25 research outputs found

    Visualizing and Quantifying Protein PolySUMOylation at the Single-Molecule Level

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    Protein polySUMOylation, the attachment of small ubiquitin-like modifier (SUMO) chains to the target protein, is associated with a variety of physiological processes. However, the analysis of protein polySUMOylation is often complicated by the heterogeneity of SUMO–target conjugates. Here, we develop a new strategy to visualize and quantify polySUMOylation at the single-molecule level by integrating the tetracysteine (TC) tag labeling technology and total internal reflection fluorescence (TIRF)-based single-molecule imaging. As a proof-of-concept, we employ the human SUMO-2 as the model. The addition of TC tag to SUMO-2 can specifically translate the SUMO-mediated modification into visible fluorescence signal without disturbing the function of SUMO-2. The SUMO monomers display homogeneous fluorescence spots at the single-molecule level, whereas the mixed SUMO chains exhibit nonuniform fluorescence spots with a wide range of intensities. Analysis of the number and the brightness of fluorescence spots enable quantitative measurement of the polySUMOylation degree inside the cells under different physiological conditions. Due to the frequent occurrence of posttranslational modification by polymeric chains in cells, this single-molecule strategy has the potential to be broadly applied for studying protein posttranslational modification in normal cellular physiology and disease etiology

    Highly Sensitive Detection of Protein with Aptamer-Based Target-Triggering Two-Stage Amplification

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    Highly sensitive detection of proteins is essential to biomedical research as well as clinical diagnosis. However, so far most detection methods rely on antibody-based assays and are usually laborious and time-consuming with poor sensitivity. Here, we develop a simple and sensitive method for the detection of a biomarker protein, platelet-derived growth factor BB (PDGF-BB), based on aptamer-based target-triggering two-stage amplification. With the involvement of an aptamer-based probe and an exponential amplification reaction (EXPAR) template, our method combines strand displacement amplification (SDA) and EXPAR, transforming the probe conformational change induced by target binding into two-stage amplification and distinct fluorescence signal. This detection method exhibits excellent specificity and high sensitivity with a detection limit of 9.04 × 10<sup>–13</sup> M and a detection range of more than 5 orders of magnitude, which is comparable with or even superior to most currently used approaches for PDGF-BB detection. Moreover, this detection method has significant advantages of isothermal conditions required, simple and rapid without multiple separation and washing steps, low-cost without the need of any labeled DNA probes. Furthermore, this method might be extended to sensitive detection of a variety of biomolecules whose aptamers undergo similar conformational changes

    Analysis of MicroRNA-Induced Silencing Complex-Involved MicroRNA-Target Recognition by Single-Molecule Fluorescence Resonance Energy Transfer

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    MicroRNAs (miRNAs) are important regulators of gene expression that control almost every physiological and pathological process. Although the complementarity between the seed region of a miRNA and its target mRNA is usually deemed as the key determinant in the miRNA-target recognition in animals, the mechanism of their recognition still remains enigmatic as more and more exceptions challenge the seed rule. Herein, we employ single-molecule fluorescence resonance energy transfer (smFRET) to investigate human miRNA-induced silencing complex (miRISC)-involved miRNA-target recognition with either perfect base pairing or poor seed match in real time. Our results demonstrate that the recognition between mammalian miRNA and its target with perfect base pairing proceeds in a two-state model as prokaryotic guide DNA-mediated recognition, suggesting a conserved pattern of guide RNA/DNA strand recognition. In addition to the general rule of miRNA-target recognition, our results reveal that annealing between miRNA and its target with poor seed match proceeds in a stepwise way, which is in accordance with the increase in the number of conformational states of miRNA-target duplex accommodated by the miRISC, suggesting the structural plasticity of human miRISC to conciliate the mismatches in seed region. This new dynamic information revealed by smFRET has an important implication for comprehensive understanding of the role of miRISC in the target recognition in mammals

    Simple and Accurate Quantification of Quantum Yield at the Single-Molecule/Particle Level

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    Quantum yield represents one of most fundamental and important properties of photoluminescent materials and eventually determines the suitability of materials for the applications in optical devices, analysis, biosensing, and fluorescence imaging. Despite that a variety of methods have been developed to measure the quantum yield, its accurate quantification still remains a great challenge. Here, we develop a new approach with the capability to quantify the quantum yield at the single-molecule/particle level. The quantum yield obtained by the single-molecule/particle detection is in agreement with that obtained by the conventional optical method. Importantly, this method can accurately measure not only the quantum yield of organic dyes but also that of quantum dots and can be further extended to measure the quantum yield of various fluorescent materials, including the nontransparent sample whose quantum yield is impossible to obtain using the conventional optical method

    Sensitive Detection of MicroRNAs with Hairpin Probe-Based Circular Exponential Amplification Assay

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    MicroRNAs (miRNAs) play important regulatory roles in a wide range of biological processes, and their aberrant expression is associated with cancer development and a variety of diseases. Here, we develop a simple, sensitive, and specific miRNA assay on the basis of circular exponential amplification in combination with the hairpin probes. The binding of target miRNA with a linear DNA template initiates the first strand displacement amplification (SDA) and generates the universal triggers which are complementary to the 3′ protruding end of a hairpin probe. These universal triggers function not only as the primers to unfold the hairpin probes through an extension reaction, generating distinct fluorescence signals, but also as the amplification templates to initiate the second SDA reaction. Moreover, the second SDA reaction can release new triggers to initiate the above two consecutive SDA reactions, thus constituting a circular exponential amplification which enables the conversion of a small amount of miRNAs to a large number of universal triggers to unfold abundant hairpin probes. This hairpin probe-based circular exponential amplification assay exhibits high sensitivity with a detection limit of 3.80 × 10<sup>–13</sup> M and a detection range of 4 orders of magnitude. It can even discriminate single-nucleotide difference between miRNA family members and perform well in real sample analysis. Notably, in this assay, the long-stem hairpin probes are unfolded through an extension reaction rather than through a conventional hybridization reaction controlled by the thermodynamic equilibrium in the case of molecular beacons, making the design of hairpin probes very simple. This hairpin probe-based circular exponential amplification assay holds a great promise for further application in biomedical research and early clinical diagnosis

    Toward Biocompatible Semiconductor Quantum Dots: From Biosynthesis and Bioconjugation to Biomedical Application

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    Toward Biocompatible Semiconductor Quantum Dots: From Biosynthesis and Bioconjugation to Biomedical Applicatio

    Ultrasensitive Detection of Transcription Factors Using Transcription-Mediated Isothermally Exponential Amplification-Induced Chemiluminescence

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    Transcription factors (TFs) are important cellular components that modulate gene expression, and the malregulation of transcription will lead to a variety of diseases such as cancer and developmental syndromes. However, the conventional methods for transcription factor assay are generally cumbersome and costly with low sensitivity. Here, we develop a label-free strategy for ultrasensitive detection of transcription factors using a cascade signal amplification of RNA transcription, dual isothermally exponential amplification reaction (EXPAR), and G-quadruplex DNAzyme-driven chemiluminescence. Briefly, the specific binding of TF with the detecting probe prevents the cleavage of the detecting probe by exonuclease and subsequently facilitates the conversion of TF signal to abundant RNA triggers in the presence of T7 RNA polymerase. The obtained RNA triggers can initiate the strand displacement amplification to yield abundant DNAzymes and DNA triggers, and the released DNA triggers can further initiate the next rounds of EXPAR reaction. The synergistic operation of dual EXPAR reaction can produce large amounts of DNAzymes, which subsequently catalyze the oxidation of luminol by H<sub>2</sub>O<sub>2</sub> to yield an enhanced chemiluminescence signal with the assistance of cofactor hemin. Conversely, in the absence of target TF, the naked detecting probes will be completely digested by exonucleases, leading to neither the transcription-mediated EXPAR nor the DNAzyme-driven chemiluminescence signal. This method has a low detection limit of as low as 6.03 × 10<sup>–15</sup> M and a broad dynamic range from 10 fM to 1 nM and can even measure the NF-κB p50 of crude cell nuclear extracts. Moreover, this method can be used to measure a variety of DNA-binding proteins by simply substituting the target-specific binding sequence in the detecting probes

    Sensitive Detection of Transcription Factors by Isothermal Exponential Amplification-Based Colorimetric Assay

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    Transcription factors regulate gene expression by binding to specific DNA sequences within the regulatory regions of genes and have become potential targets in clinical diagnosis and drug development. However, traditional approaches for the detection of transcription factors are usually laborious and time-consuming with a low sensitivity. Here, we develop an isothermal exponential amplification reaction (EXPAR)-based colorimetric assay for simple and sensitive detection of transcription factor NF-κB p50. In this assay, the presence of NF-κB p50 is converted to the reporter oligonucleotides through protein–DNA interaction, exonuclease III digestion, and isothermal exponential amplification. The subsequent sandwich hybridization of the reporter oligonucleotides with the gold nanoparticle (AuNP)-labeled DNA probes generates a red-to-purple color change, allowing the visual detection of NF-κB p50 with the naked eye. Notably, this method converts the detection of transcription factors to the detection of DNA without the requirement of DNA marker-linked antibodies in the case of immuno-PCR and can sensitively measure NF-κB p50 with a detection limit of 3.8 pM, which has improved by as much as 4 orders of magnitude as compared with the conventional AuNP-based colorimetric assay and the label-free luminescence assay and up to 4 orders of magnitude as compared with fluorescence resonance energy transfer (FRET)-based assay as well. Importantly, this method can be used to measure TNF-α-induced endogenous NF-κB p50 in HeLa cell nuclear extracts and might be further applied for the detection of various DNA-binding proteins and aptamer-binding molecules

    Phosphorylation-Directed Assembly of a Single Quantum Dot Based Nanosensor for Protein Kinase Assay

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    Protein kinases play crucial roles in intracellular signal transduction and metabolic pathways, and the monitoring of protein kinase activity is essential to the understanding of fundamental biochemical processes and the clinical diagnosis. Here, we demonstrate the phosphorylation-directed assembly of a single quantum dot (QD)-based nanosensor for sensitive detection of cAMP-dependent protein kinase (PKA). This assay involves (1) the PKA-directed simultaneous phosphorylation and biotinylation of cyanine 5 (Cy5)-labeled substrate peptides, (2) the assembly of phosphorylated and biotinylated peptides onto the surface of the QD, and (3) the illumination of Cy5 by means of fluorescence resonance energy transfer (FRET) between the QD and Cy5. With an adenosine triphosphate (ATP) analogue, γ-biotin-ATP, as the phosphoryl donor, the PKA-catalyzed phosphorylation reaction incorporates the biotin-conjugated phosphate group into the substrate peptides to form the biotinylated peptides. The biotin entity subsequently drives the assembly of peptides onto the surface of streptavidin-functionalized QD to form the sandwiched Cy5–peptide–QD nanostructure, enabling the occurrence of FRET between the QD and Cy5. The FRET signal can be easily recorded by either the conventional fluorescence spectrometer or the total internal reflection fluorescence (TIRF) microscope. In contrast, the absence of PKA cannot lead to the formation of Cy5–peptide–QD complex and no Cy5 signal can be detected. This protein kinase-actuated FRET assay is straightforward, without the involvement of either washing or separation steps, and has a significant advantage of high sensitivity with a detection limit of 9.3 × 10<sup>–6</sup> U/μL. Moreover, this method can be used to estimate the half-maximal inhibitory concentration (IC<sub>50</sub>) value of PKA inhibitor H-89 (<i>N</i>-[2-(<i>p</i>-bromocinnamylamino)­ethyl]-5-isoquinolinesulfonamide dihydrochloride) and to monitor forskolin (Fsk)/3-isobutyl-1-methylxanthine (IBMX)-triggered activation of PKA in cell lysates, thus holding great potential for further applications in protein kinase-related biological researches and drug discovery

    Isothermally Sensitive Detection of Serum Circulating miRNAs for Lung Cancer Diagnosis

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    Tumor-derived miRNAs in serum are emerging as the new noninvasive biomarkers for the diagnosis of human cancers, especially at their early stage. An ideal method with high sensitivity, excellent selectivity, a simple procedure, and small amounts of starting materials is imperative for the detection of clinic circulating miRNAs. Here, we develop a new method for isothermally sensitive detection of serum miRNAs using hairpin probe-based rolling circle amplification (HP-RCA). This method exhibits ultrahigh sensitivity toward lung cancer-related miR-486-5p with a detection limit of as low as 10 fM and a large dynamic range of 6 orders of magnitude, and it can even discriminate miR-486-5p from both miRNAs with high sequence homology and its precursors (pre-miRNAs). More importantly, this method can directly and accurately distinguish the expression of serum miR-486-5p among six nonsmall-cell lung carcinoma (NSCLC) patients and six healthy persons, holding a great potential for further applications in the clinical diagnosis of lung cancers
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