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Dna aptamer

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https://www.readbyqxmd.com/read/28530298/aptabody-aptatope-interactions-in-aptablotting-assays
#1
Simranjeet Singh Sekhon, Hyun-Ju Um, Woo-Ri Shin, Sang-Hee Lee, Jiho Min, Ji-Young Ahn, Yang-Hoon Kim
We demonstrate an aptablotting assay method that involves direct and indirect aptabody recognition. Nanoscale single-stranded DNA aptamers against GST and DIG-tags are utilized as aptabodies (GST-2 and DIG-1, respectively), and the GST-2 aptabody binding site, or aptatope, as predicted by a MOE-docking simulation of the protein-aptamer complex, shows the interaction of the GST-2 aptabody at the catalytically active region. The aptabody-aptatope interaction was evaluated by an in vitro enzyme inhibitory analysis...
May 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28525850/highly-sensitive-aptasensor-based-on-fluorescence-resonance-energy-transfer-between-l-cysteine-capped-zns-quantum-dots-and-graphene-oxide-sheets-for-the-determination-of-edifenphos-fungicide
#2
Majid Arvand, Aazam A Mirroshandel
With the advantages of excellent optical properties and biocompatibility, single-strand DNA-functionalized quantum dots have been widely applied in biosensing and bioimaging. A new aptasensor with easy operation, high sensitivity, and high selectivity was developed by immobilizing the aptamer on water soluble l-cysteine capped ZnS quantum dots (QDs). Graphene oxide (GO) sheets are mixed with the aptamer-QDs. Consequently, the aptamer-conjugated QDs bind to the GO sheets to form a GO/aptamer-QDs ensemble. This aptasensor enables the energy transfer based on a fluorescence resonance energy transfer (FRET) from the QDs to the GO sheets, quenching the fluorescence of QDs...
May 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28522812/selection-and-characterization-of-a-dna-aptamer-inhibiting-coagulation-factor-xia
#3
David A Donkor, Varsha Bhakta, Louise J Eltringham-Smith, Alan R Stafford, Jeffrey I Weitz, William P Sheffield
Factor XIa (FXIa) is a serine protease that catalyzes the activation of Factor IX (FIX) in the blood coagulation cascade. FXIa and its precursor FXI are emergent therapeutic targets for the development of safer anticoagulant agents. Here, we sought a novel DNA-based agent to inhibit FXIa. Towards this goal, an 80 base, single-stranded DNA aptamer library (containing a 40 base randomized core) was screened for FXIa-binding candidates, using ten rounds of positive and negative selection. After selection, 6 of 89 different sequences inhibited FXIa-mediated chromogenic substrate S2366 cleavage...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522308/development-of-a-ssdna-aptamer-for-detection-of-residual-benzylpenicillin
#4
A-Young Lee, Na-Reum Ha, In-Pil Jung, Sang-Heon Kim, A-Ru Kim, Moon-Young Yoon
Antibiotics are useful for improving the living conditions of livestock. However, residual antibiotics induce several human diseases such as food-borne illness and infection of carbapenem-resistant Enterobacteriaceae (CRE). In this study, the identification of a benzylpenicillin-specific aptamer was selected by rGO-SELEX (reduced Graphene Oxide-Systematic Evolution of Ligands by EXponential enrichment). A random ssDNA library was incubated with rGO for adsorption and eluted with benzylpenicillin. As a result of the selection process, a DNA aptamer was found that specifically bound to benzylpenicillin with high binding affinity, Kd = 383...
May 15, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28520392/gold-nanostar-enhanced-surface-plasmon-resonance-detection-of-an-antibiotic-at-attomolar-concentrations-via-an-aptamer-antibody-sandwich-assay
#5
Suhee Kim, Hye Jin Lee
A new sandwich assay for tetracycline (TC) involving a DNA aptamer and antibody pair is demonstrated in conjunction with gold nanostar (GNS) enhanced surface plasmon resonance (SPR) to achieve detection in the low attomolar range. GNS particles were covalently functionalized with the antibody probe (antiTC) and integrated into a surface sandwich assay in conjunction with a SPR gold chip modified with the TC-specific aptamer. After it was demonstrated that both affinity probes can bind simultaneously to TC, optimization of the assay was performed using either antiTC only or GNS-antiTC conjugates to interact with aptamer/TC complexes present on the chip surface...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28515761/oligonucleotide-aptamers-potential-novel-molecules-against-viral-hepatitis
#6
REVIEW
Mina Mirian, Hossein Khanahmad, Leila Darzi, Mansour Salehi, Hojjat Sadeghi-Aliabadi
Viral hepatitis, as an international public health concern, seriously affects communities and health system. In recent years, great strides have been taken for development of new potential tools against viral hepatitis. Among these efforts, a valuable strategy introduced new molecules called "aptamers". Aptamers as potential alternatives for antibodies could be directed against any protein in infected cells and any components of viral particles. In this review, we will focus on recent advances in the diagnosis and treatment of viral hepatitis based on aptamer technology...
April 2017: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28514955/label-free-biosensing-of-salmonella-enterica-serovars-at-single-cell-level
#7
Bin Wang, Bosoon Park, Bingqian Xu, Yongkuk Kwon
BACKGROUND: The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium...
May 17, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28514850/dna-dendrimer-streptavidin-nanocomplex-an-efficient-signal-amplifier-for-construction-of-biosensing-platforms
#8
Yan Zhao, Shichao Hu, Huaming Wang, Kaiwen Yu, Yan Guan, Xiaoyun Liu, Na Li, Feng Liu
We develop a DNA dendrimer-streptavidin (SA) nanocomplex as a novel signal amplifier to create biosensing platforms for disease-related species. The DNA dendrimer-SA nanocomplex is fabricated by crosslinking the nonlinear hybridization chain reaction based DNA dendrimer with the SA-coupled linker DNA, and possesses multiple sticky ends, a high molecular weight, and a hyperbranched nanostructure with large numbers of DNA duplexes. Taking advantages of the DNA dendrimer-SA nanocomplex and a label-free quartz crystal microbalance (QCM) technology, we first construct a mass-sensitive QCM biosensing platform for nucleic acids, which displays high selectivity and sensitivity with the detection limit of 0...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#9
REVIEW
Bruno Macedo, Yraima Cordeiro
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrP(C)) into the pathogenic conformer (PrP(Sc)) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrP(C) to PrP(Sc)...
May 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28507706/ph-and-ligand-induced-release-of-loads-from-dna-acrylamide-hydrogel-microcapsules
#10
Wei-Ching Liao, Sivan Lilienthal, Jason S Kahn, Marianna Riutin, Yang Sung Sohn, Rachel Nechushtai, Itamar Willner
Herein, a method to construct stimuli-responsive DNA-acrylamide-based hydrogel microcapsules has been presented. This method involves the use of polyacrylamide chains modified with predesigned nucleic acid hairpin units and optionally single-strand tethers that provide the required hybridization and recognition functions to yield substrate-loaded stimuli-responsive hydrogel-based microcapsules. The synthesis of the microcapsules involves the loading of CaCO3 microparticles with the respective load substrates and the functionalization of the CaCO3 template particles with nucleic acid promoter units...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28507681/complementary-oligonucleotides-regulate-induced-fit-ligand-binding-in-duplexed-aptamers
#11
Jeffrey D Munzar, Andy Ng, Mario Corrado, David Juncker
Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1...
March 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28505560/integrated-signal-probe-based-aptasensor-for-dual-analyte-detection
#12
Juan Xiang, Xiaomei Pi, Xiaoqing Chen, Lei Xiang, Minghui Yang, Hao Ren, Xiaojuan Shen, Ning Qi, Chunyan Deng
For the multi-analyte detection, although the sensitivity has commonly met the practical requirements, the reliability, reproducibility and stability need to be further improved. In this work, two different aptamer probes labeled with redox tags were used as signal probe1 (sP1) and signal probe2 (sP2), which were integrated into one unity DNA architecture to develop the integrated signal probe (ISP). Comparing with the conventional independent signal probes for the simultaneous multi-analyte detection, the proposed ISP was more reproducible and accurate...
April 26, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28501211/metastatic-cancer-cell-and-tissue-specific-fluorescence-imaging-using-a-new-dna-aptamer-developed-by-cell-selex
#13
Baoyin Yuan, Xiaochun Jiang, Yuanyuan Chen, Qiuping Guo, Kemin Wang, Xiangxian Meng, Zhixiang Huang, Xiaohong Wen
Metastasis, which derived from a primary tumor, accounts for 90% of mortality caused by cancer. Early diagnosis of cancer metastasis may significantly improve cure rate of patients who are at high risk for developing metastasis. In this study, we successfully achieved metastatic cancer cell and tissue-specific fluorescence imaging by using a new aptamer developed by cell-based systematic evolution of ligands by exponential enrichment (Cell-SELEX). With metastatic colorectal carcinoma LoVo cells as selection target, the aptamer named J3 which bind to metastatic cancer cells with good affinity and specificity was obtained...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28499196/binding-induced-dna-walker-for-signal-amplification-in-highly-selective-electrochemical-detection-of-protein
#14
Yuhang Ji, Lei Zhang, Longyi Zhu, Jianping Lei, Jie Wu, Huangxian Ju
A binding-induced DNA walker-assisted signal amplification was developed for highly selective electrochemical detection of protein. Firstly, the track of DNA walker was constructed by self-assembly of the high density ferrocene (Fc)-labeled anchor DNA and aptamer 1 on the gold electrode surface. Sequentially, a long swing-arm chain containing aptamer 2 and walking strand DNA was introduced onto gold electrode through aptamers-target specific recognition, and thus initiated walker strand sequences to hybridize with anchor DNA...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28496951/can-aptameric-ligands-specific-to-plasma-coagulation-factor-vii-bind-the-recombinant-form-with-high-affinity-affinity-measurement-by-fluorescence-method
#15
Maryam Tabarzad, Marzieh Jafari, Nastaran Nafissi-Varcheh
BACKGROUND: Among diverse protein purification systems, affinity chromatography is the most attractive one in the purification process of coagulation factors. Coagulation factor VII is a plasma serine protease that has a significant role in natural human hemostasis and its recombinant form such as AryoSeven(™), has been applied in clinical treatment of bleeding disorders. Immunoaffinity chromatography is the purification method of choice that is currently applied in the development of coagulation factor VIIa products...
April 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28496460/doxorubicin-loaded-dna-aptamer-linked-myristilated-chitosan-nanogel-for-targeted-drug-delivery-to-prostate-cancer
#16
Fereshteh Atabi, Seyed Latif Mousavi Gargari, Mehrdad Hashemi, Parichehreh Yaghmaei
Recently, specific attention has been paid to aptamers, short DNA or RNA, as a tool for cancer diagnosis and therapy. In the present study MCS nanogels were prepared by Myristate: Chitosan at 1:9 ratio and were characterized by several techniques. A selected ssDNA aptamer (Apt) capable of detecting LNCaP cells was linked to Myristilated Chitosan nanogels (Apt-MCS) by glutaraldehyde and loaded with Doxorubicin (DOX) to be used in targeted drug delivery against the Prostate cancer cells. LNCaP and PC-3 cells were treated with Apt-MCS-DOX complex and the binding efficiency was estimated by flow cytometry...
2017: Iranian Journal of Pharmaceutical Research: IJPR
https://www.readbyqxmd.com/read/28494740/nucleic-acids-based-nanotherapeutics-crossing-the-blood-brain-barrier
#17
Noha Nafee, Noha Gouda
The restless endeavors revealing the molecular pathways underlying many neurodegenerative diseases and brain tumors have paved the way for the introduction of the selective exogenous gene-based therapeutics. The implicated active biomolecules encompass mainly negatively-charged nucleic acids ranging from DNA, mRNA, non-coding RNAs (small-interfering RNA, siRNA, and microRNA, miRNA), to antisense oligonucleotides. They selectively interfere with the genes translational and/or transcriptional processes. Although many reviews previously addressed brain targeting, a thorough correlation between the molecular properties of these biomacromolecules, the nature of blood brain barrier (BBB) in the accompanying pathological condition, the intracellular targets, as well as the design of the delivery system which will transport the bioactive cargo to the target cells attempting efficient delivery to the active sites in the brain will be appraised...
May 10, 2017: Current Gene Therapy
https://www.readbyqxmd.com/read/28492073/polyvalent-and-thermosensitive-dna-nanoensembles-for-cancer-cell-detection-and-manipulation
#18
Jinlu Tang, Yanru Yu, Hui Shi, Xiaoxiao He, Yanli Lei, Jingfang Shangguan, Xue Yang, Zhenzhen Qiao, Kemin Wang
Development of smart DNA nanostructures is of great value in cancer studies. Here, by integrating rolling circle amplification (RCA) into split aptamer design, a novel strategy of polyvalent and thermosensitive DNA nanoensembles was first proposed for cancer cell detection and manipulation. In this strategy, a long nanosolo ssDNA with repeated Split-b and Poly T regions was generated through RCA. Split-b supplied polyvalent binding sites while Poly T supported signal output by hybridizing with fluorophore-labeled poly A...
May 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28485436/silver-nanoparticle-plasmonic-enhanced-f%C3%A3-rster-resonance-energy-transfer-fret-imaging-of-protein-specific-sialylation-on-the-cell-surface
#19
Tingbi Zhao, Ting Li, Yang Liu
A large amount of proteins are post-translationally modified with a sialic acid terminal oligosaccharide, and sialylation directly affects the function of glycoproteins and adjusts relevant biological processes. Herein, we developed a method for imaging analysis of protein-specific sialylation on the cell surface via silver nanoparticle (AgNPs) plasmonic enhanced Förster resonance energy transfer (FRET). In this strategy, the target monosaccharide was labelled with the FRET acceptor of Cy5 via bioorthogonal chemistry...
May 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/28482608/electrochemical-switching-with-a-dna-aptamer-based-electrochemical-sensor
#20
Shabnam Beiranvand, Azadeh Azadbakht
The present study was focused on the application of NH2-functionalized Fe3O4/gold nanoparticles (Fe3O4/AuNPs)-decorated carbon nanotubes (CNTs) in the development of electrochemical sensor for bisphenol A (BPA) detection. After the nanocomposite synthesis and its characterization, the optimization of the measurement conditions and working parameters of sensors were evaluated. Aminated detection probe (DNA aptamer) was surface confined on the NH2-functionalized Fe3O4/AuNPs surface using glutaraldehyde as a linker...
July 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
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