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1
Kimoto, Michiko, Yun Wei Shermane Lim, and Ichiro Hirao. "Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA." Nucleic Acids Research 47, no. 16 (August 8, 2019): 8362–74. http://dx.doi.org/10.1093/nar/gkz688.
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Abstract Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10−12 to 10−8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10−9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improved the lower-affinity aptamers’ applicabilities. These aptamer affinity rulers could be useful for evaluating and improving aptamer applicabilities.
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Ruff, Patrick, Rekha B. Pai, and Francesca Storici. "Real-Time PCR-Coupled CE-SELEX for DNA Aptamer Selection." ISRN Molecular Biology 2012 (August 8, 2012): 1–9. http://dx.doi.org/10.5402/2012/939083.
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Aptamers are short nucleic acid or peptide sequences capable of binding to a target molecule with high specificity and affinity. Also known as “artificial antibodies,” aptamers provide many advantages over antibodies. One of the major hurdles to aptamer isolation is the initial time and effort needed for selection. The systematic evolution of ligands by exponential enrichment (SELEX) is the traditional procedure for generating aptamers, but this process is lengthy and requires a large quantity of target and starting aptamer library. A relatively new procedure for generating aptamers using capillary electrophoresis (CE), known as CE-SELEX, is faster and more efficient than SELEX but requires laser-induced fluorescence (LIF) to detect the aptamer-target complexes. Here, we implemented an alternative system without LIF using real-time- (RT-) PCR to indirectly measure aptamer-target complexes. In three rounds of selection, as opposed to ten or more rounds common in SELEX protocols, a specific aptamer for bovine serum albumin (BSA) was obtained. The specificity of the aptamer to BSA was confirmed by electrophoretic mobility shift assays (EMSAs), an unlabeled competitor assay, and by a supershift assay. The system used here provides a cost effective and a highly efficient means of generating aptamers.
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Sakai, Yusuke, Md Sirajul Islam, Martyna Adamiak, Simon Chi-Chin Shiu, Julian Alexander Tanner, and Jonathan Gardiner Heddle. "DNA Aptamers for the Functionalisation of DNA Origami Nanostructures." Genes 9, no. 12 (November 23, 2018): 571. http://dx.doi.org/10.3390/genes9120571.
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DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.
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Yang, Darong, Xianghe Meng, Qinqin Yu, Li Xu, Ying Long, Bin Liu, Xiaohong Fang, and Haizhen Zhu. "Inhibition of Hepatitis C Virus Infection by DNA Aptamer against Envelope Protein." Antimicrobial Agents and Chemotherapy 57, no. 10 (July 22, 2013): 4937–44. http://dx.doi.org/10.1128/aac.00897-13.
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ABSTRACTHepatitis C virus (HCV) envelope protein (E1E2) is essential for virus binding to host cells. Aptamers have been demonstrated to have strong promising applications in drug development. In the current study, a cDNA fragment encoding the entire E1E2 gene of HCV was cloned. E1E2 protein was expressed and purified. Aptamers for E1E2 were selected by the method of selective evolution of ligands by exponential enrichment (SELEX), and the antiviral actions of the aptamers were examined. The mechanism of their antiviral activity was investigated. The data show that selected aptamers for E1E2 specifically recognize the recombinant E1E2 protein and E1E2 protein from HCV-infected cells. CD81 protein blocks the binding of aptamer E1E2-6 to E1E2 protein. Aptamers against E1E2 inhibit HCV infection in an infectious cell culture system although they have no effect on HCV replication in a replicon cell line. Beta interferon (IFN-β) and IFN-stimulated genes (ISGs) are not induced in virus-infected hepatocytes with aptamer treatment, suggesting that E1E2-specific aptamers do not induce innate immunity. E2 protein is essential for the inhibition of HCV infection by aptamer E1E2-6, and the aptamer binding sites are located in E2. Q412R within E1E2 is the major resistance substitution identified. The data indicate that an aptamer against E1E2 exerts its antiviral effects through inhibition of virus binding to host cells. Aptamers against E1E2 can be used with envelope protein to understand the mechanisms of HCV entry and fusion. The aptamers may hold promise for development as therapeutic drugs for hepatitis C patients.
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Moreno, Miguel, María Fernández-Algar, Javier Fernández-Chamorro, Jorge Ramajo, Encarnación Martínez-Salas, and Carlos Briones. "A Combined ELONA-(RT)qPCR Approach for Characterizing DNA and RNA Aptamers Selected against PCBP-2." Molecules 24, no. 7 (March 28, 2019): 1213. http://dx.doi.org/10.3390/molecules24071213.
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Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.
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Mao, Yu, Jimmy Gu, Dingran Chang, Lei Wang, Lili Yao, Qihui Ma, Zhaofeng Luo, Hao Qu, Yingfu Li, and Lei Zheng. "Evolution of a highly functional circular DNA aptamer in serum." Nucleic Acids Research 48, no. 19 (October 6, 2020): 10680–90. http://dx.doi.org/10.1093/nar/gkaa800.
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Abstract Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery of a circular aptamer, named CTBA4T-B1, that exhibits very high binding affinity (with a dissociation constant of 19 pM), excellent anticoagulation activity (with the half maximal inhibitory concentration of 90 pM) and high stability (with a half-life of 8 h) in human serum, highlighting the advantage of performing aptamer selection directly in the environment where the application is intended. CTBA4T-B1 is predicted to adopt a unique structural fold with a central two-tiered guanine quadruplex capped by two long stem–loops. This structural arrangement differs from all known thrombin binding linear DNA aptamers, demonstrating the added advantage of evolving aptamers from circular DNA libraries. The method described here permits the derivation of circular DNA aptamers directly in biological fluids and could potentially be adapted to generate other types of aptamers for therapeutic applications.
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Zavyalova, Elena, Valeriia Legatova, Rugiya Alieva, Arthur Zalevsky, Vadim Tashlitsky, Alexander Arutyunyan, and Alexey Kopylov. "Putative Mechanisms Underlying High Inhibitory Activities of Bimodular DNA Aptamers to Thrombin." Biomolecules 9, no. 2 (January 24, 2019): 41. http://dx.doi.org/10.3390/biom9020041.
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Nucleic acid aptamers are prospective molecular recognizing elements. Similar to antibodies, aptamers are capable of providing specific recognition due to their spatial structure. However, the apparent simplicity of oligonucleotide folding is often elusive, as there is a balance between several conformations and, in some cases, oligomeric structures. This research is focused on establishing a thermodynamic background and the conformational heterogeneity of aptamers taking a series of thrombin DNA aptamers having G-quadruplex and duplex modules as an example. A series of aptamers with similar modular structures was characterized with spectroscopic and chromatographic techniques, providing examples of the conformational homogeneity of aptamers with high inhibitory activity, as well as a mixture of monomeric and oligomeric species for aptamers with low inhibitory activity. Thermodynamic parameters for aptamer unfolding were calculated, and their correlation with aptamer functional activity was found. Detailed analysis of thrombin complexes with G-quadruplex aptamers bound to exosite I revealed the similarity of the interfaces of aptamers with drastically different affinities to thrombin. It could be suggested that there are some events during complex formation that have a larger impact on the affinity than the states of initial and final macromolecules. Possible mechanisms of the complex formation and a role of the duplex module in the association process are discussed.
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Bruno, John G. "Potential Use of Antifreeze DNA Aptamers for the Cryopreservation of Human Erythrocytes." Advanced Science, Engineering and Medicine 12, no. 7 (July 1, 2020): 870–74. http://dx.doi.org/10.1166/asem.2020.2628.
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This article summarizes proof of concept experiments which clearly demonstrated the ability of DNA aptamers selected against a molecular mimic of early ice crystal nuclei to protect the integrity of human erythrocytes following a slow freeze-thaw cycle. Following 10 cycles of selection and DNA amplification of rare candidate DNA aptamers against a copper-organic ligand complex which holds water molecules in a conformation resembling early ice crystal nuclei, the aptamers were tested for their ability to preserve erythrocyte morphology by phase-contrast microscopy versus controls without aptamers and with the original randomized aptamer DNA library template following slow freezing and storage overnight at -20 °C with slow thawing at 25 °C. Those experiments revealed that a minimum of 32 μg/ml of the final selected aptamer pool of DNA molecules was required to completely protect nearly 100% of the erythrocytes. By contrast, the treatment groups without the aptamers or with the randomized aptamer template DNA at 32 μg/ml produced only fragmented erythrocytes and cellular debris (no intact cells), thus indicating that specifically selected DNA conformations were required to bind and limit the size of forming ice crystals to cryoprotect the erythrocytes.
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Poturnayová, Alexandra, Maja Šnejdárková, and Tibor Hianik. "DNA aptamer configuration affects the sensitivity and binding kinetics of thrombin." Acta Chimica Slovaca 5, no. 1 (April 1, 2012): 53–58. http://dx.doi.org/10.2478/v10188-012-0009-z.
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DNA aptamer configuration affects the sensitivity and binding kinetics of thrombinThrombin is serine protease involved in the coagulation cascade, which converts soluble fibrinogen into insoluble strands of fibrin - a matrix of the blood clot formation. Development of the sensitive method of the thrombin detection in nanomolar level is important for clinical practice. In this work we applied acoustic thickness shear mode method (TSM) for study the binding of human thrombin depending on DNA aptamer configuration. We compared sensitivity of detection and binding kinetics of the thrombin to the conventional DNA aptamers and aptamer dimers immobilized at the surface of quartz crystal transducer. We have shown that aptasensors based on aptamer dimers more sensitively detect thrombin. The aptamer-thrombin complexes were also more stable as revealed from equilibrium dissociation constant,KD, that was 4 times lower for aptamer dimers in comparison with conventional aptamers. Determination of motional resistance,Rm, from acoustic impedance analysis allowed us to find important differences in physico-chemical properties of layers formed by conventional aptamers and aptamer dimers.
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Asadzadeh, Homayoun, Ali Moosavi, Georgios Alexandrakis, and Mohammad R. K. Mofrad. "Atomic Scale Interactions between RNA and DNA Aptamers with the TNF-α Protein." BioMed Research International 2021 (July 16, 2021): 1–11. http://dx.doi.org/10.1155/2021/9926128.
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Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.
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Lin, Jun Sheng, and Kenneth P. McNatty. "Aptamer-Based Regionally Protected PCR for Protein Detection." Clinical Chemistry 55, no. 9 (September 1, 2009): 1686–93. http://dx.doi.org/10.1373/clinchem.2009.127266.
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Abstract Background: DNA aptamers are single-stranded nucleotide sequences that bind specifically to target molecules. By combining the advantages of PCR for amplifying specific DNA sequences and aptamer technology, we have developed a new strategy to detect target molecules such as proteins. Methods: Ovine follicle-stimulating hormone α subunit (oFSHα) was used as the model protein to generate a specific DNA aptamer via an in vitro evolutionary process. A targeted regional-mapping approach and a target-capturing assay were used to identify the binding region on the aptamer molecule. In the detection assay, referred to as “aptamer-based regionally protected PCR” (ARP-PCR), the aptamer was allowed to bind to the target protein in solution before digestion with DNase I. The region of the aptamer bound to the target was protected from DNase I cleavage. The target-binding region of the aptamer protected from the enzymatic treatment was then amplified by the PCR. Results: Aptamers against oFSHα were generated. Six sequences of 20 selected aptamer clones were identical. This aptamer sequence was divided into 4 regions according to the aptamer’s secondary structure. From examination of the target-binding ability of each region, we determined the specific binding region, for which primers were designed. With the aptamer and primers to detect oFSHα by means of the ARP-PCR method, we were able to detect the target protein at concentrations as low as 10−14 mol/L. Conclusions: Combining the use of a DNA aptamer with the PCR is a potentially useful analytic tool for detection of proteins at low concentrations. .
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Sullivan, Richard, Mary Catherine Adams, Rajesh R. Naik, and Valeria T. Milam. "Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS." Molecules 24, no. 8 (April 21, 2019): 1572. http://dx.doi.org/10.3390/molecules24081572.
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In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.
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Schilling-Loeffler, Katja, Rachel Rodriguez, and Jacquelina Williams-Woods. "Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers." International Journal of Molecular Sciences 22, no. 16 (August 18, 2021): 8868. http://dx.doi.org/10.3390/ijms22168868.
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Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.
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Solovarov, I. S., M. A. Khasnatinov, N. A. Liapunova, I. G. Kondratov, and G. A. Danchinova. "Development of DNA aptamer selection approach based on membrane ultrafiltration of aptamer/target complex." Acta Biomedica Scientifica 7, no. 6 (December 29, 2022): 119–27. http://dx.doi.org/10.29413/abs.2022-7.6.12.
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Background. Aptamers are small single-stranded DNA or RNA molecules that have an affinity for a specific target molecule. The main method of aptamers construction is the technology of systematic evolution of ligands with exponential enrichment (SELEX). However, the exact approach depends on the nature of target molecules, and is selected and optimized by each researcher independently. The article describes the technique of production of aptamers to the tick-borne encephalitis virus (TBEV) using membrane ultrafiltration with a molecular weight cut-off of 100 kDa. As a result, the pool of aptamers with observable affinity for TBEV is successfully selected and enriched.The aim. To develop the technique suitable for selection of specific DNA aptamers to a live, crude TBEV suspension directly in cell culture supernatant.Materials and methods. The selection of aptamers was carried out using a modified SELEX DNA aptamer technology in combination with semipermeable membrane ultrafiltration using Vivaspin 6 (Sartorius, Germany) concentrators of molecular weight cut-off of 100 kDa. Enrichment of a specific pool of aptamers was performed using real time polymerase chain reaction. Aptamers were sequenced with automated Sanger sequencing method. The direct virucidal effect of the aptamers was determined by the decrease in the titer of the infectious virus after incubation with the aptamer.Results. The pool of aptamers to TBEV was selected and enriched. This aptamer pool expressed affinity both to the infectious TBEV and to the TBEV antigen. Sixteen aptamers were sequenced from this pool and four of them were synthesized and tested for antiviral activity against TBEV. No antiviral activity was observed.Conclusions. The technique developed that can be successfully used to select aptamers to a live virus culture for the viruses comparable in size to TBEV or larger.
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Andrianova, Mariia, and Alexander Kuznetsov. "Logic Gates Based on DNA Aptamers." Pharmaceuticals 13, no. 11 (November 23, 2020): 417. http://dx.doi.org/10.3390/ph13110417.
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DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.
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Lu, Chang, Anand Lopez, Jinkai Zheng, and Juewen Liu. "Using the Intrinsic Fluorescence of DNA to Characterize Aptamer Binding." Molecules 27, no. 22 (November 12, 2022): 7809. http://dx.doi.org/10.3390/molecules27227809.
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The reliable, readily accessible and label-free measurement of aptamer binding remains a challenge in the field. Recent reports have shown large changes in the intrinsic fluorescence of DNA upon the formation of G-quadruplex and i-motif structures. In this work, we examined whether DNA intrinsic fluorescence can be used for studying aptamer binding. First, DNA hybridization resulted in a drop in the fluorescence, which was observed for A30/T30 and a 24-mer random DNA sequence. Next, a series of DNA aptamers were studied. Cortisol and Hg2+ induced fluorescence increases for their respective aptamers. For the cortisol aptamer, the length of the terminal stem needs to be short to produce a fluorescence change. However, caffeine and adenosine failed to produce a fluorescence change, regardless of the stem length. Overall, using the intrinsic fluorescence of DNA may be a reliable and accessible method to study a limited number of aptamers that can produce fluorescence changes.
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Kohlberger, Michael, Sabrina Wildner, Christof Regl, Christian G. Huber, and Gabriele Gadermaier. "Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies." PLOS ONE 15, no. 11 (November 5, 2020): e0241560. http://dx.doi.org/10.1371/journal.pone.0241560.
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The monoclonal anti-CD20 IgG1 antibody rituximab is used as a first-line treatment for B cell lymphoma. Like all therapeutic antibodies, it is a complex protein for which both safety and efficacy heavily depend on the integrity of its three-dimensional structure. Aptamers, short oligonucleotides with a distinct fold, can be used to detect minor modifications or structural variations of a molecule or protein. To detect antibody molecules in a fold state occurring prior to protein precipitation, we generated DNA aptamers that were selected for extensively heat-treated rituximab. Using the magnetic bead-based systematic evolution of ligands by exponential enrichment (SELEX), we obtained six DNA aptamer sequences (40-mers) specific for 80°C heat-treated rituximab. In silico fold prediction and circular dichroism analysis revealed a G-quadruplex structure for one aptamer, while all others exhibited a B-DNA helix. Binding affinities ranging from 8.8–86.7 nM were determined by an enzyme-linked apta-sorbent assay (ELASA). Aptamers additionally detected structural changes in rituximab treated for 5 min at 70°C, although with lower binding activity. Notably, none of the aptamers recognized rituximab in its native state nor did they detect the antibody after it was exposed to lower temperatures or different physical stressors. Aptamers also reacted with the therapeutic antibody adalimumab incubated at 80°C suggesting similar aptamer binding motifs located on extensively heat-treated IgG1 antibodies. Within this work, we obtained the first aptamer panel, which is specific for an antibody fold state specifically present prior to protein aggregation. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals.
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Hosseini, Seyed Mohammad Hasan, Mohammad Reza Bassami, Alireza Haghparast, Mojtaba Sankian, and Gholamreza Hashemi Tabar. "Identification of Aptamers that Specifically Bind to A1 Antigen by Performing Cell-on Human Erythrocytes." Galen Medical Journal 9 (June 27, 2020): 1657. http://dx.doi.org/10.31661/gmj.v9i0.1657.
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Background: The apply of aptamers as a new generation’s way to probe diagnostic for the detection of target molecules has gained ground. Aptamers can be used as alternatives to diagnostic antibodies for detection of blood groups due to their unique features. This study was aimed to produce DNA diagnostic aptamer detecting the antigen of A1 blood group using the Cell-Selex method. Materials and Methods: DNA aptamer was isolated against A1 RBC antigen after ten stages of Cell-Selex and amplification by an asymmetric polymerase chain reaction. The progress of the stages of selection was evaluated using flow cytometry analysis, which the DNA aptamer isolated from the tenth cycle with an affinity of 70% fluorescent intensity, was selected from four positive colonies followed by determination of the sequences and secondary structures. Results: The aptameric sequence obtained from C4 cloning was calculated with the highest binding affinity to A1 antigen having an apparent dissociation constant (Kd value) of at least 29.5 ± 4.3 Pmol, which was introduced as the selected aptamer-based on ΔG obtained from a colony of C4 equal to –13.13. Conclusion: The aptamer obtained from using Cell-Selex method could be used as an example for the development of diagnostic tools such as biosensors for detecting A1 blood group antigens. [GMJ.2020;9:e1657]
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Siddiqui, Saika, and Jie Yuan. "Binding Characteristics Study of DNA based Aptamers for E. coli O157:H7." Molecules 26, no. 1 (January 3, 2021): 204. http://dx.doi.org/10.3390/molecules26010204.
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E. coli O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for E. coli O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (Kd) and binding capacity (Bmax) of DNA-based aptamers for E. coli O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to E. coli 157:H7 and the highest specificity over non-pathogenic E. coli strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5′ end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg2+ ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1.
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Gariepy, Jean, Ismat Khatri, Reginald Gorczynski, Ashley Young, Lindsay Woo, Chung-Wai Chow, Marzena Cydzik, and Aaron Prodeus. "A cross species CD200R1 immune checkpoint agonist with potent anti-inflammatory properties." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 194.24. http://dx.doi.org/10.4049/jimmunol.198.supp.194.24.
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Abstract Functional aptamers displaying agonistic or antagonistic properties are showing great promise in terms of modulating immune responses. Our group has recently developed pegylated DNA aptamers that can either block inflammatory responses (CD200R1agonist) or restore tumor-directed immune responses (PD-1 antagonist) in vivo. Here, we report the derivation and design of a cross species mouse/human CD200R1 DNA aptamer agonist that blocks inflammatory responses in mouse models of skin graft rejection and asthma. This DNA aptamer was discovered by performing NGS and comparing the resulting aptamer motifs derived from independently screening mouse and human CD200R1 as targets. Importantly, this m/hCD200R1 agonistic aptamer does not suppress cytotoxic T-lymphocyte (CTL) induction in 5 day allo-mixed lymphocyte cultures (MLCs) derived from CD200R1 knockout mice, indicating that its mode of action is directly linked to CD200R1 activation. This study suggests that one can derive agonistic DNA aptamers that can be verified as immunomodulators in mouse models with outcomes translatable to the treatment of human conditions.
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Alkhamis, Obtin, Weijuan Yang, Rifat Farhana, Haixiang Yu, and Yi Xiao. "Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease." Nucleic Acids Research 48, no. 20 (October 14, 2020): e120-e120. http://dx.doi.org/10.1093/nar/gkaa849.
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Abstract In vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.
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Mallikaratchy, Prabodhika, Alessandro Ruggiero, William Maguire, Kelly Piersanti, Jeffrey Gardner, Carlos Villa, Freddy Escorcia, et al. "Multivalent DNA Aptamer-Based Therapeutic Agents for Lymphoma and Leukemia." Blood 114, no. 22 (November 20, 2009): 2711. http://dx.doi.org/10.1182/blood.v114.22.2711.2711.
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Abstract Abstract 2711 Poster Board II-687 Non-Hodgkins lymphomas affect 450,000 patients in the United States and even with recent advances in antibody-based therapies; more than 20,000 people will die of their disease annually. The goal of this work was to develop a high affinity, stable aptamer selective for B-cell leukemias and lymphomas. Aptamers are small DNA molecules that have the ability to bind to proteins with high affinity and specificity. They are also ideal candidates as therapeutic carriers. Aptamer binding is based on the ability of small oligonucleotide polymers (typically 20–80mers) to fold into unique three-dimensional structures that can interact with a specific target. Based on nature of this interaction, aptamers could be considered to be antibody analogs. Compared to antibodies however, one of the inherent properties of aptamers is that their small size (typically 10–20,000 daltons for aptamers vs 150,000 daltons for antibodies,) might address some difficult pharmacologic issues of antibodies, which penetrate slowly into tumors and clear the blood slowly. Recently, the TDO5 aptamer was identified and it was found to bind to membrane bound human IgM, a component of the BCR complex in B-Cell neoplasms. In contrast to currently available monoclonal antibodies, TD05 binds to membrane bound human IgM only and not with soluble IgM, eliminating the possibility of competitive inhibition by soluble IgM in the serum. The specificity of the aptamer was confirmed by screening with 24 cell lines and fresh clinical leukemia samples. Out of 24 cell lines, the IgM-negative cells, including T-cell leukemias and solid tumor lines such as breast, kidney, and colon and ovarian, showed no binding with TD05 indicating there is no non-specific adhesion with cell lines. One of the challenges of using the current form of TD05 as a drug carrier is that it is not yet suitable for use in vivo because of low avidity (>10uM) and stability (t ½= 1min) at physiological conditions. In order to increase the affinity of this aptamer, a new truncated multivalent and nuclease stable aptamer was designed. First, truncation of the original version of TD05 was considered because reduced size may lead to more efficient chemical syntheses and better pharmacologic properties. The resulting TD05.1 has a 5-fold increased affinity compared to original version of TD05. Second, bivalent (BV) aptamers utilizing TD05.1 with various polyethylene glycol (PEG) linker lengths were designed. Linker length is critical in designing multivalent aptamers to avoid loss of binding due to steric hindrance and to optimize the binding geometry, both of which would affect binding affinity. An optimal linker length of ∼16nm was chosen after empiric binding studies. Nuclease stability was also addressed by the introduction of chemical functionalities into TD05.1. The introduction of non-natural bases such as LNA bases (Locked Nucleic Acids), have been demonstrated to be effective in this regard. The stability of LNA stems from the bicyclic furanose unit locked in a sugar conformation. In order to retain the specific recognition and 3-dimensional nature of the aptamer's folding, LNA analogues were only introduced at the regions that are not involved in binding. Additionally, to further improve nuclease resistance, increase circulation time in vivo and to prevent non-specific adhesion to serum proteins and cells, the LNA modified BV aptamer TD05.1 was modified with polyethylene glycol at the 3' and 5' ends. The introduction of LNA and polyethylene glycol further stabilized the secondary structure, increasing the affinity and nuclease resistance in serum from one minute to seven hours(t ½> 420 min). We then constructed a trivalent analog of the aptamer with multiple functionalities, including chelators and fluorophores, which showed ∼25-fold higher affinity compared to monomeric aptamer at physiological conditions. In conclusion, this study demonstrates the development of a trivalent, high affinity aptamer selective for the membrane bound human IgM found in B-cell leukemias and lymphoma. Studies to assess the biological activity and the use of this construct as a drug carrier to treat B-NHL and B-CLL are in progress. Disclosures: No relevant conflicts of interest to declare.
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Wang, Zhong, Xiuying Yang, Nicholas Zhou Lee, and Xudong Cao. "Multivalent Aptamer Approach: Designs, Strategies, and Applications." Micromachines 13, no. 3 (March 12, 2022): 436. http://dx.doi.org/10.3390/mi13030436.
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Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.
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Sepehri Zarandi, Hamideh, Mandana Behbahani, and Hassan Mohabatkar. "In Silico Selection of Gp120 ssDNA Aptamer to HIV-1." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 9 (May 26, 2020): 1087–93. http://dx.doi.org/10.1177/2472555220923331.
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Nucleic acid aptamers that specifically bind to other molecules are mostly obtained through the systematic evolution of ligands by exponential enrichment (SELEX). Because SELEX is a time-consuming procedure, the in silico design of specific aptamers has recently become a progressive approach. HIV-1 surface glycoprotein gp120, which is involved in the early stages of HIV-1 infection, is an attractive target for RNA and DNA aptamer selection. In this study, four single-stranded DNA aptamers, referred to as HD2, HD3, HD4, and HD5, that had the ability of HIV-1 inhibition were designed in silico. In a proposed non-SELEX approach, some parts of the B40 aptamer sequence, which interacted with gp120, were isolated and considered as a separate aptamer sequence. Then, to obtain the best docking scores of the HDOCK server and Hex software, some modifications, insertions, and deletions were applied to each selected sequence. Finally, the cytotoxicity and HIV inhibition of the selected aptamers were evaluated experimentally. Results demonstrated that the selected aptamers could inhibit HIV-1 infection by up to 80%, without any cytotoxicity. Therefore, this new non-SELEX approach could be considered a simple, fast, and efficient method for aptamer selection.
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Zhang, Li, and John C. Chaput. "In Vitro Selection of an ATP-Binding TNA Aptamer." Molecules 25, no. 18 (September 13, 2020): 4194. http://dx.doi.org/10.3390/molecules25184194.
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Recent advances in polymerase engineering have made it possible to isolate aptamers from libraries of synthetic genetic polymers (XNAs) with backbone structures that are distinct from those found in nature. However, nearly all of the XNA aptamers produced thus far have been generated against protein targets, raising significant questions about the ability of XNA aptamers to recognize small molecule targets. Here, we report the evolution of an ATP-binding aptamer composed entirely of α-L-threose nucleic acid (TNA). A chemically synthesized version of the best aptamer sequence shows high affinity to ATP and strong specificity against other naturally occurring ribonucleotide triphosphates. Unlike its DNA and RNA counterparts that are susceptible to nuclease digestion, the ATP-binding TNA aptamer exhibits high biological stability against hydrolytic enzymes that rapidly degrade DNA and RNA. Based on these findings, we suggest that TNA aptamers could find widespread use as molecular recognition elements in diagnostic and therapeutic applications that require high biological stability.
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Lorenzo-Gómez, Ramón, Daniel González-Robles, Rebeca Miranda-Castro, Noemí de-los-Santos-Álvarez, and María Jesús Lobo-Castañón. "On the Electrochemical Detection of Alpha-Fetoprotein Using Aptamers: DNA Isothermal Amplification Strategies to Improve the Performance of Weak Aptamers." Biosensors 10, no. 5 (April 30, 2020): 46. http://dx.doi.org/10.3390/bios10050046.
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Affinity characterization is essential to develop reliable aptamers for tumor biomarker detection. For alpha-fetoprotein (AFP), a biomarker of hepatocellular carcinoma (HCC), two DNA aptamers were described with very different affinity. In this work, we estimate the dissociation constant of both of them by means of a direct assay on magnetic beads modified with AFP and electrochemical detection on carbon screen-printed electrodes (SPCE). Unlike previous works, both aptamers showed similar dissociation constant (Kd) values, in the subµM range. In order to improve the performance of these aptamers, we proposed the isothermal amplification of the aptamers by both terminal deoxynucleotidyl transferase (TdT) and rolling circle amplification (RCA). Both DNA amplifications improved the sensitivity and also the apparent binding constants from 713 nM to 189 nM for the short aptamer and from 526 nM to 32 nM for the long aptamer. This improvement depends on the true affinity of the binding pair, which ultimately limits the analytical usefulness.
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Morais, Liliane Monteiro de, Thiago Santos Chaves, Marco Alberto Medeiros, Kaique Alves Brayner Pereira, Patrícia Barbosa Jurgilas, Sheila Maria Barbosa de Lima, Sotiris Missailidis, and Ana Maria Bispo de Filippis. "Selection and Characterization of Single-Stranded DNA Aptamers of Diagnostic Potential against the Whole Zika Virus." Viruses 14, no. 9 (August 25, 2022): 1867. http://dx.doi.org/10.3390/v14091867.
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Zika virus became a major public health problem in early 2015, when cases of Guillain–Barré syndrome and microcephaly were associated with viral infection. Currently, ZIKV is endemic in all tropical areas of the world, and the chance for future Zika epidemics remains very real and accurate diagnosis is crucial. The aim of this work was to select specific ssDNA aptamers that bind to the entire Zika virus and can be used to compose specific diagnostics, without cross-reactivity with other flaviviruses. Zika virus was cultivated in Vero cells and used as a target for aptamer selection. Aptamers specific for the ZIKV were selected using whole-virus SELEX, with counterselection for other flavivirus. Secondary and tertiary structures were evaluated and the molecular anchoring between the aptamers and target were simulated by the HDOCK server. Aptamer interaction was evaluated by ELISA/ELASA and the dissociation constant (Kd) was calculated by thermophoresis. Four ZIKV-specific aptamers were selected. The best two were further characterized and proved to be specific for ZIKV. Aptamers are capable of binding specifically to the ZIKV and differentiate from Dengue virus. The aptamers selected in this work can be used as capture agents in the composition of diagnostic tests to specifically detect ZIKV infection.
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Kato, Teru, Ippei Shimada, Ryota Kimura, and Masumi Hyuga. "Light-up fluorophore–DNA aptamer pair for label-free turn-on aptamer sensors." Chemical Communications 52, no. 21 (2016): 4041–44. http://dx.doi.org/10.1039/c5cc08816j.
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A DNA aptamer binding to the environment-sensitive fluorophore, dapoxyl, which increased the fluorescence upon binding, was selected and used to construct aptamer sensors by fusion with analyte-binding DNA aptamers.
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Tsukakoshi, Kaori, Yasuko Yamagishi, Mana Kanazashi, Kenta Nakama, Daiki Oshikawa, Nasa Savory, Akimasa Matsugami, et al. "G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol." Nucleic Acids Research 49, no. 11 (June 7, 2021): 6069–81. http://dx.doi.org/10.1093/nar/gkab388.
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Abstract Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Beyer, Stefan, Wendy U. Dittmer, Andreas Reuter, and Friedrich C. Simmel. "Controlled Release of Thrombin Using Aptamer-Based Nanodevices." Advances in Science and Technology 53 (October 2006): 116–21. http://dx.doi.org/10.4028/www.scientific.net/ast.53.116.
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Aptamers are DNA or RNA single strands that have been selected from random pools based on their ability to bind ligands. Like antibodies, aptamers are highly specific to their targets, and thus have many potential uses in biomedicine and biotechnology. We report here on the construction of a protein-binding molecular device based on a DNA aptamer, which can be instructed to hold or release the human blood-clotting factor, α-thrombin, depending on an operator DNA sequence addressing it. In the operation of this DNA nanodevice, the thrombin-binding DNA aptamer is switched between a binding and a non-binding form. This is achieved by sequentially hybridizing and removing a DNA single strand to the protein binding region of the aptamer. This principle of operation is limited as the switching sequence is determined by the protein-binding sequence. To overcome this limitation we introduce a DNA signal translation device that allows the operation of aptamers with arbitrary sequences. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences.
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Liu, Xiangzhong, Jing Hu, Yu Ning, Haijia Xu, Hantao Cai, Aofei Yang, Zhengshuai Shi, and Zhanghua Li. "Aptamer Technology and Its Applications in Bone Diseases." Cell Transplantation 32 (January 2023): 096368972211449. http://dx.doi.org/10.1177/09636897221144949.
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Aptamers are single-stranded nucleic acids (DNA, short RNA, or other artificial molecules) produced by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, which can be tightly and specifically combined with desired targets. As a comparable alternative to antibodies, aptamers have many advantages over traditional antibodies such as a strong chemical stability and rapid bulk production. In addition, aptamers can bind targets in various ways, and are not limited like the antigen–antibody combination. Studies have shown that aptamers have tremendous potential to diagnose and treat clinical diseases. However, only a few aptamer-based drugs have been used because of limitations of the aptamers and SELEX technology. To promote the development and applications of aptamers, we present a review of the methods optimizing the SELEX technology and modifying aptamers to boost the selection success rate and improve aptamer characteristics. In addition, we review the application of aptamers to treat bone diseases.
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Nurul Amilia, Bugi Ratno Budiarto, Apon Zaenal Mustopa, Tegar Aprilian, Baso Manguntungi, and Endang Saepudin. "Isolation of DNA Aptamers for Enteropathogenic Escherichia coli (EPEC) Detection using Bacterial-SELEX Approach." HAYATI Journal of Biosciences 29, no. 6 (July 6, 2022): 789–98. http://dx.doi.org/10.4308/hjb.29.6.789-798.
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Enteropathogenic Escherichia coli (EPEC) is a Gram-negative pathogenic bacterium that causes diarrheal disease, especially in infants and children. Aptamers are short chain oligonucleotides that have high affinity, specificity, and selectivity to their targets, which have potential to be developed as a method for diagnosing pathogens. In this study, aptamer was isolated through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method using whole cells bacteria (Bacterial-SELEX) for recognizing pathogenic E. coli EPEC K1.1 which was isolated from children with diarrhea in Indonesia. Ten rounds of bacterial-SELEX procedure were conducted with modification conditions by using Top10, DH5a E. coli cells, Listeria monocytogenes, and Lactobacillus plantarum S34 as counter-selections. The selection process was started with a pool of ssDNA random library consisting of a random base with 40-nucleotides long flanked with fixed primers sequence for aptamer amplification purpose. Short single-stranded DNA amplification was done by symmetric and asymmetric PCR. The highly enriched oligonucleotide pools (pooled 8, 9, and 10) were cloned and the resulting ssDNA aptamers were identified by Sanger DNA sequencing. Finally, twelve aptamers with unique sequences and various secondary structures including G-quadruplex sequence motif within aptamers were obtained as candidates specific aptamer for detection and capturing of EPEC K1.1.
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Hanžek, Antonija, Frédéric Ducongé, Christian Siatka, and Anne-Cécile Duc. "Identification and Characterization of Aptamers Targeting Ovarian Cancer Biomarker Human Epididymis Protein 4 for the Application in Urine." Cancers 15, no. 2 (January 10, 2023): 452. http://dx.doi.org/10.3390/cancers15020452.
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Ovarian cancer is the deadliest gynecological cancer. With non-specific symptoms of the disease and the lack of effective diagnostic methods, late diagnosis remains the crucial hurdle of the poor prognosis. Therefore, development of novel diagnostic approaches are needed. The purpose of this study is to develop DNA-based aptamers as potential diagnostic probes to detect ovarian cancer biomarker Human epididymis protein 4 (HE4) in urine. HE4 is a protein overexpressed in ovarian cancer, but not in healthy or benign conditions. With high stability and diagnostic value for detection of ovarian cancer, urine HE4 appears as an attractive non-invasive biomarker. The high-affinity anti-HE4 DNA aptamers were selected through 10 cycles of High Fidelity Systematic Evolution of Ligands by EXponential enrichment (Hi-Fi SELEX), a method for aptamer selection based on digital droplet PCR. The anti-HE4 aptamers were identified using DNA sequencing and bioinformatics analysis. The candidate aptamer probes were characterized in urine for binding to HE4 protein using thermofluorimetry. Two anti-HE4 aptamers, AHE1 and AHE3, displayed binding to HE4 protein in urine, with a constant of dissociation in the nanomolar range, with Kd (AHE1) = 87 ± 9 nM and Kd (AHE3) aptamer of 127 ± 28 nM. Therefore, these aptamers could be promising tools for application in diagnostics and future development of urine tests or biosensors for ovarian cancer.
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Li, Ting, Fengjiao Yao, Yacong An, Xundou Li, Jinhong Duan, and Xian-Da Yang. "Novel Complex of PD-L1 Aptamer and Holliday Junction Enhances Antitumor Efficacy in Vivo." Molecules 26, no. 4 (February 18, 2021): 1067. http://dx.doi.org/10.3390/molecules26041067.
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Blocking the PD-1/PD-L1 pathway can diminish immunosuppression and enhance anticancer immunity. PD-1/PD-L1 blockade can be realized by aptamers, which have good biocompatibility and can be synthesized in quantity economically. For in vivo applications, aptamers need to evade renal clearance and nuclease digestion. Here we investigated whether DNA nanostructures could be used to enhance the function of PD-L1 aptamers. Four PD-L1 aptamers (Apt) were built into a Holliday Junction (HJ) to form a tetravalent DNA nanostructure (Apt-HJ). The average size of Apt-HJ was 13.22 nm, which was above the threshold for renal clearance. Apt-HJ also underwent partial phosphorothioate modification and had improved nuclease resistance. Compared with the monovalent PD-L1 aptamer, the tetravalent Apt-HJ had stronger affinity to CT26 colon cancer cells. Moreover, Apt-HJ markedly boosted the antitumor efficacy in vivo vs. free PD-L1 aptamers without raising systemic toxicity. The results indicate that multiple aptamers attached to a DNA nanostructure may significantly improve the function of PD-L1 aptamers in vivo.
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Tang, Zhiwen, Parag Parekh, Pete Turner, Richard W. Moyer, and Weihong Tan. "Generating Aptamers for Recognition of Virus-Infected Cells." Clinical Chemistry 55, no. 4 (April 1, 2009): 813–22. http://dx.doi.org/10.1373/clinchem.2008.113514.
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Abstract Background: The development of molecular probes capable of recognizing virus-infected cells is essential to meet the serious clinical, therapeutic, and national-security challenges confronting virology today. We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. Methods: To create aptamer probes capable of recognizing virus-infected cells, we used cell-SELEX (systematic evolution of ligands via exponential enrichment), which uses intact infected live cells as targets for aptamer selection. In this study, vaccinia virus–infected and –uninfected lung cancer A549 cells were chosen to develop our model probes. Results: A panel of aptamers has been evolved by means of the infected cell–SELEX procedure. The results demonstrate that the aptamers bind selectively to vaccinia virus–infected A549 cells with apparent equilibrium dissociation constants in the nanomolar range. In addition, these aptamers can specifically recognize a variety of target infected cell lines. The aptamers’ target is most likely a viral protein located on the cell surface. Conclusions: The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell–SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells.
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Trinh, Kien Hong, Ulhas Sopanrao Kadam, Jinnan Song, Yuhan Cho, Chang Ho Kang, Kyun Oh Lee, Chae Oh Lim, Woo Sik Chung, and Jong Chan Hong. "Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion." International Journal of Molecular Sciences 22, no. 19 (October 7, 2021): 10846. http://dx.doi.org/10.3390/ijms221910846.
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Fenitrothion is an insecticide belonging to the organophosphate family of pesticides that is widely used around the world in agriculture and living environments. Today, it is one of the most hazardous chemicals that causes severe environmental pollution. However, detection of fenitrothion residues in the environment is considered a significant challenge due to the small molecule nature of the insecticide and lack of molecular recognition elements that can detect it with high specificity. We performed in vitro selection experiments using the SELEX process to isolate the DNA aptamers that can bind to fenitrothion. We found that newly discovered DNA aptamers have a strong ability to distinguish fenitrothion from other organophosphate insecticides (non-specific targets). Furthermore, we identified a fenitrothion-specific aptamer; FenA2, that can interact with Thioflavin T (ThT) to produce a label-free detection mode with a Kd of 33.57 nM (9.30 ppb) and LOD of 14 nM (3.88 ppb). Additionally, the FenA2 aptamer exhibited very low cross-reactivity with non-specific targets. This is the first report showing an aptamer sensor with a G4-quadruplex-like structure to detect fenitrothion. Moreover, these aptamers have the potential to be further developed into analytical tools for real-time detection of fenitrothion from a wide range of samples.
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Van Riesen, Abigail J., Kaila L. Fadock, Prashant S. Deore, Ahmed Desoky, Richard A. Manderville, Shahin Sowlati-Hashjin, and Stacey D. Wetmore. "Manipulation of a DNA aptamer–protein binding site through arylation of internal guanine residues." Organic & Biomolecular Chemistry 16, no. 20 (2018): 3831–40. http://dx.doi.org/10.1039/c8ob00704g.
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Chemically modified aptamers have the opportunity to increase aptamer target binding affinity and provide structure–activity relationships to enhance our understanding of molecular target recognition by the aptamer fold.
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Gan, Zixuen, Muhamad Aidilfitri Mohamad Roslan, Mohd Yunus Abd Shukor, Murni Halim, Nur Adeela Yasid, Jaafar Abdullah, Ina Salwany Md Yasin, and Helmi Wasoh. "Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application." Biosensors 12, no. 11 (October 25, 2022): 922. http://dx.doi.org/10.3390/bios12110922.
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Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.
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Santosh, Baby, and Pramod K. Yadava. "Nucleic Acid Aptamers: Research Tools in Disease Diagnostics and Therapeutics." BioMed Research International 2014 (2014): 1–13. http://dx.doi.org/10.1155/2014/540451.
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Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.
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Hassanzadeh, Leila, Suxiang Chen, and Rakesh Veedu. "Radiolabeling of Nucleic Acid Aptamers for Highly Sensitive Disease-Specific Molecular Imaging." Pharmaceuticals 11, no. 4 (October 15, 2018): 106. http://dx.doi.org/10.3390/ph11040106.
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Aptamers are short single-stranded DNA or RNA oligonucleotide ligand molecules with a unique three-dimensional shape, capable of binding to a defined molecular target with high affinity and specificity. Since their discovery, aptamers have been developed for various applications, including molecular imaging, particularly nuclear imaging that holds the highest potential for the clinical translation of aptamer-based molecular imaging probes. Their easy laboratory production without any batch-to-batch variations, their high stability, their small size with no immunogenicity and toxicity, and their flexibility to incorporate various functionalities without compromising the target binding affinity and specificity make aptamers an attractive class of targeted-imaging agents. Aptamer technology has been utilized in nuclear medicine imaging techniques, such as single photon emission computed tomography (SPECT) and positron emission tomography (PET), as highly sensitive and accurate biomedical imaging modalities towards clinical diagnostic applications. However, for aptamer-targeted PET and SPECT imaging, conjugation of appropriate radionuclides to aptamers is crucial. This review summarizes various strategies to link the radionuclides to chemically modified aptamers to accomplish aptamer-targeted PET and SPECT imaging.
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Yuan, Shuofeng, Naru Zhang, Kailash Singh, Huiping Shuai, Hin Chu, Jie Zhou, Billy K. C. Chow, and Bo-Jian Zheng. "Cross-Protection of Influenza A Virus Infection by a DNA Aptamer Targeting the PA Endonuclease Domain." Antimicrobial Agents and Chemotherapy 59, no. 7 (April 27, 2015): 4082–93. http://dx.doi.org/10.1128/aac.00306-15.
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ABSTRACTAmino acid residues in the N-terminal of the PA subunit (PAN) of the influenza A virus polymerase play critical roles in endonuclease activity, protein stability, and viral RNA (vRNA) promoter binding. In addition, PANis highly conserved among different subtypes of influenza virus, which suggests PANto be a desired target in the development of anti-influenza agents. We selected DNA aptamers targeting the intact PA protein or the PANdomain of an H5N1 virus strain using systematic evolution of ligands by exponential enrichment (SELEX). The binding affinities of selected aptamers were measured, followed by an evaluation ofin vitroendonuclease inhibitory activity. Next, the antiviral effects of enriched aptamers against influenza A virus infections were examined. A total of three aptamers targeting PA and six aptamers targeting PANwere selected. Our data demonstrated that all three PA-selected aptamers neither inhibited endonuclease activity nor exhibited antiviral efficacy, whereas four of the six PAN-selected aptamers inhibited both endonuclease activity and H5N1 virus infection. Among the four effective aptamers, one exhibited cross-protection against infections of H1N1, H5N1, H7N7, and H7N9 influenza viruses, with a 50% inhibitory concentration (IC50) of around 10 nM. Notably, this aptamer was identified at the 5th round but disappeared after the 10th round of selection, suggesting that the identification and evaluation of aptamers at early rounds of selection may be highly helpful for screening effective aptamers. Overall, our study provides novel insights for screening and developing effective aptamers for use as anti-influenza drugs.
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Aljohani, Maher M., Dana Cialla-May, Jürgen Popp, Raja Chinnappan, Khaled Al-Kattan, and Mohammed Zourob. "Aptamers: Potential Diagnostic and Therapeutic Agents for Blood Diseases." Molecules 27, no. 2 (January 7, 2022): 383. http://dx.doi.org/10.3390/molecules27020383.
Full textAbstract:
Aptamers are RNA/DNA oligonucleotide molecules that specifically bind to a targeted complementary molecule. As potential recognition elements with promising diagnostic and therapeutic applications, aptamers, such as monoclonal antibodies, could provide many treatment and diagnostic options for blood diseases. Aptamers present several superior features over antibodies, including a simple in vitro selection and production, ease of modification and conjugation, high stability, and low immunogenicity. Emerging as promising alternatives to antibodies, aptamers could overcome the present limitations of monoclonal antibody therapy to provide novel diagnostic, therapeutic, and preventive treatments for blood diseases. Researchers in several biomedical areas, such as biomarker detection, diagnosis, imaging, and targeted therapy, have widely investigated aptamers, and several aptamers have been developed over the past two decades. One of these is the pegaptanib sodium injection, an aptamer-based therapeutic that functions as an anti-angiogenic medicine, and it is the first aptamer approved by the U.S. Food and Drug Administration (FDA) for therapeutic use. Several other aptamers are now in clinical trials. In this review, we highlight the current state of aptamers in the clinical trial program and introduce some promising aptamers currently in pre-clinical development for blood diseases.
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Vázquez-González, Margarita, and Itamar Willner. "Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications." International Journal of Molecular Sciences 22, no. 4 (February 11, 2021): 1803. http://dx.doi.org/10.3390/ijms22041803.
Full textAbstract:
Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions “nucleoapzymes”. In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.
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Kumar Kulabhusan, Prabir, Babar Hussain, and Meral Yüce. "Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents." Pharmaceutics 12, no. 7 (July 9, 2020): 646. http://dx.doi.org/10.3390/pharmaceutics12070646.
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Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.
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Oliveira, Ricardo, Eva Pinho, Ana Luísa Sousa, Óscar Dias, Nuno Filipe Azevedo, and Carina Almeida. "Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking." PLOS ONE 17, no. 3 (March 23, 2022): e0264701. http://dx.doi.org/10.1371/journal.pone.0264701.
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Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures. Such conformation is crucial for aptamers’ ability to bind to a target with high affinity and specificity. Unnatural nucleotides have been used to develop nucleic acid mimic (NAM) aptamers with increased performance, such as biological stability. Prior knowledge of aptamer-target interactions is critical for applying post-SELEX modifications with unnatural nucleotides since it can affect aptamers’ structure and performance. Here, we describe an easy-to-apply in silico workflow using free available software / web servers to predict the tertiary conformation of NAM, DNA and RNA aptamers, as well as the docking with the target molecule. Representative 2ʹ-O-methyl (2ʹOMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. All aptamers’ tertiary structure and docking models were successfully predicted with good structural similarity to the experimental data. Thus, this workflow will boost the development of aptamers, particularly NAM aptamers, by assisting in the rational modification of specific nucleotides and avoiding trial-and-error approaches.
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Chen, Xinhuan, Yangyang Zhang, Yanli Shi, Tingting Niu, Bo Li, Linyan Guo, Yan Qiao, Jimin Zhao, Baoyin Yuan, and Kangdong Liu. "Evolution of DNA aptamers against esophageal squamous cell carcinoma using cell-SELEX." Analyst 146, no. 13 (2021): 4180–87. http://dx.doi.org/10.1039/d1an00634g.
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Trunzo, Nevina E., and Ka Lok Hong. "Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications." International Journal of Molecular Sciences 21, no. 14 (July 18, 2020): 5074. http://dx.doi.org/10.3390/ijms21145074.
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Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.
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Morita, Yoshihiro, Macall Leslie, Hiroyasu Kameyama, David Volk, and Takemi Tanaka. "Aptamer Therapeutics in Cancer: Current and Future." Cancers 10, no. 3 (March 19, 2018): 80. http://dx.doi.org/10.3390/cancers10030080.
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Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.
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Ratanabunyong, Siriluk, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee, and Kiattawee Choowongkomon. "Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase." Molecules 27, no. 1 (January 3, 2022): 285. http://dx.doi.org/10.3390/molecules27010285.
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The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 μM and 0.15–2 μM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT.
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Nahar, Nusrat, Ridwan Bin Rashid, and Mohammad Sharifur Rahman. "Applications of Aptamers in Medicine: A Mini Review." Bangladesh Pharmaceutical Journal 20, no. 1 (April 5, 2017): 99–104. http://dx.doi.org/10.3329/bpj.v20i1.32099.
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Aptamers are single-stranded DNA or RNA molecules that bind to its target with high affinity and specificity. Nucleic acid aptamers are an attractive class of carrier molecules because of their tissue penetration capability, high chemical flexibility, low immunogenicity, low toxicity and cost effective production. These characteristics make aptamers an alternative to the antibody. An aptamer can be developed for the treatment of age-related macular degeneracy disease, blood clotting, cancer and auto-immune diseases etc. Macugen is so far the only aptamer-based drug that received FDA approval. Cancer patients are treated by targeting two proteins named nucleolin and CXCL12. Targeted delivery of aptamers has been successfully developed that reduce the occurrence of the unwanted off-target effects. Aptamers are susceptible to renal filtration and endonuclease cleavage. Conjugation with PEG or cholesterol and chemical modification can decrease renal clearance and increase serum stability.Bangladesh Pharmaceutical Journal 20(1): 99-104, 2017