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Biomedical subjects

Dai-Wen Pang

Publications and source records attributed to Dai-Wen Pang.

At least 19 recordsLinked to original sources
PubMed2025

Spatial Mapping and Interactome Profiling of m6A-Modified R-Loops via Chemically Inducible Split-APEX2 Proximity Labeling.

m6A-Modified R-loops (m6A-R-loops) play crucial roles in epigenetic regulation and genome stability, yet resolving their spatial distribution and protein interactomes in live cells remains challenging. To address this, we developed m6A-R-loop proximity labeling (m6A-RLPL), a chemically inducible split-APEX2 proximity labeling technology integrating dual-target recognition using the RNA-DNA hybrid binding domain of RNase H1 for R-loop targeting and m6A reader protein's YTH domain for m6A recognition, coupled with an abscisic acid (ABA)-inducible dimerization system for signal amplification. This technology revealed host m6A-R-loops enriched with nucleoli under normal conditions. When applied to herpes simplex virus (HSV) infection, it further demonstrated viral m6A-R-loops undergoing dramatic accumulation within phase-separated granules in replication compartments during late-stage infection. Proximity proteomics identified ZC3H4 and CCDC124 as essential regulators maintaining these structures, which serve as transcription sites for HSV late genes, with disruption selectively impairing viral transcription. m6A-RLPL establishes a generalizable approach for spatially resolved profiling of m6A-R-loop interactomes and organizational dynamics in living systems.

Humans↗
PubMed2006

Quantum-dot-labeled DNA probes for fluorescence in situ hybridization (FISH) in the microorganism Escherichia coli.

Semiconductor quantum dots (QDs) as a kind of nonisotopic biological labeling material have many unique fluorescent properties relative to conventional organic dyes and fluorescent proteins, such as composition- and size-dependent absorption and emission, a broad absorption spectrum, photostability, and single-dot sensitivity. These properties make them a promising stable and sensitive label, which can be used for long-term fluorescent tracking and subcellular location of genes and proteins. Here, a simple approach for the construction of QD-labeled DNA probes was developed by attaching thiol-ssDNA to QDs via a metal-thiol bond. The as-prepared QD-labeled DNA probes had high dispersivity, bioactivity, and specificity for hybridization. Based on such a kind of probe with a sequence complementary to multiple clone sites in plasmid pUC18, fluorescence in situ hybridization of the tiny bacterium Escherichia coli has been realized for the first time.

DNA Probes↗
PubMed2006

[Quantum dots and their applications in cancer research].

Quantum dots are semiconductor nanocrystals with physical dimensions smaller than the exciton Bohr radius. As their fluorescence emissions are size-tunable, we can acquire any spectrum from ultraviolet (UV) to near-infrared by changing the particles' radiuses. The large Stokes shifts of quantum dots can be used to further improve detection sensitivity. The luminescence intensity is high and stable. Single quantum dots have longer excited state lifetimes, and they appear 10-20 times brighter than organic fluorescent dyes. And they have good biocompatibility because quantum dots with appropriate shells don't interfere with physiological processes, such as growth, development, signaling and motility. With the development of optical labeling and imaging technology, many present conventional biomedical methods have limitations in microcosmic direct real-time researches of bio-molecular interactions and early diagnosis of malignant tumors. The invention of quantum dots and their biomedical applications make them as good markers for tumor cell tracing and targeting in cancer research, such as prostate cancer, mammary cancer, cervical cancer, basal cell carcinoma, liver cancer, and melanoma. The current research is focused on tumor markers imaging and molecular interaction based on tangible carriers such as cells and tissues. The next research orientation would be to tap the potential of this highly sensitive technology to image tumor biomarkers in serum and other body fluids, so as to increase the early diagnosis rate of malignant tumors.

Animals↗
PubMed2006

[Synthesis and spectral studies of functionalized L-Cys-CdS nanoparticles as fluorescence probes].

In this work, nano-CdS was successfully prepared. The nano-CdS was also modified with L-cysteine. Absorption and fluorescence spectra of CdS nanoparticles for different pH values, reaction times and different Cys/Cd2+/S ratios were investigated. Meanwhile a fluorescence enhancing effect was observed between trace zinc ions and the functionalized L-Cys-CdS nanoparticles. The response is linearly proportional to the concentration of zinc ions from 1.0 to 15 micromol x L(-1). The functionalized nanoparticles are hopeful of use as fluorescence probes in detecting trace elements in biological samples.

Cadmium Compounds↗
PubMed2005

Core/shell quantum-dot-photosensitized nano-TiO2 films: fabrication and application to the damage of cells and DNA.

Through the use of monodisperse core/shell quantum dots (QDs) as photosensitizers for the first time, a novel strategy for the fabrication of QD-photosensitized nano-TiO2 films was demonstrated. Core/shell QDs were self-assembled on nano-TiO2 films through carboxyls as anchoring groups to metal oxides. Atomic force microscopy and some other experiments showed the fabrication strategy is successful. Reactive oxygen species detection experiments indicated that such films have photosensitization ability. The results of bactericidal and DNA damage experiments demonstrate that such films have excellent photoactivity.

DNA↗
PubMed2005

DNA-binding and cleavage studies of novel copper(II) complex with L-phenylalaninate and 1,4,8,9-tetra-aza-triphenylene ligands.

DNA-binding properties of novel copper(II) complex [Cu(l-Phe)(TATP)(H(2)O)](+), where L-Phe=L-phenylalaninate and TATP=1,4,8,9-tetra-aza-triphenylene are investigated using electronic absorption spectroscopy, fluorescence spectroscopy, voltammetry and viscosity measurement. It is found that the presence of calf thymus DNA results in a hypochromism and red shift in the electronic absorption, a quenching effect on fluorescence nature of ethidium bromide-DNA system, an enhanced response on voltammograms of [Co(phen)(3)](3+/2+)-DNA system, and an obvious change in viscosity of DNA. From absorption titration, fluorescence analysis and voltammetric measurement, the binding constant of the complex with DNA is calculated. The latter two methods reveal the stronger binding of [Cu(l-Phe)(TATP)(H(2)O)](+) complex to double strand DNA by the moderate intercalation than [Co(phen)(3)](3+). Such a binding induces the cleavage of plasmid pBR322 DNA in the presence of H(2)O(2).

Aza Compounds↗
PubMed2005

Direct electrochemistry and electrocatalysis of heme proteins entrapped in agarose hydrogel films in room-temperature ionic liquids.

The electrochemistry and electrocatalysis of a number of heme proteins entrapped in agarose hydrogel films in the room-temperature ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) have been investigated. UV-vis and FTIR spectroscopy show that the heme proteins retain their native structure in agarose film. The uniform distribution of hemoglobin in agarose-dimethylformamide film was demonstrated by atomic force microscopy. Cyclic voltammetry shows that direct electron transfer between the heme proteins and glassy carbon electrode is quasi-reversible in [bmim][PF(6)]. The redox potentials for hemoglobin, myoglobin, horseradish peroxidase, cytochrome c, and catalase were found to be more negative than those in aqueous solution. The charge-transfer coefficient and the apparent electron-transfer rate constant for these heme proteins in [bmim][PF(6)] were calculated from the peak-to-peak separation as a function of scan rate. The heme proteins catalyze the electroreduction of trichloroacetic acid and tert-butyl hydroperoxide in [bmim][PF(6)]. The kinetic parameter I(max) (maximum current at saturation concentration of substrate) and the apparent K(m) (Michaelis-Menten constant) for the electrocatalytic reactions were evaluated.

Biosensing Techniques↗
PubMed2005

Electrochemical DNA sensing based on gold nanoparticle amplification.

A hybridization signal-amplified method based on a gold nanoparticle-supported DNA sequence for electrochemical DNA sensing has been investigated by cyclic voltammetry, differential-pulse voltammetry, and atomic-force microscopy (AFM). Quantitative analysis showed that the peak current increment (DeltaIp) is linearly dependent on the concentration of the gold nanoparticle-supported DNA sequence Au2 over the range 0.51-8.58 pmol L(-1). AFM results indicated that the extent of surface hybridization was dependent on the concentration of the gold-nanoparticle-supported DNA sequence. Moreover, a new pair of peaks, which might arise from the special configuration of the gold-nanoparticle-supported DNA sequence, appeared in the cyclic voltammogram after hybridization. Although quite sensitive, this DNA sensing surface was not easily regenerated, so this kind of amplified method was suitable for disposable DNA sensors and chip-based gene diagnosis sensors.

Base Sequence↗
PubMed2005

Preparation and characterization of overcoated II-VI quantum dots.

A convenient route for the synthesis of high-quality overcoated II-VI quantum dots (QDs) is reported in this paper. Simple salts, such as Cd(Ac)2 and Zn(Ac)2 were used to replace organometallics, whose disadvantage is obvious. Size-tunable core/shell structured QDs (CdSe/ZnS, CdSe/CdS, etc.) were synthesized. They were of narrow size distribution and had good monodispersivity and photoluminescence (PL) properties. The spectrum was symmetrical and sharp-pointed (with the full width at half-maximum (fwhm) of about 20-30 nm). The quantum yield (QY) was improved to 60-80% from 20-30% for bare QDs and remained stable at least for 6 months. The primary overcoated QDs were modified with biomacromolecules by a direct mechanical rubbing strategy, which is very simple and fast. The results obtained by UV-vis, PL, atomic force microscopy (AFM), and fluorescence microscopy imaging showed that the modified QDs were of good fluorescent and monodisperse characteristics. They are likely to be used further for biological labels.

Cadmium Compounds↗
PubMed2004

Combing DNA on CTAB-coated surfaces.

A fluorescence microscope (FM) coupled with an intensified charge-coupled device (ICCD) camera was used to investigate the combing of DNA on cetyltrimethyl ammonium bromide (CTAB)-coated glass surfaces. DNA molecules can be combed uniform and straight on CTAB-coated surfaces. Different combing characteristics at different pH values were found. At lower pH (ca. 5.5), DNA molecules were stretched 30% longer than the unextended and DNA extremities bound with CTAB-coated surfaces via hydrophobic interaction. At high pH values (e.g., 6.4 and 6.5), DNA molecules were extended about 10% longer and DNA extremities bound with CTAB-coated surfaces via electrostatic attraction. At pH 6.0, DNA molecules could be extended 30% longer on 0.2-mM CTAB-coated surfaces. CTAB cationic surfactant has both a hydrophobic motif and a positively charged group. So, CTAB-coated surfaces can bind DNA extremities via hydrophobic effect or electrostatic attraction at different pH values. It was also found that combing of DNA on CTAB-coated surfaces is reversible. The number of DNA base pairs binding to CTAB-coated surfaces was calculated.

Bacteriophage lambda↗
PubMed2004

Direct electrochemistry and electrocatalysis of heme-proteins entrapped in agarose hydrogel films.

Three heme-proteins, including myoglobin (Mb), hemoglobin (Hb) and horseradish peroxidase (HRP), were immobilized on edge-plane pyrolytic graphite (EPG) electrodes by agarose hydrogel. The proteins entrapped in the agarose film undergo fast direct electron transfer reactions, corresponding to FeIII = e- --> FeII. The formal potential (E degrees'), the apparent coverage (Gamma), the electron transfer coefficient (alpha) and the apparent electron transfer rate constant (ks) were calculated by integrating cyclic voltammograms or performing nonlinear regression analysis of square wave voltammetric (SWV) experimental data. The E degrees's are linearly dependent on solution pH (redox Bohr effect), indicating that the electron transfer was proton-coupled. Ultraviolet visible (UV-Vis) and reflection-absorption infrared (RAIR) spectra suggest that the conformation of proteins in the agarose film are little different from that proteins alone, and the conformation changes reversibly in the range of pH 3.0-10.0. Atomic force microscopy (AFM) images of the agarose film indicate a stable and crystal-like structure formed possibly due to the synergistic interaction of hydrogen bonding between N,N-dimethylformamide (DMF), agarose hydrogel and heme-proteins. This suggests a strong interaction between the heme-proteins and the agarose hydrogel. DMF plays an important role in immobilizing proteins and enhancing electron transfer between proteins and electrodes. The mechanisms for catalytic reduction of hydrogen peroxide and nitric oxide (NO) by proteins entrapped in agarose hydrogel were also explored.

Absorption↗
PubMed2004

Functionalized CdSe quantum dots as selective silver ion chemodosimeter.

CdSe quantum dots (QDs) have been prepared and modified with mercaptoacetic acid. They are water-soluble and biocompatible. To improve their fluorescence intensity and stability in water solution, bovine serum albumin (BSA) was absorbed onto their surface. Based on the quench of fluorescence signals of the functionalized CdSe QDs in the 543 nm wavelength and enhancement of them in the 570-700 nm wavelength range by Ag(I) ions at pH 5.0, a simple, rapid and specific method for Ag(I) determination was proposed. In comparison with single organic fluorophores, these nanoparticles are brighter, more stable against photobleaching, and do not suffer from blinking. Under the optimum conditions, the response is linearly proportional to the concentration of Ag(I) between 4.0 x 10(-7) and 1.5 x 10(-5) mol L(-1), and the limit of detection is 7.0 x 10(-8) mol L(-1). The mechanism of reaction is also discussed.

Journal Article↗
PubMed2004

Improvement of homogeneity of analytical biodevices by gene manipulation.

Homogeneity is proposed for evaluation of the quality of analytical biodevices, such as biosensors and biochips. As a demonstration, glucose oxidase (GOx) was modified at its C-terminal with a linker peptide with a cysteine residue at the end. The fusion structure (GOx-linker-cysteine) enables the enzyme to immobilize on gold surfaces with a Cys-S-Au bond or to immobilize on a silanized glass surface via disulfide chemistry. With this fusion structure, the enzyme can be anchored onto the substrate with well-controlled orientation, thus forming a homogeneous biological layer on biodevices. The linker peptide between GOx and the cysteine acts as a spacer to reduce the steric hindrance caused by the bulky body of the enzyme. Biochemistry experiments showed that this genetically modified glucose oxidase (shortened to GOxm) retained most of its catalytic characteristics, with K(m) and K(cat) similar to those of the wild-type GOx. Electrochemistry experiments showed that GOxm-modified electrode gave higher and more stable current responses than the electrode modified with GOx which has no free -SH on its surface. The coefficients of variation (used for evaluation of the interchangeability of the enzyme device from the same batch preparation) were 9.5% for the GOxm gold electrode and 20.0% for the GOx gold electrode and the GOxm oxygen electrode. The relative errors (used for evaluation of the precision of the individual enzyme device) were 2.9% for the GOxm gold electrode, 12.0% for the GOx gold electrode, and 11.2% for the GOxm oxygen electrode. Atomic force microscopy images revealed that GOxm formed a self-assembled monolayer in a hexagonal-like lattice packing arrangement on the gold surface, while GOx formed multilayer assembling or aggregated particles. The homogeneity of the protein chips, the GOxm array that was prepared through -S-S- formation, and the GOx array that was prepared through nonspecific adsorption was evaluated. The coefficients of variation, calculated with the signal level of all dots, were 5.4% for the GOxm array and 81.8% for the GOx array. All experimental results pointed to the fact that the homogeneity of the analytical biodevices could be considerably improved by using the proposed method.

Aspergillus niger↗
PubMed2004

Transport, location, and quantal release monitoring of single cells on a microfluidic device.

A novel microfluidic device has been developed for on-chip transport, location, and quantal release monitoring of single cells. The microfluidic device consists of a plate of PDMS containing channels for introducing cells and stimulants and a glass substrate into which a cell micro-chamber was etched. The two tightly reversibly sealed plates can be separated for respective cleaning, which significantly extends the lifetime of the microchip that is frequently clogged in cell analysis experiments. Using hydraulic pressure, single cells were transported and located on the microfluidic chip. After location of a single PC12 cell on the microfluidic chip, the cell was stimulated by nicotine that was also introduced through the micro-channels, and the quantum release of dopamine from the cell was amperometricly detected with our designed carbon fiber microelectrode. The results have demonstrated the convenience and efficiency of using the microfluidic chip for monitoring of quantal release from single cells and have offered a facile method for the analysis of single cells on microfluidic devices.

Journal Article↗
PubMed2003

Amplified voltammetric detection of DNA hybridization via oxidation of ferrocene caps on gold nanoparticle/streptavidin conjugates.

Gold nanoparticle/streptavidin conjugates covered with 6-ferrocenylhexanethiol were attached onto a biotinylated DNA detection probe of a sandwich DNA complex. Due to the elasticity of the DNA strands, the ferrocene caps on gold nanoparticle/streptavidin conjugates are positioned in close proximity to the underlying electrode modified with a mixed DNA capture probe/hexanethiol self-assembled monolayer and can undergo reversible electron-transfer reactions. A detection level, down to 2.0 pM (10 amol for the 5 microL of sample needed) for oligodeoxynucleotide samples was obtained. The amplification of the voltammetric signals was attributed to the attachment of a large number of redox (ferrocene) markers per DNA duplex formed. The ferrocene oxidation current increased with the target concentration and began to level off at a target concentration of 10 nM. An Excellent linearity was found within the range between 6.9 and 150.0 pM and reasonable relative standard deviations (between 3.0 and 13.0%) were obtained. The amenability of this method to the analyses of polynucleotides (i.e., PCR products of the pre-S gene of hepatitis B virus in serum samples) was also demonstrated. The method is shown to be simple, selective, reproducible, and cost-effective and does not require labeling of the DNA targets.

DNA↗