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Dna aptamer

Xiaofang Zheng, Ruizi Peng, Xi Jiang, Yaya Wang, Shuai Xu, Guoliang Ke, Ting Fu, Qiaoling Liu, Shuang-Yan Huan, Xiaobing Zhang
We have developed a DNA nanoprobe for adenosine triphosphate (ATP) sensing in living cells, based on the split aptamer and the DNA triangular prism (TP). In which nucleic acid aptamer was split into two fragments, the stem of the split aptamer was respectively labeled donor and acceptor fluorophores that underwent an fluorescence resonance energy transfer if two ATP molecules were bound as target molecule to the recognition module. Hence, ATP as a target induced the self-assembly of split aptamer fragments and thereby brought the dual fluorophores into close proximity for high FRET efficiency...
September 21, 2017: Analytical Chemistry
Nan Wang, Miaomiao Zhang, Xuejuan Chen, Xingxing Ma, Chen Li, Zhe Zhang, Jilin Tang
Mucin 1 (MUC1) is an attractive tumor marker for cancer diagnosis. An advanced atomic force microscopy (AFM) mode, peak-force tapping AFM with an aptamer functionalized tip, was introduced to map the specific interaction sites of an aptamer and MUC1. Single molecular force spectroscopy (SMFS) was used to investigate dynamic parameters of the aptamer-MUC1.
September 20, 2017: Analyst
Jian Xu, Xixi Zhang, Shuanghai Zhou, Junjun Shen, Dawei Yang, Jing Wu, Xiaoyang Li, Meiling Li, Xiufen Huang, Joshua E Sealy, Munir Iqbal, Yongqing Li
Bovine herpesvirus 1 (BoHV-1) is an important pathogen of domestic and wild cattle responsible for major economic losses in dairy and beef industries throughout the world. Inhibition of viral entry plays a crucial role in the control of BoHV-1 infection and aptamers have been reported to inhibit viral replication. In this study, nine DNA aptamers that target BoHV-1 were generated using systemic evolution of ligands by exponential enrichment. Of the nine candidates, aptamer IBRV-A4 exhibited the highest affinity and specificity for BoHV-1, which bound to BoHV-1 with a Kd value of 3...
September 18, 2017: Scientific Reports
Bo-Tsang Huang, Wei-Yun Lai, Yi-Chung Chang, Jen-Wei Wang, Shauh-Der Yeh, Emily Pei-Ying Lin, Pan-Chyr Yang
The successful translation of cytotoxic T lymphocyte antigen-4 (CTLA-4) blockade has revolutionized the concept of cancer immunotherapy. Although monoclonal antibody therapeutics remain the mainstream in clinical practice, aptamers are synthetic oligonucleotides that encompass antibody-mimicking functions. Here, we report a novel high-affinity CTLA-4-antagonizing DNA aptamer (dissociation constant, 11.84 nM), aptCTLA-4, which was identified by cell-based SELEX and high-throughput sequencing. aptCTLA-4 is relatively stable in serum, promotes lymphocyte proliferation, and inhibits tumor growth in cell and animal models...
September 15, 2017: Molecular Therapy. Nucleic Acids
Glory Ranches, Melanie Lukasser, Herbert Schramek, Andreas Ploner, Taras Stasyk, Gert Mayer, Günter Mayer, Alexander Hüttenhofer
Chronic kidney disease (CKD) is a progressive pathological condition marked by a gradual loss of kidney function. Treatment of CKD is most effective when diagnosed at an early stage and patients are still asymptomatic. However, current diagnostic biomarkers (e.g., serum creatinine and urine albumin) are insufficient for prediction of the pathogenesis of the disease. To address this need, we applied a cell-SELEX (systematic evolution of ligands by exponential enrichment) approach and identified a series of DNA aptamers, which exhibit high affinity and selectivity for cytokine-stimulated cells, resembling some aspects of a CKD phenotype...
September 15, 2017: Molecular Therapy. Nucleic Acids
Mengmeng Zhao, Peilong Wang, Yajuan Guo, Lixu Wang, Fang Luo, Bin Qiu, Longhua Guo, Xiaoou Su, Zhenyu Lin, Guonan Chen
Aflatoxin B1 (AFB1) can cause great threat to human health, so the development of convenient and portable device for sensitive detection of AFB1 is highly desired. The portable pH meter has the characters of facile operation, low cost, and easy availability. Therefore, in this study, we investigate the applicability of utilizing a pH meter as the readout to develop a portable sensor for AFB1. The specific detection of AFB1 is realized via the combination of AFB1-responsive aptamer-cross-linked hydrogel. Upon the addition of AFB1, AFB1 binds to its aptamer with high affinity in lieu of aptamer/DNA complex, causing the collapse of hydrogel network and results in the releasing of urease into the solution...
January 1, 2018: Talanta
Ichiro Hirao, Michiko Kimoto, Kyung Hyun Lee
A novel aptamer generation method to greatly augment the affinity and stability of DNA aptamers was developed by genetic alphabet expansion combined with mini-hairpin DNA technology. The genetic alphabet expansion increases the physicochemical and structural diversities of DNA aptamers by introducing extra components, unnatural bases, as a fifth base, allowing for the enhancement of DNA aptamer affinities. Furthermore, the mini-hairpin DNA technology stabilizes DNA aptamers against nuclease digestion and thermal denaturation, by introducing an extraordinarily stable mini-hairpin DNA containing a GCGAAGC sequence...
September 12, 2017: Biochimie
Sofia G Meirinho, Luís G Dias, António M Peres, Lígia R Rodrigues
A DNA aptamer with affinity and specificity for human osteopontin (OPN), a potential breast cancer biomarker, was selected using the SELEX process, considering its homology rate and the stability of its secondary structures. This aptamer exhibited a satisfactory affinity towards OPN, showing dissociation constants lower than 2.5 nM. It was further used to develop a simple, label-free electrochemical aptasensor against OPN. The aptasensor showed good sensitivity towards OPN in standard solutions, being the square wave voltammetry (SWV), compared to the cyclic voltammetry, the most sensitive technique with detection and quantification limits of 1...
September 22, 2017: Analytica Chimica Acta
Chia-Chen Chang, Guoqing Wang, Tohru Takarada, Mizuo Maeda
A colorimetric method for fast, simple, and selective detection of Cu2+ was developed using I--mediated etching of triangular gold nanoplates (AuNPLs). The method was based on our finding that Cu2+ efficiently promoted this etching in the presence of SCN-. The etching process was accompanied by a dramatic color change from blue to red, allowing for visual and spectroscopic detection of Cu2+ with a detection limit of 10 μM and 1 μM, respectively. By incorporating molecular recognition by a DNA aptamer into this method, visual detection of chloramphenicol was also achieved with a detection limit of 5 μM...
September 14, 2017: ACS Applied Materials & Interfaces
Irina V Belyanina, Tatiana N Zamay, Galina S Zamay, Sergey S Zamay, Olga S Kolovskaya, Tatiana I Ivanchenko, Valery V Denisenko, Andrey K Kirichenko, Yury E Glazyrin, Irina V Garanzha, Valentina V Grigorieva, Alexandr V Shabanov, Dmitry V Veprintsev, Alexey E Sokolov, Vladimir M Sadovskii, Ana Gargaun, Maxim V Berezovski, Anna S Kichkailo
Biomedical applications of magnetic nanoparticles under the influence of a magnetic field have been proved useful beyond expectations in cancer therapy. Magnetic nanoparticles are effective heat mediators, drug nanocarriers, and contrast agents; various strategies have been suggested to selectively target tumor cancer cells. Our study presents magnetodynamic nanotherapy using DNA aptamer-functionalized 50 nm gold-coated magnetic nanoparticles exposed to a low frequency alternating magnetic field for selective elimination of tumor cells in vivo...
2017: Theranostics
Chengyi Li, Min Qian, Shanshan Wang, Huilin Jiang, Yilin Du, Jianxin Wang, Weiyue Lu, Niren Murthy, Rongqin Huang
In this report, we present a mesoporous carbon nanosphere that can target drugs to tumors and image tumor biomarkers. A single-strand DNA (P0 aptamer) aptavalve was capped on the surface of doxorubicin-loaded oxide mesoporous carbon nanospheres (Dox-OMCN-P0) through π-π stacking for real-time imaging-guided on-demand targeting drug delivery. The Dox-OMCN-P0 could not only realize the detection of MUC1 tumor marker with a wide linear range (0.1 - 10.6 μmol/L) and a low detection limit (17.5 nmol) based on different apparatuses, but also achieve in-situ targeting imaging of cellular MUC1 concentration in vitro and in vivo via "off-on" fluorescence biosensing...
2017: Theranostics
Meng Liu, Qingxin Yin, John D Brennan, Yingfu Li
Rapid and accurate diagnosis of Clostridium difficile infections (CDI) is crucial for patient treatment, infection control and epidemiological monitoring. As an important antigen, glutamate dehydrogenase (GDH) has been proposed as a preliminary screening test target for CDI. However, current assays based on GDH activity or GDH immunoassays have suboptimal sensitivity and specificity. Herein, we described the selection and characterization of single-stranded DNA aptamers that specifically targeted GDH. After 10 rounds of selection, high-throughput sequencing was used to identify enriched aptamer candidates...
September 4, 2017: Biochimie
Xiao Zhou, Xiaoye Su, Pravin Pathak, Ryan Vik, Brittany Vinciguerra, Lyle Isaacs, Janarthanan Jayawickramarajah
Host-guest complexes are emerging as powerful components in functional systems with applications ranging from materials to biomedicine. In particular, CB7 based host-guest complexes have received much attention for the controlled release of drugs due to the remarkable ability of CB7 toward binding input molecules in water with high affinity leading to displacement of CB7 from included pharmacophores (or from drug loaded porous particles). However, the release of bound guests from CB7 in response to endogenous biological molecules remains limited since the input biomolecule needs to have the appropriate chemical structure to bind tightly into the CB7 cavity...
September 7, 2017: Journal of the American Chemical Society
Huayi Shi, Na Chen, Yuanyuan Su, Houyu Wang, Yao He
Rapid, sensitive, and accurate detection of adenosine triphosphate (ATP), the primary energy molecule, is critical for the elucidation of its unique roles in cell signaling and many cellular reactions. Up to date, a major challenge is still remaining for fabricating surface-enhanced Raman scattering (SERS) aptamer sensors (aptasensors) suitable for accurate and reliable quantification of ATP. Herein, we develop the ratiometric silicon SERS aptasensor for ATP detection, which is made of uniform silver nanoparticles (Ag NPs)-modified silicon wafer (Ag NPs@Si), followed by the functionalization with double-stranded DNA (dsDNA I)...
September 21, 2017: Analytical Chemistry
Kazuki Hirose, Maho Tsuchida, Hinako Asakura, Koji Wakui, Keitaro Yoshimoto, Keisuke Iida, Makoto Sato, Masami Shibukawa, Masami Suganuma, Shingo Saito
A single-round DNA aptamer selection for mammalian cells was successfully achieved for the first time using a capillary electrophoresis (CE)-based methodology called polymer-enhanced capillary transient isotachophoresis (PectI). The PectI separation yielded a single peak for the human lung cancer cell line (PC-9) complexed with DNA aptamer candidates, which was effectively separated from a free randomized DNA library peak, ensuring no contamination from free DNA in the PC-9-DNA aptamer complex fraction. The DNA aptamer candidates obtained after a single-round selection employing counter selection with HL-60 were proven to bind selectively and form kinetically stable complexes with PC-9 cells...
September 6, 2017: Analyst
Yu Gu, Juan Song, Mei-Xing Li, Tingting Zhang, Wei Zhao, Jing-Juan Xu, Maili Liu, Hong-Yuan Chen
Quantification of trace serum circulate microRNAs is extremely important in clinical diagnosis but remains a great challenge. Herein we developed an ultra-sensitive platform for microRNA 141 (miR-141) detection based on a silver coated gold nanorods (Au@Ag NRs) etching process accompanied by surface plasmon resonance (SPR) shift. Both SPR absorption and scattering responses were monitored. Combined amplification cascades of catalyzed hairpin assembly (CHA) and hybridization chain reaction (HCR) with the sensitive SPR responses of plasmonic Au@Ag NRs, the proposed bioassay exhibited ultra-high sensitivity toward miRNA-141 with dynamic range from 5...
September 5, 2017: Analytical Chemistry
Jian Zhao, Keyao Tu, Yanlei Liu, Yulei Qin, Xiwei Wang, Lifeng Qi, Donglu Shi
Dual surfaced dumbbell-like gold magnetic nanoparticles (Au-Fe3O4) were synthesized for targeted aptamers delivery. Their unique biological properties were characterized as a smart photo-controlled drug carrier. DNA aptamers targeting vascular endothelial growth factor (VEGF) were assembled onto the surface of Au-Fe3O4 by electrostatic absorption. The binding capacity of the nanoparticles with VEGF aptamers was confirmed by gel electrophoresis. The targeted recognization of ovarian cancer cells by the aptamers-functionalized Au-Fe3O4 nanoparticles (Apt-Au-Fe3O4 NPs) was observed by confocal microscopy...
November 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
Feng Chen, Yi Liu, Rong Liao, Hang Gong, Chunyan Chen, Xiaoming Chen, Changqun Cai
This paper describes a reduced graphene oxide (RGO)-based resonance light-scattering (RLS) method for thrombin detection by using double strand DNA (dsDNA) as a binding element. dsDNA is obtained by hybridizing DNA1 and DNA2, which respectively consist of one aptamer of thrombin and the complementary strand of the other aptamer of thrombin. When thrombin is added, the specific binding of two aptamers to thrombin results in a complex (DNA1-thrombin-DNA2) and triggers the release of the complementary strand of two aptamers from dsDNA...
September 8, 2017: Analytica Chimica Acta
Gregory R Wiedman, Yanan Zhao, Arkady Mustaev, Jinglei Ping, Ramya Vishnubhotla, A T Charlie Johnson, David S Perlin
This technical report describes the development of an aptamer for sensing azole antifungal drugs during therapeutic drug monitoring. Modified synthetic evolution of ligands through exponential enrichment (SELEX) was used to discover a DNA aptamer recognizing azole class antifungal drugs. This aptamer undergoes a secondary structural change upon binding to its target molecule, as shown through fluorescence anisotropy-based binding measurements. Experiments using circular dichroism spectroscopy revealed a unique G-quadruplex structure that was essential and specific for binding to the azole antifungal target...
July 2017: MSphere
Yanyan Yu, Gaoxing Su, Hongyan Zhu, Qing Zhu, Yong Chen, Bohui Xu, Yuqin Li, Wei Zhang
In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR) for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes...
2017: International Journal of Nanomedicine
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