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Dna aptamer

Marzieh Jafari, Mohsen Rezaei, Heibatullah Kalantari, Maryam Tabarzad, Bahram Daraei
DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and Aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to difference between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive Aflatoxin B1 DNA based biosensors...
March 22, 2017: Biotechnology and Applied Biochemistry
Galina S Zamay, Tatiana I Ivanchenko, Tatiana N Zamay, Valentina L Grigorieva, Yury E Glazyrin, Olga S Kolovskaya, Irina V Garanzha, Andrey A Barinov, Alexey V Krat, Gleb G Mironov, Ana Gargaun, Dmitry V Veprintsev, Sergey S Bekuzarov, Andrey K Kirichenko, Ruslan A Zukov, Marina M Petrova, Andrey A Modestov, Maxim V Berezovski, Anna S Zamay
Nucleic acid aptamers are becoming popular as molecular probes for identification and imaging pathology and, at the same time, as a convenient platform for targeted therapy. Recent studies have shown that aptamers may be effectively used for tumor characterization and as commercially available monoclonal antibodies. Here we present three DNA aptamers binding to whole transformed lung cancer tissues, including tumor cells, connective tissues, and blood vessels. Protein targets have been revealed using affinity purification followed by mass spectrometry analyses, and they have been validated using a panel of correspondent antibodies and 3D imaging of tumor tissues...
March 17, 2017: Molecular Therapy. Nucleic Acids
Nicholas G Welch, Judith A Scoble, Benjamin W Muir, Paul J Pigram
Orientation of surface immobilized capture proteins, such as antibodies, plays a critical role in the performance of immunoassays. The sensitivity of immunodiagnostic procedures is dependent on presentation of the antibody, with optimum performance requiring the antigen binding sites be directed toward the solution phase. This review describes the most recent methods for oriented antibody immobilization and the characterization techniques employed for investigation of the antibody state. The introduction describes the importance of oriented antibodies for maximizing biosensor capabilities...
March 16, 2017: Biointerphases
Cristina Romero-López, Alfredo Berzal-Herranz
Aptamers are short DNA or RNA oligonucleotides specialized in the specific and efficient binding to a target molecule. They are obtained by in vitro selection or evolution processes. It was in 1990 that two independent research groups described the bases of a new in vitro technology for the identification of RNA molecules able to specifically bind to a target [1,2]. Tuerk and Gold established the principals of the in vitro selection process that was named SELEX (Systematic Evolution of Ligands by Exponential enrichment), which is based on iterative cycles of binding, partitioning, and amplification of oligonucleotides from a pool of variant sequences [2]...
March 16, 2017: Pharmaceuticals
Mohammad Ramezani, Khalil Abnous, Seyed Mohammad Taghdisi
Detection and quantitation of antibiotic residues in blood serum and foodstuffs are in great demand. We have developed aptasensors for detection of streptomycin using electrochemical and optical methods. In the first method, an electrochemical aptasensor was developed for sensitive and selective detection of streptomycin, based on combination of exonuclease I (Exo I), complementary strand of aptamer (CS), arch shaped structure of aptamer (Apt)-CS conjugate, and gold electrode. The designed electrochemical aptasensor exhibited high selectivity toward streptomycin with a limit of detection (LOD) as low as 11...
2017: Methods in Molecular Biology
Yanbin Li, Ronghui Wang
Aptamers are single-stranded RNA or DNA oligonucleotides which have specific three-dimensional (3D) structures for high affinity and specific recognition to their target. In diagnostic and detection assays, aptamers represent an alternative to antibodies as recognition agents and offer advantages, such as reduced cost, rapid and reproducible synthesis, controllable modification, and improved stability. Aptamers are favorably used in biosensors as sensitive and selective bio-receptors coupled with a variety of transducers such as optical, mass-sensitive, and electrochemical sensors, the so-called aptasensors...
2017: Methods in Molecular Biology
Sai Wang, Liqin Zhang, Shuo Wan, Sena Cansiz, Cheng Cui, Yuan Liu, Ren Cai, Chengyi Hong, I-Ting Teng, Muling Shi, Yuan Wu, Yiyang Dong, Weihong Tan
Exosomes are extracellular vesicles (50-100 nm) circulating in biofluids as intercellular signal transmitters. Although the potential of cancerous exosomes as tumor biomarkers is promising, sensitive and rapid detection of exosomes remains challenging. Herein, we combined the strengths of advanced aptamer technology, DNA-based nanostructure, and portable electrochemical devices to develop a nanotetrahedron (NTH)-assisted aptasensor for direct capture and detection of hepatocellular exosomes. The oriented immobilization of aptamers significantly improved the accessibility of an artificial nucleobase-containing aptamer to suspended exosomes, and the NTH-assisted aptasensor could detect exosomes with 100-fold higher sensitivity when compared to the single-stranded aptamer-functionalized aptasensor...
March 20, 2017: ACS Nano
Xinya Jiang, Haijun Wang, Huijun Wang, Ying Zhuo, Ruo Yuan, Yaqin Chai
Herein, we fabricated a novel electrochemiluminescence (ECL) biosensor for ultrasensitive detection of mucin 1 (MUC1) based on a three-dimensional (3-D) DNA nanomachine signal probe powered by protein-aptamer binding complex. The assembly of 3-D DNA nanomachine signal probe achieved the cyclic reuse of target protein based on the protein-aptamer binding complex induced catalyzed hairpin assembly (CHA), which overcame the shortcoming of protein conversion with enzyme cleavage or polymerization in the traditional examination of protein...
March 20, 2017: Analytical Chemistry
Debapriya Mazumdar, Tian Lan, Yi Lu
Real-time, on-site detection and quantification of different trace analytes is a challenge that requires both searching a general class of molecules to recognize a broad range of contaminants and translating this recognition to easily detectable signals. Functional nucleic acids, which include DNAzymes (DNA with catalytic activity) and aptamers (nucleic acids that bind an analyte), are ideal candidates for the target recognition. These nucleic acids can be selected by a combinatorial biology method called in vitro selection to interact with a particular analyte with high specificity and sensitivity...
2017: Methods in Molecular Biology
Delia J Scoville, Tae Kyu Brian Uhm, Jamie A Shallcross, Rebecca J Whelan
CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman's risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides...
2017: Journal of Nucleic Acids
E Goux, E Dausse, V Guieu, L Azéma, G Durand, M Henry, L Choisnard, J-J Toulmé, C Ravelet, E Peyrin
Herein, we report a novel approach for the design of a colorimetric aptasensor based on functionalized gold nanoparticle probes. This approach relies on the conjugation of nanoparticles by two functional DNA and RNA hairpins that engage specific kissing (loop-loop) interactions in response to the addition of a small analyte ligand, leading to particle aggregation and then red-to-purple colour change of the colloidal solution.
March 9, 2017: Nanoscale
Min Young Song, Dung Nguyen, Seok Won Hong, Byoung Chan Kim
Conventional cell-SELEX aims to isolate aptamers to a single unique target bacteria species. We propose a method to isolate single-stranded DNA aptamers that have broad reactivity to multiple bacterial targets belonging to different genera. The key of the proposed method is that targets of interest are changed sequentially at each SELEX round. The general scheme was examined using six bacteria from different genera, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Citrobacter freundii, Bacillus subtilis, and Staphylococcus epidermidis (four gram-negative and two gram-positive bacteria)...
March 8, 2017: Scientific Reports
Wenjing Bi, Xue Bai, Fan Gao, Congcong Lu, Ye Wang, Guijin Zhai, Shanshan Tian, Enguo Fan, YuKui Zhang, Kai Zhang
Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and non-covalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-crosslinking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another comple-mentary DNA with a photo-active group and reporter group was modified as capture probe (CP)...
March 7, 2017: Analytical Chemistry
Bharat N Gawande, John C Rohloff, Jeffrey D Carter, Ira von Carlowitz, Chi Zhang, Daniel J Schneider, Nebojsa Janjic
The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid-like modifications on both pyrimidine bases...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
Shimaa Eissa, Mohammed Zourob
This article reports a novel aptamer-based impedimetric detection of carbendazim, a commonly used benzimidazole fungicide in agriculture. High affinity and specificity DNA aptamers against carbendazim were successfully selected using systematic evolution of ligand by exponential enrichment (SELEX). The dissociation constants (Kds) of the selected DNA aptamers after 10 in vitro selection cycles were characterized using fluorescence-based assays showing values in the nanomolar range. The aptamer which showed the highest degree of affinity and conformation change was used to fabricate an electrochemical aptasensor via self-assembly of thiol-modified aptamer on gold electrodes...
March 7, 2017: Analytical Chemistry
Aozhe Zhang, Dingran Chang, Zijian Zhang, Fan Li, Weihong Li, Xu Wang, Yingfu Li, Qian Hua
Geniposide is a key iridoid glycoside from Gardenia jasminoides fructus widely used in traditional Chinese herbal medicine. However, detection of this small molecule represents a significant challenge mostly due to the lack of specific molecular recognition elements. In this study, we have performed in vitro selection experiments to isolate DNA aptamers that can specifically bind geniposide. Using a stringent selection procedure, we have isolated DNA aptamers that can distinguish geniposide from genipin and glucose, two structural analogs of geniposide...
February 28, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Brian J F Swift, Jared A Shadish, Cole A DeForest, François Baneyx
Combining bioorthogonal chemistry with the use of proteins engineered with adhesive and morphogenetic solid-binding peptides is a promising route for synthesizing hybrid materials with the economy and efficiency of living systems. Using optical sensing of chloramphenicol as a proof of concept, we show here that a GFP variant engineered with zinc sulfide and silica-binding peptides on opposite sides of its β-barrel supports the fabrication of protein-capped ZnS:Mn nanocrystals that exhibit the combined emission signatures of organic and inorganic fluorophores...
March 13, 2017: Journal of the American Chemical Society
Hirotaka Minagawa, Kentaro Onodera, Hiroto Fujita, Taiichi Sakamoto, Joe Akitomi, Naoto Kaneko, Ikuo Shiratori, Masayasu Kuwahara, Katsunori Horii, Iwao Waga
We have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers' attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated...
March 3, 2017: Scientific Reports
Heidi-Kristin Walter, Jens Bauer, Jeannine Steinmeyer, Akinori Kuzuya, Christof M Niemeyer, Hans-Achim Wagenknecht
A split aptamer for adenosine triphosphate (ATP) was embedded as a recognition unit into two levers of a nanomechanical DNA origami construct by extension and modification of selected staple strands. An additional optical module in the stem of the split aptamer comprised two different cyanine-styryl dyes that underwent an energy transfer from green (donor) to red (acceptor) emission if two ATP molecules were bound as target molecule to the recognition module and thereby brought the dyes in close proximity. As a result, the ATP as a target triggered the DNA origami shape transition and yielded a fluorescence color change from green to red as readout...
March 8, 2017: Nano Letters
Feng Zhang, Alexandra Correia, Ermei Mäkilä, Wei Li, Jarno Salonen, Jouni J Hirvonen, Hongbo Zhang, Hélder A Santos
Negatively charged surface-modified drug delivery systems are promising for in vivo applications as they have more tendency to accumulate in tumor tissues. However, the inefficient cell uptake of these systems restricts their final therapeutic performance. Here, we have fabricated a receptor-mediated surface charge inversion nanoparticle made of undecylenic acid modified, thermally hydrocarbonized porous silicon (UnTHCPSi) nanoparticles core and sequentially modified with polyethylenimine (PEI), methotrexate (MTX), and DNA aptamer AS1411 (herein termed as UnTHCPSi-PEI-MTX@AS1411) for enhancing the cell uptake of nucleolin-positive cells...
March 22, 2017: ACS Applied Materials & Interfaces
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