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Aptamers

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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
#1
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/28525848/an-amplified-comparative-fluorescence-resonance-energy-transfer-immunosensing-of-ca125-tumor-marker-and-ovarian-cancer-cells-using-green-and-economic-carbon-dots-for-bio-applications-in-labeling-imaging-and-sensing
#2
Somayeh Hamd-Ghadareh, Abdollah Salimi, Fardin Fathi, Saman Bahrami
CA125, is a marker in the clinical diagnosis of several cancers and currently is the best serum-based tumor marker for ovarian cancer. Here, we developed an ultrasensitive antibody-ssDNA aptamer sandwich-type fluorescence immunosensor for CA125 detection. Based on a novel signal amplification strategy the carbon dots (CDs) functionalized with aptamer (CD-aptamer) used as detection probe and PAMAM-Dendrimers/AuNPs was used for covalent attachment of CA125-antibody and completing the sandwich assay method. By measuring of fluorescence resonance energy transfer (FRET) signals between CDs and AuNPs as nanoquenchers, the fluorescence signal quenched during sandwich complex formed between anti-CA125, CA125 and CDs-Aptamer and decreasing of fluorescence response signal is related to CA125 concentrations...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28525643/synthetic-mrna-devices-that-detect-endogenous-proteins-and-distinguish-mammalian-cells
#3
Shunsuke Kawasaki, Yoshihiko Fujita, Takashi Nagaike, Kozo Tomita, Hirohide Saito
Synthetic biology has great potential for future therapeutic applications including autonomous cell programming through the detection of protein signals and the production of desired outputs. Synthetic RNA devices are promising for this purpose. However, the number of available devices is limited due to the difficulty in the detection of endogenous proteins within a cell. Here, we show a strategy to construct synthetic mRNA devices that detect endogenous proteins in living cells, control translation and distinguish cell types...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28522812/selection-and-characterization-of-a-dna-aptamer-inhibiting-coagulation-factor-xia
#4
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
#5
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/28522194/aptamer-mediated-gene-therapy-enhanced-antitumor-activity-against-human-hepatocellular-carcinoma-in-vitro-and-in-vivo
#6
Shuangli Xiao, Zhongbing Liu, Ruolan Deng, Chunhong Li, Shaozhi Fu, Guilan Chen, Xiaoqin Zhang, Famin Ke, Siyun Ke, Xin Yu, Shurong Wang, Zhirong Zhong
A recombinant adenovirus carrying the tumor suppressor gene PTEN (Ad5-PTEN) is an effective antitumor agent against liver cancer. But the application of Ad5-PTEN has been greatly hindered by its auto-immunogenicity, non-specific toxicity to normal tissues, as well as poor stability in blood stream because of neutralizing antibody. Epithelial cell adhesion molecule (EpCAM) is over-expressed in most solid tumors and it has been identified to be a cancer stem cell surface marker in liver cancer. An RNA aptamer EpDT3 could specially bind with EpCAM and target EpCAM-positive cells...
May 15, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
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
#7
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/28516771/highly-selective-cerebral-atp-assay-based-on-micrometer-scale-ion-current-rectification-at-polyimidazolium-modified-micropipettes
#8
Kailin Zhang, Xiulan He, Yang Liu, Ping Yu, Junjie Fei, Lanqun Mao
Development of new principles and methods for cerebral ATP assay is highly imperative not only for determining ATP dynamics in brain but also for understanding physiological and pathological processes related to ATP. Herein, we for the first time demonstrate that micrometer scale ion current rectification (MICR) at a polyimidazolium-modified micropipet can be used as the signal transduction output for the cerebral ATP assay with high selectivity. The rationale for ATP assay is essentially based on the competitive binding of the negatively charged ATP aptamer toward positively charged polyimidazolium and ATP...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28515761/oligonucleotide-aptamers-potential-novel-molecules-against-viral-hepatitis
#9
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
#10
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
#11
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/28513559/detecting-and-discriminating-shigella-sonnei-using-an-aptamer-based-fluorescent-biosensor-platform
#12
Myeong-Sub Song, Simranjeet Singh Sekhon, Woo-Ri Shin, Hyung Cheol Kim, Jiho Min, Ji-Young Ahn, Yang-Hoon Kim
In this paper, a Whole-Bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against Shigella sonnei. Real-time PCR amplification and post-SELEX experiment revealed that the selected aptmers possessed a high binding affinity and specificity for S. sonnei. Of the 21 aptamers tested, the C(t) values of the SS-3 and SS-4 aptamers (Ct = 13.89 and Ct = 12.23, respectively) had the lowest value compared to other aptamer candidates. The SS-3 and SS-4 aptamers also displayed a binding affinity (KD) of 39...
May 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#13
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
#14
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
#15
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
#16
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/28505431/a-stepping-library-based-post-selex-strategy-approaching-to-the-minimized-aptamer-in-spr
#17
Xiaoqin He, Lei Guo, Junlin He, Hua Xu, Jianwei Xie
When evolved from SELEX (systematic evolution of ligands by exponential enrichment), aptamers are generally ca. 70-130 nucleotides in length, and needed to be effectively truncated for further diagnosis or therapeutic uses. Post-SELEX optimization is then aroused to simplify the aptamer sequence and improve the affinity property. In this work, we report a new post-SELEX strategy based on a stepping library for the first time. With a hypothesis that one nucleobase can influence the whole binding affinity through its adjacent base stacking and potential steric hydrogen bonding interaction, we designed a stepping library composed of all probable nucleotide truncation directions...
May 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28504865/real-time-crystallographic-studies-of-the-adenine-riboswitch-using-an-x-ray-free-electron-laser
#18
REVIEW
J R Stagno, Y R Bhandari, C E Conrad, Y Liu, Y-X Wang
Structures of the four reaction states of the adenine riboswitch aptamer domain, including a transient intermediate state were solved by serial femtosecond crystallography. The structures not only demonstrate the use of X-ray free electron lasers for RNA crystallography but have also proven that transient states can be determined in real time by mix-and-inject crystallography. These results illustrate the structural basis for the ligand-induced conformational changes associated with the molecular "switch". This article is protected by copyright...
May 15, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28501211/metastatic-cancer-cell-and-tissue-specific-fluorescence-imaging-using-a-new-dna-aptamer-developed-by-cell-selex
#19
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/28501180/detection-of-a%C3%AE-oligomers-based-on-magnetic-field-assisted-separation-of-aptamer-functionalized-fe3o4-magnetic-nanoparticles-and-bayf5-yb-er-nanoparticles-as-upconversion-fluorescence-labels
#20
Ling-Feng Jiang, Bo-Cheng Chen, Ben Chen, Xue-Jian Li, Hai-Lin Liao, Hong-Miao Huang, Zhan-Jing Guo, Wen-Yan Zhang, Lin Wu
A sensitive and stable bioassay for the detection of Aβ oligomer (Aβo), a potentially promising candidate biomarker for Alzheimer's disease (AD) diagnosis, was developed using Fe3O4 magnetic nanoparticles (MNPs) as the recognition and concentration elements and BaYF5:Yb,Er upconversion nanoparticles (UCNPs) as highly sensitive labels, conjugated with the Aβo aptamer (DNA1) and the complementary oligonucleotide of the Aβo aptamer (DNA2), respectively. The DNA1 hybridized with DNA2 to form the duplex structure on the surface of the MNPs/UCNPs nanocomposites probe...
August 1, 2017: Talanta
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