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Dna aptamer

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https://www.readbyqxmd.com/read/28633099/simultaneous-and-specific-enrichment-of-several-amphenicol-antibiotics-residues-in-food-based-on-novel-aptamer-functionalized-magnetic-adsorbents-using-hplc-dad
#1
Shengfeng Huang, Ning Gan, Haibo Liu, You Zhou, Yinji Chen, Yuting Cao
In this work, a novel aptamer functionalized magnetic adsorbent was developed and combined with magnetic dispersive solid phase extraction (MDSPE) for selective enrichment of several amphenicol antibiotics residues (chloramphenicol(CAP), thiamphenicol(TAP) and florphenicol(FF)) in foodstuff then determined by High Performance Liquid Chromatography (HPLC)-Diode array detector(DAD). Firstly, a magnetic silica-coated Fe3O4 microsphere(Fe3O4@SiO2) was synthetized by sol-gel method, then it was functionalized by amino groups through 3-Aminopropyltriethoxysilane (APTES) reagent to form Fe3O4@SiO2-NH2; Thirdly, the amino group on Fe3O4@SiO2-NH2 was transferred to carboxylic group via the succinic anhydride to form Fe3O4@SiO2-COOH...
June 12, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28629023/heparin-dna-aptamer-co-assembled-multifunctional-catecholamine-coating-for-epc-capture-and-improved-hemocompatibility-of-vascular-devices
#2
Jinchuan Deng, Shuheng Yuan, Xin Li, Kebing Wang, Lingxia Xie, Na Li, Jin Wang, Nan Huang
Good hemocompatibility and rapid endothelialization are two key factors in the success of stent interventional therapy. In this study, aptamers with the ability to capture endothelial progenitors and anticoagulant molecular heparin were successfully immobilized on the surface of dopamine/polyethylenimine (PDA/PEI) copolymer coating via electrostatic interaction. The results of X-ray spectroscopy (XPS), water contact angle (WCA), and immunofluorescence staining tests confirmed the successful introduction of heparin and aptamers...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28626560/selective-single-molecule-nanopore-sensing-of-proteins-using-dna-aptamer-functionalised-gold-nanoparticles
#3
Xiaoyan Lin, Aleksandar P Ivanov, Joshua B Edel
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28625157/purification-of-single-stranded-dna-by-co-polymerization-with-acrylamide-and-electrophoresis
#4
Tulsi Ram Damase, Andrew D Ellington, Peter B Allen
Single-stranded DNA (ssDNA) oligonucleotides are useful as aptamers, hybridization probes and for emerging applications in DNA nanotechnology. Current methods to purify ssDNA require both a strand-separation step and a separate size-separation step but may still leave double-stranded DNA (dsDNA) impurities in the sample. Here, we use commercially available acrydite DNA primers to immobilize one strand of a PCR product within a polyacrylamide matrix. Electrophoresis moves the non-crosslinked DNA into the gel where the single-stranded product of desired size can be recovered...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28624215/periostin-binding-dna-aptamer-treatment-ameliorates-peritoneal-dialysis-induced-peritoneal-fibrosis
#5
Bo Young Nam, Jung Tak Park, Young Eun Kwon, Jung Pyo Lee, Jong Ha Jung, Youndong Kim, Seonghun Kim, Jimin Park, Jae Eun Um, Meiyan Wu, Seung Hyeok Han, Tae-Hyun Yoo, Shin-Wook Kang
Peritoneal fibrosis is a major complication in peritoneal dialysis (PD) patients, which leads to dialysis discontinuation. Periostin, increased by transforming growth factor β1 (TGF-β1) stimulation, induces the expression of extracellular matrix (ECM) genes. Aberrant periostin expression has been demonstrated to be associated with PD-related peritoneal fibrosis. Therefore, the effect of periostin inhibition by an aptamer-based inhibitor on peritoneal fibrosis was evaluated. In vitro, TGF-β1 treatment upregulated periostin, fibronectin, α-smooth muscle actin (α-SMA), and Snail expression and reduced E-cadherin expression in human peritoneal mesothelial cells (HPMCs)...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28623657/aptamer-magnetic-bead-quantum-dot-sandwich-assays-for-foodborne-pathogen-detection-pros-cons-and-lessons-learned
#6
John G Bruno, Jeffrey C Sivils, Taylor Phillips
DNA and RNA aptamers have been extensively investigated as potential competitors for antibodies for a variety of applications including food safety testing. Ultrasensitive fluorescence detection of foodborne pathogenic bacteria as low as 1-10 cells/mL has been achieved using aptamers coupled to quantum dots in clear pristine buffers for environmental sample detection. Quantum dots offer other advantages, including single UV or blue light source multiplex (multicolored) detection. However, quantum dots can exhibit decreased fluorescence in some food matrixes and even completely fail to fluoresce in some fatty matrixes, as documented in this report...
June 16, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28622804/g-quadruplex-based-exo-iii-assisted-signal-amplification-aptasensor-for-the-colorimetric-detection-of-adenosine
#7
Lei Xu, Xin Shen, Bingzhi Li, Chunhong Zhu, Xuemin Zhou
Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28620670/pesticide-vapor-sensing-using-an-aptamer-nanopore-and-agarose-gel-on-a-chip
#8
Satoshi Fujii, Aiko Nobukawa, Toshihisa Osaki, Yuya Morimoto, Koki Kamiya, Nobuo Misawa, Shoji Takeuchi
A pesticide vapor sensor was developed using an agarose gel-based chip containing a nanopore sensing system. Vaporized omethoate was detected by the absorption into the gel, the complex formation with a DNA aptamer, and its obstruction at the nanopore. This strategy is applicable to other vapors, expanding the versatility of nanopore sensors.
June 16, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28614699/a-signal-amplification-probe-enhances-sensitivity-of-antibodies-and-aptamers-based-immuno-diagnostic-assays
#9
Ofer Nussbaum, Michal Bar Oz, Tal Tilayov, Helly Atiya, Shlomo Dagan
One major unmet need is improving the sensitivity of immune-diagnostic assays. This is particularly important in the field of biomarker discoveries and monitoring. We have established a novel signal amplification probe system enabling a highly sensitive target detection platform to be used in immuno-assays. The probe consists of a double stranded DNA that can carry a large number of signaling elements such as biotin or fluorescent molecules. The DNA probe anchors to the recognition unit, whether an antibody or an aptamer, by covalent conjugation or by a simple and rapid molecular association process...
June 11, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28605461/determining-the-folding-and-binding-free-energy-of-dna-based-nanodevices-and-nanoswitches-using-urea-titration-curves
#10
Andrea Idili, Francesco Ricci, Alexis Vallée-Bélisle
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28603040/a-real-time-control-system-of-gene-expression-using-ligand-bound-nucleic-acid-aptamer-for-metabolic-engineering
#11
Jing Wang, Xun Cui, Le Yang, Zhe Zhang, Liping Lv, Haoyuan Wang, Zhenmin Zhao, Ningzi Guan, Lichun Dong, Rachel Chen
Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS...
June 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28598605/metal-sensing-by-dna
#12
Wenhu Zhou, Runjhun Saran, Juewen Liu
Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers...
June 9, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28595725/ultrasensitive-detection-of-nucleic-acids-and-proteins-using-quartz-crystal-microbalance-and-surface-plasmon-resonance-sensors-based-on-target-triggering-multiple-signal-amplification-strategy
#13
Wenbo Sun, Weiling Song, Xiaoyan Guo, Zonghua Wang
In this study, quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensors were combined with template enhanced hybridization processes (TEHP), rolling circle amplification (RCA) and biocatalytic precipitation (BCP) for ultrasensitive detection of DNA and protein. The DNA complementary to the aptamer was released by the specific binding of the aptamer to the target protein and then hybridized with the capture probe and the assistant DNA to form a ternary "Y" junction structure. The initiation chain was generated by the template-enhanced hybridization process which leaded to the rolling circle amplification reaction, and a large number of repeating unit sequences were formed...
July 25, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28592206/molecular-modeling-and-spri-investigations-of-interleukin-6-il6-protein-and-dna-aptamers
#14
Kristen L Rhinehardt, Stephen A Vance, Ram V Mohan, Marinella Sandros, Goundla Srinivas
Interleukin 6 (IL6), an inflammatory response protein has major implications in immune related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes...
June 7, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28591844/new-insights-into-a-classic-aptamer-binding-sites-cooperativity-and-more-sensitive-adenosine-detection
#15
Zijie Zhang, Olatunji Oni, Juewen Liu
The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed...
June 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28588614/optimization-of-aflatoxin-b1-aptasensing
#16
Marzieh Jafari, Mohsen Rezaei, Heibatullah Kalantari, Maryam Tabarzad, Bahram Daraei
Combination of aptamers with DNAzymes attracted intense attention for development of DNA-based biosensors for detection of mycotoxins. In the present study a combination of aflatoxin B1 specific aptamer and HRP- (horseradish peroxidase-) mimicking DNAzyme was optimized for detecting aflatoxin B1. Detecting approach is based on the binding affinity of aflatoxin B1 to its specific aptamer and conversion of substrate to a detectable colorimetric signal by a linked DNAzyme. Compared to conventional methods for aflatoxin B1 detection, DNA-based assay has the advantages of low cost, long-term stability, and rapid, simple, and user-friendly steps...
2017: Journal of Toxicology
https://www.readbyqxmd.com/read/28585149/inhibition-of-adhesion-and-metastasis-of-hepg2-hepatocellular-carcinoma-cells-in-vitro-by-dna-aptamer-against-sialyl-lewis-x
#17
Xiao-Kang Wang, Yan Peng, Hao-Ran Tao, Fen-Fang Zhou, Chi Zhang, Fei Su, Shi-Pei Wang, Qing Liu, Li-Hua Xu, Xue-Kai Pan, Wei Xie, Mao-Hui Feng
The sialyl Lewis X (SLe(x)) antigen encoded by the FUT7 gene is the ligand of endotheliam-selectin (E-selectin). The combination of SLe(x) antigen and E-selectin represents an important way for malignant tumor metastasis. In the present study, the effect of the SLe(x)-binding DNA aptamer on the adhesion and metastasis of hepatocellular carcinoma HepG2 cells in vitro was investigated. Reverse transcription-polymerase chain reaction (RT-PCR) and immunofluorescence staining were conducted to detect the expression of FUT7 at both transcriptional and translational levels...
June 2017: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/28581004/dna-origami-gold-nanorod-hybrid-nanostructures-for-the-circumvention-of-drug-resistance
#18
Linlin Song, Qiao Jiang, Jianbing Liu, Na Li, Qing Liu, Luru Dai, Yuan Gao, Weili Liu, Dongsheng Liu, Baoquan Ding
We herein demonstrate that DNA origami can work as a multifunctional platform integrating a chemotherapeutic drug (doxorubicin), gold nanorods and a tumour-specific aptamer MUC-1, to realize the effective circumvention of drug resistance. Doxorubicin (DOX) was loaded efficiently onto DNA origami through base pair intercalation and surface-modified gold nanorods (AuNRs) were assembled onto the DNA origami through DNA hybridization. Due to the active targeting effect of the assembled aptamers, the multifunctional nanostructures achieved increased cellular internalization of DOX and AuNRs...
June 5, 2017: Nanoscale
https://www.readbyqxmd.com/read/28579776/aptamer-conjugated-pegylated-quantum-dots-targeting-epidermal-growth-factor-receptor-variant-iii-for-fluorescence-imaging-of-glioma
#19
Jiaze Tang, Ning Huang, Xiang Zhang, Tao Zhou, Ying Tan, Jiangli Pi, Li Pi, Si Cheng, Huzhi Zheng, Yuan Cheng
The extent of resection is a significant prognostic factor in glioma patients. However, the maximum safe resection level is difficult to determine due to the inherent infiltrative character of tumors. Recently, fluorescence-guided surgery has emerged as a new technique that allows safe resection of glioma. In this study, we constructed a new kind of quantum dot (QD)-labeled aptamer (QD-Apt) nanoprobe by conjugating aptamer 32 (A32) to the QDs surface, which can specially bind to the tumors. A32 is a single-stranded DNA capable of binding to the epidermal growth factor receptor variant III (EGFRvIII) specially distributed on the surface of glioma cells...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28578167/novel-label-free-and-high-throughput-microchip-electrophoresis-platform-for-multiplex-antibiotic-residues-detection-based-on-aptamer-probes-and-target-catalyzed-hairpin-assembly-for-signal-amplification
#20
Ye Wang, Ning Gan, You Zhou, Tianhua Li, Futao Hu, Yuting Cao, Yinji Chen
Novel label-free and multiplex aptasensors have been developed for simultaneous detection of several antibiotics based on a microchip electrophoresis (MCE) platform and target catalyzed hairpin assembly (CHA) for signal amplification. Kanamycin (Kana) and oxytetracycline (OTC) were employed as models for testing the system. These aptasensors contained six DNA strands termed as Kana aptamer-catalysis strand (Kana apt-C), Kana inhibit strand (Kana inh), OTC aptamer-catalysis strand (OTC apt-C), OTC inhibit strand (OTC inh), hairpin structures H1 and H2 which were partially complementary...
May 10, 2017: Biosensors & Bioelectronics
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