Analysis of poly(ADP-ribose) polymerase-1 by enzyme-initiated auto-PARylation-controlled aggregation of hemin-graphene nanocomposites

Construction of a Dendritic Nanoassembly-Based Fluorescent Biosensor for Electrostatic Interaction-Independent and Label-Free Measurement of Human Poly(ADP-ribose) Polymerase 1 in Lung Tissues

Poly(ADP-ribose) polymerase 1 (PARP-1) is responsible for catalyzing the creation of poly(ADP-ribose) polymer and involved in DNA replication and repair. Sensitive measurement of PARP-1 is critical for clinical diagnosis. However, the conventional electrostatic attraction-based PAPR-1 assays usually involve laborious procedures, poor sensitivity, and false positives. Herein, we demonstrate the construction of a dendritic nanoassembly-based fluorescent biosensor for electrostatic interaction-independent and label-free measurement of human PARP-1 in lung tumor tissues. When PARP-1 is present, the specific double-stranded DNA (dsDNA)-activated PARP-1 transfers the ADP-ribosyl group from nicotinamide adenine dinucleotide (NAD+)/biotinylated NAD+ to the PARP-1 itself, resulting in the formation of biotinylated dsDNA-PARP-1-PAR polymer bioconjugates that can be captured by magnetic beads. Upon the addition of TdT, APE1, and NH2-modified T-rich probe, the captured dsDNAs with dual 3'-OH termini initiate TdT-activated APE1-mediated hyperbranched amplification to produce abundant dendritic DNA nanoassemblies that can be stained by SYBR Green I to generate a high fluorescence signal. This biosensor is characterized by a template-free, electrostatic interaction-independent, high sensitivity, and label-free assay. It enables rapid (less than 3 h) measurement of PARP-1 with a limit of detection of 4.37 × 10-8 U/μL and accurate measurement of cellular PARP-1 activity with single-cell sensitivity. Moreover, it is capable of screening potential inhibitors and discriminating the PARP-1 level in normal person tissues and lung cancer patient tissues, with great potential in PARP-1-related clinical diagnosis and drug discovery.

Streptavidin-Conjugated DNA for the Boronate Affinity-Based Detection of Poly(ADP-Ribose) Polymerase-1 with Improved Sensitivity

This work reports the development of a fluorescence method for the detection of poly(ADP-ribose) polymerase-1 (PARP1), in which a phenylboronic acid-modified fluorescein isothiocyanate dye (FITC-PBA) was used to recognize the formed poly(ADP-ribose) (PAR) polymer. The detection system was designed by conjugating recombinant streptavidin (rSA) with PARP1-specific double-stranded DNA (dsDNA) through streptavidin-biotin interaction. Capture of PARP1 via rSA-biotin-dsDNA allowed for the poly-ADP-ribosylation (PARylation) of both rSA and PARP1 in a homogeneous solution. The resulting rSA-biotin-dsDNA/PAR conjugates were then captured and separated via the commercialized nitrilotriacetic acid-nickel ion-modified magnetic bead (MB-NTA-Ni) through the interaction between NTA-Ni on MB surface and oligohistidine (His₆) tag in rSA. The PAR polymer could capture the dye of FITC-PBA through the borate ester interaction between the boronic acid moiety in PBA and the cis-diol group in ribose, thus causing a decrease in fluorescence signal. The PARylation of streptavidin and the influence of steric hindrance on PARylation efficiency were confirmed using reasonable detection strategies. The method showed a wide linear range (0.01~20 U) and a low detection limit (0.01 U). This work should be valuable for the development of novel biosensors for the detection of poly(ADP-ribose) polymerases and diol-containing species.

Background-Quenched Aggregation-Induced Emission through Electrostatic Interactions for the Detection of Poly(ADP-ribose) Polymerase-1 Activity

Poly(ADP-ribose) polymerase-1 (PARP1) is a potential biomarker and therapeutic target for cancers that can catalyze the poly-ADP-ribosylation of nicotinamide adenine dinucleotide (NAD⁺) onto the acceptor proteins to form long poly(ADP-ribose) (PAR) polymers. Through integration with aggregation-induced emission (AIE), a background-quenched strategy for the detection of PARP1 activity was designed. In the absence of PARP1, the background signal caused by the electrostatic interactions between quencher-labeled PARP1-specitic DNA and tetraphenylethene-substituted pyridinium salt (TPE-Py, a positively charged AIE fluorogen) was low due to the fluorescence resonance energy transfer effect. After poly-ADP-ribosylation, the TPE-Py fluorogens were recruited by the negatively charged PAR polymers to form larger aggregates through electrostatic interactions, thus enhancing the emission. The detection limit of this method for PARP1 detection was found to be 0.006 U with a linear range of 0.01~2 U. The strategy was used to evaluate the inhibition efficiency of inhibitors and the activity of PARP1 in breast cancer cells with satisfactory results, thus showing great potential for clinical diagnostic and therapeutic monitoring.

Deciphering the functional mechanism of zinc ions of PARP1 binding with single strand breaks and double strand breaks

Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for the treatment of cancer-related diseases, and plays an important role in biological processes such as DNA repair, regulating a variety of metabolic and signal transduction processes. Understanding the dynamic binding mechanisms between each domain of PARP1 and DNA is of great significance to deepen the understanding on the function of PARP1 and to facilitate the design of inhibitors. Herein, strategies such as classical molecular dynamics simulation, conformational analysis, binding free energy calculation and energy decomposition were used to shed light on the binding mechanisms of different DNA binding domains (DBDs, including ZnF1, ZnF2 and ZnF3) in PARP1 with DNA and on the influences of zinc ions on the binding process. On one hand, during binding with DNA, ZnF2 tends to expand its space to identify the DNA damage sites and ZnF1/ZnF2 recognizes the interfaces on both sides of DNA damage rather than one side during the process of DNA repair. More importantly, the stable secondary structure of L₂ of ZnF2 (PRO146 to MET153) is the key conformational change for ZnF1 and ZnF2 to recognize DNA damage. Meanwhile, ZnF3 has little effect on the binding mechanisms of PARP1. On the other hand, for the structural differences of DBD domains, zinc ions in ZnF1 and ZnF2 (Zn1 and Zn2) have an impact not only on the conformational changes of PARP1, but also on the conformational changes brought by the interaction of double strand breaks (DSB) and single strand breaks (SSB). And meanwhile, Zn3 also has little effect on ZnF3 for the system of ZnF3/DSB. The findings presented in this work deepen the understanding on the functional mechanism of PARP1 and provide a theoretical basis for further study on the interaction between different inhibitors and DBD domains to design more potential inhibitors.

Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for treatment of cancer-related diseases. Detailed structural changes DBD in PARP1 during the binding process with DNA were investigated and the dynamic conformational differences of DBD caused by zinc ions were revealed.

Role of PGC-1α in the Mitochondrial NAD+ Pool in Metabolic Diseases

Mitochondria play vital roles, including ATP generation, regulation of cellular metabolism, and cell survival. Mitochondria contain the majority of cellular nicotinamide adenine dinucleotide (NAD⁺), which an essential cofactor that regulates metabolic function. A decrease in both mitochondria biogenesis and NAD⁺ is a characteristic of metabolic diseases, and peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) orchestrates mitochondrial biogenesis and is involved in mitochondrial NAD⁺ pool. Here we discuss how PGC-1α is involved in the NAD⁺ synthesis pathway and metabolism, as well as the strategy for increasing the NAD⁺ pool in the metabolic disease state.

An electrochemical platform based on a hemin-rGO-cMWCNTs modified aptasensor for sensitive detection of kanamycin

Kanamycin (KANA) residue in meat is particularly harmful to public health and there is an urgent need to establish a fast, accurate and low-cost method to determinate KANA in food quality control. In this paper, hemin-reduced graphene oxide-carboxylated multiwalled carbon nanotubes (hemin-rGO-cMWCNTs) were designed and prepared, and the characteristics of hemin-rGO-cMWCNTs are presented. After that, an aptamer/hemin-rGO-cMWCNTs sensor for determination of KANA was developed. The electrochemical characteristics were studied by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). Under optimal conditions, the sensitive response of the aptasensor towards KANA presented a wide concentration range of 10-9 to 10-6 M and a low detection limit of 0.36 nM (S/N = 3). Meanwhile, the aptasensor showed prominent selectivity, high stability and acceptable reproducibility in the application of KANA detection. In addition, the aptasensor detection in real samples correlated well with that obtained by liquid chromatograph mass spectrometer (LCMS).

Toxic effects of the Emamectin Benzoate exposure on cultured human bronchial epithelial (16HBE) cells

Pesticides pollution has caused serious environmental problems in recent years, and mounting evidence has shown that more and more insecticides have serious risk in human health. Emamectin Benzoate formally regarded as a highly safety insecticide based on its exclusive targets, but the cytotoxicity to human lung was ignored for a long time. In the present study, bioassay experiments were used to assess the toxicity of the Emamectin Benzoatein on human non-target cells including cell viability assay, DNA damage assay, flow cytometer assay and western blotting assay. The results indicated that Emamectin Benzoatecan cause the inhibition of the proliferation, cytochrome c release, activation of caspase-3/9 and increase Bax/Bcl-2 ratio, which means it induced the cytotoxicity on 16HBE cells associated with the mitochondrial apoptosis. Besides, the DNA damge caused by the Emamectin Benzoate suggest it has a potential genotoxic effect on human lung cells.

High specificity and efficiency electrochemical detection of poly(ADP-ribose) polymerase-1 activity based on versatile peptide-templated copper nanoparticles and detection array

Poly(ADP-ribose) polymerase-1 (PARP-1) activity is closely related to tumor, which is a promising biomarker for cancer diagnosis. So far, only a few methods have been developed for PARP-1 activity assay because both PARP-1 and its catalytic products lack valuable optical or electrochemical property. Herein, we propose a more specific method to label probes on great deal of phosphate groups of PAR. Firstly, versatile peptides were used to prepare CuNPs. This peptide not only worked as reducing agent to prepare CuNPs but also had guanidine groups to label PAR autonomously and specifically. Unlike most previously reported methods based on unspecific electrostatic interactions, CuNPs probes covered by guanidine groups labelled PAR with phosphate groups via intense covalent-like interactions. On the other hand, PARP-1 catalyzed the formation of PAR in each isolated reaction container of the detection array, realizing the high-throughput detection and enhancing the detection efficiency. Ultimately, CuNPs were oxidized into Cu²⁺ and precisely detected by stripping voltammetry. Hence, selectivity and efficiency of PARP-1 detection were both improved. Meanwhile, this approach was successfully used to detect the efficiency of PARP-1 inhibitor and the PARP-1 contents in real cells, indicating its great potential for clinical diagnosis and high-throughput PARP-1 inhibitor screen.

Quartz Crystal Microbalance Detection of Poly(ADP-ribose) Polymerase-1 Based on Gold Nanorods Signal Amplification

Recent findings have thrust poly(ADP-ribose) polymerase-1 (PARP-1) into the limelight as a potential biomarker and chemotherapeutic target for cancer. Thus, a sensitive method for detection of PARP-1 is necessary for early diagnosis of cancer and drug development. However, the poor electrochemical and optical activity of PARP-1 and its product poly(ADP-ribose) (PAR) prompted researchers to develop more methods. Here, we developed an efficient method for the determination of PARP-1 by using quartz crystal microbalance (QCM) because it is mass-sensitive. Once activated by the specific DNA, PARP-1 cleaves nicotinamideadenine dinucleotide (NAD⁺) into nicotinamide and ADP-ribose to synthesize a hyperbranched poly(ADP-ribose) polymer. Although QCM is mass-sensitive, it is not sensitive enough to discern PAR effectively. So, positively charged cetyltrimethylammonium bromide (CTAB)-coated gold nanorods (GNRs) were introduced to increase the frequency change significantly because of the strong electrostatic interaction between them with negatively charged PAR. PARP-1 ranging from 0.06 to 3 nM can be facilely detected with a low detection limit of 0.04 nM. The strategy has been used to evaluate PARP-1 inhibitors and to detect PARP-1 activity in real cancer cells lysate with satisfactory results, indicating that it was a promising candidate for clinical diagnosis and drug screening in the future.

A label-free PFP-based photoelectrochemical biosensor for highly sensitive detection of PARP-1 activity

Poly(ADP-ribose) polymerase-1 (PARP-1), as an original tumor marker, has aroused wide attention in recent years. However, only a few researches have been done for PARP-1 activity detection because PARP-1 is lack of optical or electrochemical property. In this work, a label-free and high-sensitive photoelectrochemical (PEC) biosensor for PARP-1 activity detection based on poly[9,9-bis(6'-N,N,N-trimethylammonium)hexyl]fluorenylene phenylene (PFP) has been designed. To the best of our knowledge, it is the first time that PEC has been used to monitor PARP-1 activity. PARP-1 were activated under the function of activated dsDNA, as a result, branched polymers of ADP-ribose (PAR) with plentiful negative charge were formed in the presence of nicotinamide adenine dinucleotide (NAD⁺). Subsequently, positively charged PFP with good photoelectrochemical properties, were absorbed on PAR via electrostatic interaction. High photocurrent was produced under light induction, which was depended on the PARP-1 activity. The biosensor has a wide linear range from 0.01 to 2 U with a detection limit of 0.007 U. The strategy has been applied in breast and ovarian cancer cells to detection PARP-1 activity with approving results, which signifies that it is a promising tool for clinical diagnosis.