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Dna aptamer

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https://www.readbyqxmd.com/read/28108354/abcs-of-dna-aptamer-and-related-assay-development
#1
REVIEW
Tarun Kumar Sharma, John G Bruno, Abhijeet Dhiman
This review is intended to guide the novice in aptamer research and development to understand virtually all of the aptamer development options and currently available assay modalities. Aptamer development topics range from discussions of basic and advanced versions of Systematic Evolution of Ligands by EXponential Enrichment (SELEX) and SELEX variations involving incorporation of exotic unnatural nucleotides to expand library diversity for even greater aptamer affinity and specificity to improved next generation methods of DNA sequencing, screening and tracking aptamer development throughout the SELEX process and characterization of lead aptamer candidates...
January 17, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28108313/the-hsp70-inhibiting-peptide-aptamer-a17-potentiates-radiosensitization-of-tumor-cells-by-hsp90-inhibition
#2
Daniela Schilling, Carmen Garrido, Stephanie Combs, Gabriele Multhoff
The inhibition of heat shock protein 90 (Hsp90) is a promising strategy to increase the radiosensitivity of tumor cells. However, Hsp90 inhibition induces the expression of Hsp70 which is a prominent cytoprotective protein. Therefore, dual targeting of Hsp70 and Hsp90 might be beneficial to increase the radiosensitivity of tumor cells. Hsp70 inhibiting peptide aptamers have been shown to increase the sensitivity of tumor cells to apoptosis induced by different anticancer drugs. Herein, we studied the radiosensitizing activity of the Hsp70 inhibiting peptide aptamer A17 in combination with the Hsp90 inhibitor NVP-AUY922...
January 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28107987/generation-of-biostable-l-aptamers-against-achiral-targets-by-chiral-inversion-of-existing-d-aptamers
#3
Huapei Chen, Sitao Xie, Hao Liang, Cuichen Wu, Liang Cui, Shuang-Yan Huan, Xiaobing Zhang
In this paper, based on reciprocal chiral substrate specificity, taking achiral molecules, ethanolamine (EA) and malachite green (MG) as two model targets, biostable L- DNA aptamers and L-RNA aptamers were generated respectively by chiral inversion of existing D-aptamers. In the detection of EA with L-DNA aptamer-based sensors, the feasibility of our strategy was confirmed, while in the detection of MG with L-RNA aptamers, linear calibration curves were obtained in the range from 0.1 to 5µm with the detection limit of 0...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107929/highly-sensitive-aptasensor-based-on-synergetic-catalysis-activity-of-mos2-au-he-composite-using-cdna-au-god-for-signal-amplification
#4
Hai-Yan Song, Tian-Fang Kang, Li-Ping Lu, Shui-Yuan Cheng
Single or few-layer nanosheets of MoS2 (MoS2 nanosheets) and a composite composed of MoS2 nanosheets, Au nanoparticles (AuNPs) and hemin (HE) (denoted as MoS2-Au-HE) were prepared. The composites possessed high synergetic catalysis activity towards the electroreduction of hydrogen peroxide. Furthermore, glucose oxidase (GOD) and AuNPs were used as marker of the complementary DNA (cDNA) strand of kanamycin aptamer to prepare a conjugate (reffered as cDNA-Au-GOD) that was designed as the signal probe. Both cDNA-Au-GOD and MoS2-Au-HE were applied to fabricate aptasensor for kanamycin...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28105835/silver-nanoclusters-beacon-as-stimuli-responsive-versatile-platform-for-multiplex-dnas-detection-and-aptamer-substrate-complexes-sensing
#5
Guoliang Liu, Jingjing Li, Da-Qian Feng, Jun-Jie Zhu, Wei Wang
An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28100695/mapping-the-affinity-landscape-of-thrombin-binding-aptamers-on-2-f-ana-dna-chimeric-g-quadruplex-microarrays
#6
Jory Lietard, Hala Abou Assi, Irene Gómez-Pinto, Carlos González, Mark M Somoza, Masad J Damha
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2'-Fluoroarabinonucleic acid (2'F-ANA) is a prime candidate for such use in microarrays. Indeed, 2'F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28094326/remission-of-lymphoblastic-leukaemia-in-an-intravascular-fluidic-environment-by-pliable-drug-carrier-with-a-sliding-target-ligand
#7
Donghyun Jang, Yeong Mi Lee, Jaehyun Lee, Junsang Doh, Won Jong Kim
A polyrotaxane-based nanoconstruct with pliable structure carrying a chemotherapeutic drug was developed for targeting circulating lymphoblastic leukaemia cells in a fluidic environment of blood vessels in vivo. By introducing lymphoblast targeting aptamer DNA through cyclodextrin, threaded in poly(ethylene glycol) as polyrotaxane, target aptamer slides along the long polymeric chain and actively search for target ligand, leading to active targeting in dynamic fluidic system which is enhanced by up to 6-fold compared with that of control carriers with non-sliding targeting ligands...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094182/dna-duplex-linker-for-afm-selex-of-dna-aptamer-against-human-serum-albumin
#8
Musashi Takenaka, Yuzo Okumura, Tomokazu Amino, Yusuke Miyachi, Chiaki Ogino, Akihiko Kondo
DNA-duplex interactions in thymines and adenins are used as a linker for the novel methodology of Atomic Force Microscope-Systematic Evolution of Ligands by EXpotential enrichment (AFM-SELEX). This study used the hydrogen bonds in 10 mer of both thymines (T10) and adenines (A10). Initially, the interactive force in T10-A10 was measured by AFM, which returned an average interactive force of approximately 350pN. Based on this result, DNA aptamers against human serum albumin could be selected in the 4th round, and 15 different clones could be sequenced...
January 7, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28089700/new-synthetic-route-to-ethynyl-dutp-a-means-to-avoid-formation-of-acetyl-and-chloro-vinyl-base-modified-triphosphates-that-could-poison-selex-experiments
#9
Pascal Röthlisberger, Fabienne Levi-Acobas, Marcel Hollenstein
5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified...
January 6, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28087261/dna-aptamer-probes-for-detection-of-estrogen-receptor-%C3%AE-positive-carcinomas
#10
Arghya Sett, Bibhuti Bhusan Borthakur, Jagannath Dev Sharma, Amal Chandra Kataki, Utpal Bora
Estrogen receptor alpha (ERα) which is a ligand-activated transcription factor also known as NR3A1 (nuclear receptor subfamily 3, group A, member 1). It is an important biomarker for breast cancer metastasis. In the present study, we report a novel DNA aptamer candidate against estrogen receptor (ER) alpha structure. The enriched aptamer candidate was obtained after 14 iterative cycles of in vitro protein-SELEX process. Isothermal calorimetry study suggests the nanomolar sensitivity of the candidate ER_Apt1 to its target protein...
December 25, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28063413/chronopotentiometric-sensing-of-specific-interactions-between-lysozyme-and-the-dna-aptamer
#11
Veronika Ostatná, Veronika Kasalová-Vargová, László Kékedy-Nagy, Hana Černocká, Elena E Ferapontova
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes...
December 23, 2016: Bioelectrochemistry
https://www.readbyqxmd.com/read/28051347/-in-house-production-of-single-stranded-oligodeoxyribonucleotides
#12
Allan R D Nunes, Suely F Chavante, Hugo A O Rocha, Daniel C F Lanza
The most widely used technique for the production of DNA aptamers/oligonucleotides is chemical synthesis. Despite its effectiveness, this technique cannot be performed "in house", making the user fully dependent on a supplier. In this work, we present a simplified method by which it is possible to enzymatically produce DNA aptamers "in house". This new method uses the rolling circle replication followed by a unique cleavage step using the SchI endonuclease. Potentially, any oligonucleotide can be produced by the enzymatic method proposed in this study...
January 4, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/28050975/modeling-the-microscopic-electrical-properties-of-thrombin-binding-aptamer-tba-for-label-free-biosensors
#13
Eleonora Alfinito, Lino Reggiani, Rosella Cataldo, Giorgio De Nunzio, Livia Giotta, Maria Rachele Guascito
Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors...
January 4, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28045140/precipitation-selex-identification-of-dna-aptamers-for-calcium-phosphate-materials-synthesis
#14
K R Baillargeon, K Meserve, S Faulkner, S Watson, H Butts, P Deighan, A E Gerdon
DNA aptamers that enhance calcium phosphate mineral formation were identified using a novel precipitation SELEX method. The evolved DNA library was substantially enriched in G nucleotides and in predicted G-quadruplex structures, suggesting their importance in the mechanism of mineralization. This work could readily be extended to provide additional novel DNA aptamers for materials synthesis.
January 3, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28045004/target-triggered-signal-turn-on-detection-of-prostate-specific-antigen-based-on-metal-enhanced-fluorescence-of-ag-sio2-sio2-rubpy-composite-nanoparticles
#15
Yun-Liang Deng, Dang-Dang Xu, Dai-Wen Pang, Hong-Wu Tang
A three-layer core-shell nanostructure consisting of a silver core, a silica spacer, and a fluorescent dye RuBpy-doped outer silica layer was fabricated, and the optimal metal-enhanced fluorescence (MEF) distance was explored through adjusting the thickness of the silica spacer. The results show that the optimal distance is ∼10.4 nm with the maximum fluorescence enhancement factor 2.12. Then a new target-triggered MEF 'turn-on' strategy based on the optimized composite nanoparticles was successfully constructed for quantitative detection of prostate specific antigen (PSA), by using RuBpy as the energy donor and BHQ-2 as the acceptor...
January 3, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28044095/using-modified-aptamers-for-site-specific-protein-aptamer-conjugations
#16
Ruowen Wang, Danqing Lu, Huarong Bai, Cheng Jin, Guobei Yan, Mao Ye, Liping Qiu, Rongshan Chang, Cheng Cui, Hao Liang, Weihong Tan
Conjugation of DNAs to defined locations on a protein surface will offer powerful tools for positioning functional groups and molecules in biological and biomedical studies. However, tagging protein with DNA is challenging in physiological environments, which requires a bioorthogonal approach. Here we report a chemical solution to selectively conjugate DNA aptamer with a protein by protein-aptamer template (PAT)-directed reactions. Since protein-aptamer interactions are bioorthogonal, we exploit PAT as a unique platform for specific DNA-protein cross-linking...
March 1, 2016: Chemical Science
https://www.readbyqxmd.com/read/28039562/long-shelf-life-of-a-lyophilized-dna-aptamer-beacon-assay
#17
John G Bruno
An aptamer beacon previously developed to detect C-telopeptide (CTx) from human bone collagen breakdown was lyophilized and shown to give a "lights on" concentration-dependent spectral fluorescence response essentially identical to that of the fresh reagent despite storage in a dark dry environment for the past 5.5 years.
December 30, 2016: Journal of Fluorescence
https://www.readbyqxmd.com/read/28033558/dna-sequence-functionalized-with-heterogeneous-core-satellite-nanoassembly-for-novel-energy-transfer-based-photoelectrochemical-bioanalysis
#18
Yuan-Cheng Zhu, Fei Xu, Nan Zhang, Wei-Wei Zhao, Jing-Juan Xu, Hong-Yuan Chen
This work reports the use of compositionally heterogeneous asymmetric Ag@Au core-satellite nanoassembly functionalized with DNA sequence as unique signaling nanoprobes for the realization of new energy-transfer-based photoelectrochemical (PEC) immunoassay of prostate- specific antigen (PSA). Specifically, the Ag@Au asymmetric core-satellite nanoassemblies (Ag@Au ACS) were fabricated on a two-dimensional glass substrate by a modified controlled assembly technique, and then functionalized with DNA sequences containing PSA aptamers as signaling nanoprobes...
December 20, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28009914/whole-cell-selex-of-aptamers-with-a-tyrosine-like-side-chain-against-live-bacteria
#19
Marleen Renders, Emily Miller, Curtis H Lam, David M Perrin
In an effort to expand the binding and recognition capabilities of aptamers, a nucleoside triphosphate modified with a phenol that mimics the side chain of tyrosine was used in the selection of DNA aptamers against live bacteria. Of multiple modified aptamers that were isolated against Escherichia coli DH5α cells, one aptamer displays high selectivity and affinity for the target cells and is greatly enriched for phenol-modified dU nucleotides (dU(y), 47.5%). When the same sequences are synthesized with TTP, no binding is observed...
December 22, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28008436/aptamer-tagged-dna-origami-for-spatially-addressable-detection-of-aflatoxin-b1
#20
Zhisong Lu, Ying Wang, Dan Xu, Lei Pang
A DNA origami-based platform for detecting aflatoxin B1 has been constructed with the assistance of aptamer probes and its complementary ssDNA-modified gold nanoparticles. This work may open new horizons for the application of DNA origami in the detection of a variety of small molecules.
December 23, 2016: Chemical Communications: Chem Comm
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