近距离接触,发生荧光猝灭;加入与探针DNA序列互补的目标DNA,两者杂交形成双链DNA,并从银纳米粒子的表面脱离,荧光得到恢复.这种银纳米粒子构建的荧...     

Application of 3,4,9,10-perylenetetracarboxylic diimide microfibers as a fluorescent sensing platform for biomolecular detection

In this paper, we report on the use of 3,4,9,10-perylenetetracarboxylic diimide microfibers (PDIMs) as an effective fluorescent sensing platform for DNA detection for the first time. This sensing system exhibits a detection limit as low as 15 nmol L⁻¹ and has a high selectivity down to single-base mismatch. The general concept used in this approach is based on adsorption of fluorescently labeled single-stranded DNA (ssDNA) probe by PDIM due to the strong π–π stacking between unpaired DNA bases and PDIM. As a result, the fluorophore is brought into close proximity of PDIM, leading to substantial fluorescence quenching. In the presence of the target, the specific hybridization of the probe with its complementary DNA sequence generates a double stranded DNA (dsDNA) which detaches from PDIM, leading to fluorescence recovery. Its generality of this sensing platform for protein detection is also demonstrated.     

水溶性碳纳米粒子的制备及其在DNA和单核苷酸多态性分析中的应用

利用电化学氧化的方法制备了水溶性好、粒径为7～12nm的碳纳米粒子,该碳纳米粒子通过π-π相互作用吸附荧光标记的单链DNA探针,并能有效地猝灭其荧光．当单链DNA探针与匹配的DNA目标分子杂交形成双链DNA时,猝灭的荧光被恢复,由此可以检测1-200nmol／L的DNA目标分子。此外,在碳纳米粒子存在时,由荧光标记的DNA探针和DNA目标分子形成的双链DNA的熔解温度可以简便地被测定,当双链DNA有错配碱基时,其熔解温度降低,由此可方便、快速地分析单核苷酸多态性．     

A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism

Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF^T1799A oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF^T1799A DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF^T1799A DNA in complex human serum with excellent recovery (94–103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.     

Highly sensitive and selective detection of silver(I) ion using nano-C60 as an effective fluorescent sensing platform

In this Communication, we report water-soluble nano-C(60) in the first use as an effective fluorescent sensing platform for the highly sensitive and selective detection of Ag(+). The general concept used in this approach is based on a fluorescently labeled single-stranded DNA (ssDNA) probe that adsorbs on nano-C(60), leading to substantial dye fluorescence quenching; however, in the presence of Ag(+), C-Ag(+)-C coordination induces the probe to fold into a hairpin structure, which does not adsorb on nano-C(60) and thus retains the dye fluorescence. This sensing system exhibits a detection limit as low as 1 nM and has a high selectivity against other metal ions. Finally and most importantly, we demonstrate its performance in real sample analysis.     

CdS quantum dots as a fluorescent sensing platform for nucleic acid detection

We demonstrate that CdS quantum dots (QDs) can be applied to fluorescence-enhanced detection of nucleic acids in a two-step protocol. In step one, a fluorescently labeled single-stranded DNA probe is adsorbed on the QDs to quench its luminescence. In step two, the hybridization of the probe with its target ssDNA produces a double-stranded DNA which detaches from the QD. This, in turn, leads to the recovery of the fluorescence of the label. The lower detection limit of the assay is as low as 1?nM. The scheme (that was applied to detect a target DNA related to the HIV) is simple and can differentiate between perfectly complementary targets and mismatches.

A low-cost surface plasmon resonance instrument based on detection of resonance excitation wavelength

A laboratory-made surface plasmon resonance (SPR) instrument based on the detection of resonance excitation wavelength has been successfully fabricated. The performance and workability of the SPR instrument was demonstrated as a DNA biosensor. Biotinylated single-stranded oligonucleotides (ssDNA) were chemically immobilized on a gold-film surface of the SPR instrument as a DNA probe for the detection of its fully complementary, half-complementary and non-complementary ssDNA. The immobilization of the ssDNA probe was done by avidin-biotin linkage. The ssDNA used were 12-mer oligonucleotides. The sensing mechanism was based on the shift in resonance wavelength of an excitation light beam as the target ssDNA hybridized with the ssDNA on the gold-film surface. The linear dynamic ranges of the DNA biosensor for fully complementary and half-complementary ssDNA are 0.04-1.2 pM and 0.08-1.1 pM, respectively. The DNA biosensor showed higher sensitivity to fully complementary ssDNA than to half-complementary ssDNA. But no shift of resonance wavelength to the non-complementary ssDNA was observed.     

A homogeneous fluorescence sensing platform with water-soluble carbon nanoparticles for detection of microRNA and nuclease activity

Based on the high efficiency of fluorescence quenching and the different affinities of water-soluble carbon nanoparticles (CNPs) towards single-stranded DNA (ssDNA) and double-stranded DNA/RNA hybrid, a novel, rapid and cost-effective assay for detection of microRNA and nuclease activity was developed. The fluorescein-labeled ssDNA probe (FAM-P) could be adsorbed on the surface of CNPs through π-π stacking interaction giving rise to fluorescence quenching. By introduction of microRNA complementary to the DNA probe, the double-stranded DNA/miRNA hybrid could be formed and released from the surface of CNPs resulting in the fluorescence recovery. Thus, microRNA was successfully detected in homogenous fashion without any amplification or enzyme-involving reactions. Moreover, we demonstrated that the nuclease activities of RNase H and DNase I could also be sensitively monitored by using CNPs based on the fluorescence changing of the DNA probe. So, the CNPs provide an excellent homogeneous sensing platform for studying molecular diagnosis and therapeutics.     

Recent Progress in Metal-Organic Framework Based Fluorescent Sensors for Hazardous Materials Detection

Population growth and industrial development have exacerbated environmental pollution of both land and aquatic environments with toxic and harmful materials. Luminescence-based chemical sensors crafted for specific hazardous substances operate on host-guest interactions, leading to the detection of target molecules down to the nanomolar range. Particularly, the luminescence-based sensors constructed on the basis of metal-organic frameworks (MOFs) are of increasing interest, as they can not only compensate for the shortcomings of traditional detection techniques, but also can provide more sensitive detection for analytes. Recent years have seen MOFs-based fluorescent sensors show outstanding advantages in the field of hazardous substance identification and detection. Here, we critically discuss the application of MOFs for the detection of a broad scope of hazardous substances, including hazardous gases, heavy metal ions, radioactive ions, antibiotics, pesticides, nitro-explosives, and some harmful solvents as well as luminous and sensing mechanisms of MOF-based fluorescent sensors. The outlook and several crucial issues of this area are also discussed, with the expectation that it may help arouse widespread attention on exploring fluorescent MOFs (LMOFs) in potential sensing applications.     

Coordination Polymer Nanobelts as an Effective Sensing Platform for Fluorescence‐enhanced Nucleic Acid Detection

In this communication, the application of coordination polymer nanobelts (CPNs) assembled from H₂PtCl₆ and 3,3′,5,5′‐tetramethylbenzidine (TMB) are explored as an effective fluorescent sensing platform for nucleic acid detection for the first time. The suggested method has a high selectivity down to single‐base mismatch. DNA detection is accomplished by the following two steps: (1) CPN binds fluorecent dye‐labeled single‐stranded DNA (ssDNA) probe via both electrostatic attraction and π‐π stacking interactions between unpaired DNA bases and CPN. As a result, the fluorescent dye is brought into close proximity to CPN and substantial fluorescence quenching occurs due to photoinduced electron transfer from the nitrogen atom in CPN to the excited fluorophore. (2) The hybridization of adsorbed ssDNA probe with its target generates a double stranded DNA (dsDNA). The duplex cannot be adsorbed by CPN due to its rigid conformation and the absence of unpaired DNA bases, leading to an obvious fluorescence enhancement.

     

Development of a novel antifouling platform for biosensing probe immobilization from methacryloyloxyethyl phosphorylcholine-containing copolymer brushes

The immobilization of thiol-terminated poly[(methacrylic acid)-ran-(2-methacryloyloxyethyl phosphorylcholine)] (PMAMPC-SH) brushes on gold-coated surface plasmon resonance (SPR) chips was performed using the "grafting to" approach via self-assembly formation. The copolymer brushes provide both functionalizability and antifouling characteristics, desirable features mandatorily required for the development of an effective platform for probe immobilization in biosensing applications. The carboxyl groups from the methacrylic acid (MA) units were employed for attaching active biomolecules that can act as sensing probes for biospecific detection of target molecules, whereas the 2-methacryloyloxyethyl phosphorylcholine (MPC) units were introduced to suppress unwanted nonspecific adsorption. The detection efficiency of the biotin-immobilized PMAMPC brushes with the target molecule, avidin (AVD), was evaluated in blood plasma in comparison with the conventional 2D monolayer of 11-mercaptoundecanoic acid (MUA) and homopolymer brushes of poly(methacrylic acid) (PMA) also immobilized with biotin using the SPR technique. Copolymer brushes with 79 mol % MPC composition and a molecular weight of 49.3 kDa yielded the platform for probe immobilization with the best performance considering its high S/N ratio as compared with platforms based on MUA and PMA brushes. In addition, the detection limit for detecting AVD in blood plasma solution was found to be 1.5 nM (equivalent to 100 ng/mL). The results have demonstrated the potential for using these newly developed surface-attached PMAMPC brushes for probe immobilization and subsequent detection of designated target molecules in complex matrices such as blood plasma and clinical samples.     

Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease

A structure-switching-based approach for the design of fluorescent biosensors from known RNA aptazymes were demonstrated for the detection of theophylline and thiamine pyrophosphate (TPP). Taking advantages of the ability of graphene oxide (GO) to protect ssDNA from nuclease cleavage and the cyclic amplification induced by deoxyribonuclease I (DNase I), the amplified assay showed high sensitivity. In the presence of target, the target-dependent hammerhead aptazyme cleaves off. The released Shine–Dalgarno (SD) sequence was introduced into the detection system, in which a FAM labeled probe ssDNA was noncovalently assembled on GO, and the fluorescence of the dye was completely quenched. In the presence of the released sequence, the binding between the dye-labeled DNA and the SD sequence alter the conformation of dye-labeled DNA, and disturb the interaction between the dye-labeled DNA and GO, liberating dye-labeled DNA from GO. The fluorescent intensity was increased, whereupon the DNase I can cleave the free DNA in the DNA/RNA complex, thereby liberating the fluorophore and ultimately releasing the SD RNA sequence. The released SD RNA sequence then binds another DNA probe, and the cycle starts anew, which leads to significant amplification of the fluorescent signal. The strategy showed good sensitivity and the dynamic ranges were of 0.1–10 μM and 0.5–100 μM for theophylline and TPP, respectively. The approach opens up a wide range of possibilities for sensing of other small molecules in biological entities.     

A Colorimetric Biosensing Platform with Aptamers,Rolling Circle Amplification and Urease-Mediated Litmus Test

Here we report on an ultra-sensitive colorimetric sensing platform that takes advantage of both the strong amplification power of rolling circle amplification (RCA) and the high efficiency of a simple urease-mediated litmus test. The presence of a target triggers the RCA reaction, and urease-labelled DNA can hybridize to the biotinylated RCA products and be immobilized onto streptavidin-coated magnetic beads. The urease-laden beads are then used to hydrolyze urea, leading to an increase in pH that can be detected by a simple litmus test. We show this sensing platform can be easily integrated with aptamers for sensing diverse targets via the detection of human thrombin and platelet-derived growth factor (PDGF) utilizing structure-switching aptamers as well as SARS-CoV-2 in human saliva using a spike-binding trimeric DNA aptamer. Furthermore, we demonstrate that this colorimetric sensing platform can be integrated into a simple paper-based device for sensing applications.     

Electrochemical DNA Biosensor Based on Partially Reduced Graphene Oxide Modified Carbon Ionic Liquid Electrode for the Detection of Transgenic Soybean A2704‐12 Gene Sequence

In this work a partially reduced graphene oxide (p‐RGO) modified carbon ionic liquid electrode (CILE) was prepared as the platform to fabricate an electrochemical DNA sensor, which was used for the sensitive detection of target ssDNA sequence related to transgenic soybean A2704‐12 sequence. The CILE was fabricated by using 1‐butylpyridinium hexafluorophosphate as the binder and then p‐RGO was deposited on the surface of CILE by controlling the electroreduction conditions. NH₂ modified ssDNA probe sequences were immobilized on the electrode surface via covalent bonds between the unreduced oxygen groups on the p‐RGO surface and the amine group at the 5′‐end of ssDNA, which was denoted as ssDNA/p‐RGO/CILE and further used to hybridize with the target ssDNA sequence. Methylene blue (MB) was used as electrochemical indicator to monitor the DNA hybridization. The reduction peak current of MB after hybridization was proportional to the concentration of target A2704‐12 ssDNA sequences in the range from 1.0×10^?12 to 1.0×10^?6 mol/L with a detection limit of 2.9×10^?13 mol/L (3σ). The electrochemical DNA biosensor was further used for the detection of PCR products of transgenic soybean with satisfactory results.     

Detection of bar gene encoding phosphinothricin herbicide resistance in plants by electrochemical biosensor

An electrochemical biosensor for the detection of bar gene coding phosphinothricin herbicide resistance is presented. The detection was based on hybridization reaction between the specific to bar gene 19-mer probe immobilized on the electrode surface and complementary DNA in a sample. Single-stranded DNA probe specific to bar gene was covalently attached by 5'-phosphate end to the surface of carbon paste electrode. Outer layer of a conventional CPE was provided with carboxyl groups of stearic acid. ssDNA was coupled to the electrode through ethylenediamine with the use of water-soluble 1-ethyl-3(3'-dimethylaminopropyl)-carbodiimide and N-hydroxy-sulfosuccinimide as activating reagents. Hybridization reaction at the electrode surface was detected via Co(bpy)(3)(3+), which possess a much higher affinity to the resulting DNA duplex compared to ssDNA probe. Detection limit of the sensor was 0.1 microM of target DNA fragments and its response was linear from 5 to 20 microM. Hybridization event was also detected by measuring guanine peak but this approach presented distinctly higher detection limit (1 muM) and lower reproducibility. Complete time of one measurement with the use of the biosensor including covalent attachment of ethylenediamine (linker) and ssDNA probe to the electrode, hybridization with target and interaction with electroactive indicator was about 70 min.     

Synergistic Effect of MWNTs/CeO2/CHIT Film for Detection of CdSe Nanoparticle Labeled Sequence‐Specific of 35S Promoter of Cauliflower Mosaic Virus Gene

A porous composite film was fabricated combining the advantages of multiwalled carbon nanotubes, CeO₂ and chitosan. The synergistic effect of the film improved the immobilization of probe ssDNA. The loaded probe ssDNA was used for detection of CdSe quantum dots labeled target DNA. The DNA hybridization reaction was detected by differential pulse anodic stripping voltammetry of Cd²⁺ after the oxidative release of labeled CdSe quantum dots. The established DNA biosensor can discriminate different target sequences associated with 35S promoter of cauliflower mosaic virus gene with relatively wide linear range and low detection limit (2.4×10^?13 mol/L).     

A Carbon‐Dot‐Based Fluorescent Nanosensor for Simple Visualization of Bacterial Nucleic Acids

A simple and facile method for sensing of nucleic acids is in great need for disease biomarker detection and diagnosis. Herein, a fluorescent nanosensor utilizing carbon dot nanoparticles is introduced that form visible precipitates in the presence of target DNA. Carbon dot nanoparticles are fabricated by microwave pyrolysis of polyethylenimine, which emits strong photoluminescence and can form precipitates when added to target DNA oligonucleotides. The precipitates can be easily visualized by UV illumination, and data can be acquired as images using a smartphone, which are analyzed for quantification. This carbon‐dot‐based assay allowed fluorescent sensing of target oligonucleotides with various sizes and visualization even with minimal amount of DNA (≈100 pmol). Finally, the assay can be applied as a nanosensor platform for detecting bacterial DNA for the antibiotic‐resistance gene KPC‐2 from Klebsiella pneumoniae . This method provides a simple technique for detecting molecular targets, showing wide applicability for diagnostics on the bedside or point‐of‐care testing.     

Programmable and Reversible Regulation of Catalytic Hemin@MOFs Activities with DNA Structures

Metal-organic frameworks(MOFs)-based nanozyme plays an important role in biosensing,therapy and catalysis.In this study,the effects of single-stranded DNA(ssDNA)with programmable sequences and its complementary DNA(Tdna)on the intrinsic peroxidase-like activity of hemin loaded MOFs(UiO-66-NH2),denoted as he-min@UiO-66-NH2,were investigated.The hemin@UiO-66-NH2 exhibited improved catalytic activity compared with free hemin.However,the catalytic activity is inhibited in the presence of ssDNA,as ssDNA can be adsorbed by MOFs and therefore protected the active sites from contact with substrates.Upon the addition of the TDNA,double-stranded DNA(dsDNA)was formed and detached from the MOFs,resulting in the recovery of catalytic activity.Sequentially adding ssDNA or its complementary DNA strands can achieve the reversible regulation of the catalytic activity of MOFs nanozymes.Moreover,the DNA hybridization-based regulation was further applied to a cascaded catalytic system composed of the nanozyme,hemin@UiO-66-NH2,and glucose oxidase.These nanozyme based programmable and reversibly regulated catalytic systems may have potential applications in future smart biosensing and catalysis systems.     

金属有机框架化合物对溶剂分子和有机小分子荧光识别与传感研究进展

属-有机框架（MOFs）化合物由于其特定的孔道/孔洞结构以及在气体吸附/存储与分离、化学传感、光学、磁学以及荧光检测等方面的良好性能及潜在应用而成为当前人们关心和研究的热点。本文聚焦MOFs在溶剂分子和有机小分子荧光识别及传感方面的研究工作,着重介绍该领域近期的研究进展,并对该领域今后的发展进行了展望。