Defining the copper binding aptamotif and aptamer integrated recovery platform (AIRP)

Sekhon, Simranjeet Singh; Lee, Sang‐Hee; Lee, Kyeong-Ah; Min, Jiho; Lee, Byung-Tae; Kim, Kyoung-Woong; Ahn, Ji‐Young; Kim, Yang‐Hoon

doi:10.1039/c6nr09408b

Cited by 34 publications

(9 citation statements)

References 43 publications

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“…This implies that the cell specific aptamers were saturated and enriched during the SELEX processes. To further demonstrate the difference in binding ability round by round, we employed real-time PCR (RT-PCR), which proved valuable in validating the optimal state of DNA aptamer enrichment [ 20 ].…”

Section: Resultsmentioning

confidence: 99%

“…An aptamer is an artificial single-stranded oligonucleotide that can be specifically isolated through the Systematic Evolution of Ligands by exponential enrichment (SELEX) process and capable of recognizing a variety of targets in systemically designed detection platforms [ 17 , 18 , 19 , 20 ]. Some studies have reported ingenious efforts to combine the recognition ability of aptamers with advanced nanomaterials in the field of drug delivery and targeted therapeutics because of their strong stability under a wide range of temperature, pH and in-vivo/ex-vivo conditions [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

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Detecting and Discriminating Shigella sonnei Using an Aptamer-Based Fluorescent Biosensor Platform

et al. 2017

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In this paper, a Whole-Bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against Shigella sonnei. Real-time PCR amplification and post-SELEX experiment revealed that the selected aptmers possessed a high binding affinity and specificity for S. sonnei. Of the 21 aptamers tested, the C(t) values of the SS-3 and SS-4 aptamers (Ct = 13.89 and Ct = 12.23, respectively) had the lowest value compared to other aptamer candidates. The SS-3 and SS-4 aptamers also displayed a binding affinity (KD) of 39.32 ± 5.02 nM and 15.89 ± 1.77 nM, respectively. An aptamer-based fluorescent biosensor assay was designed to detect and discriminate S. sonnei cells using a sandwich complex pair of SS-3 and SS-4. The detection of S. sonnei by the aptamer based fluorescent biosensor platform consisted of three elements: (1) 5’amine-SS-4 modification in a 96-well type microtiter plate surface (N-oxysuccinimide, NOS) as capture probes; (2) the incubation with S. sonnei and test microbes in functionalized 96 assay wells in parallel; (3) the readout of fluorescent activity using a Cy5-labeled SS-3 aptamer as the detector. Our platform showed a significant ability to detect and discriminate S. sonnei from other enteric species such as E. coli, Salmonella typhimurium and other Shigella species (S. flexneri, S. boydii). In this study, we demonstrated the feasibility of an aptamer sensor platform to detect S. sonnei in a variety of foods and pave the way for its use in diagnosing shigellosis through multiple, portable designs.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detecting and Discriminating Shigella sonnei Using an Aptamer-Based Fluorescent Biosensor Platform

et al. 2017

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“… 20 − 23 Today, there are some chemiluminescence immunoassay (CLIA)-compliant diagnostic tests based on ASPH detection utilizing enzyme-linked immunosorbent assay (ELISA) to diagnose or monitor a series of cancers. 24 ASPH is also known as the target of immunohistochemical staining in some tumors including hepatocellular carcinoma, cholangiocarcinomas, and lung carcinoma. 21 , 25 − 28 Moreover, ASPH has recently attracted more attention as a potent target for tumor therapeutic applications.…”

Section: Introductionmentioning

confidence: 99%

Novel Approach to Overcome Defects of Cell-SELEX in Developing Aptamers against Aspartate β-Hydroxylase

et al. 2021

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Cell-based aptamer selection (Cell-SELEX) against predefined protein targets that benefits using the native form of the targets is the most promising approach to achieve aptamer probes capable of recognizing targets under both in vitro and in vivo conditions. The major disadvantages in Cell-SELEX are the imperfectness of the negative selection step and the lengthy procedure of selection. Here, we introduced the Counter-SELEX as part of our modified Cell-SELEX and implemented deep sequencing to overcome these shortcomings in developing aptamers against aspartate β-hydroxylase (ASPH) as a known tumor marker. In parallel with the conventional Cell-SELEX, five consecutive cycles of counter selection were accomplished using sequences bound to negative cells (the Counter-SELEX) to detect oligos that are not specific for ASPH. After high-throughput sequencing, the representative of each promising achieved family was subjected to further confirmatory analysis via flow cytometry, followed by the fluorescence immunostaining of histopathological sections. Implementing our innovative complementary method, annoying mis-selected sequences in Cell-SELEX enriched pools were effectively identified and removed. According to the affinity assay on the cells displaying ASPH, three aptamers, AP-Cell 1, AP-Cell 2, and AP-Cell 3, with K d values of 47.51, 39.38, and 65.23 nM, respectively, were obtained, while AP-Cell 1 and 3 could then successfully spot ASPH displayed on the tissues. Our study showed that the Counter-SELEX could be considered as a complementary method for Cell-SELEX to overcome the imperfectness of the negative selection step. Moreover, high-throughput nucleotide sequencing could help to shorten the overall process.

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“…In addition, easy chemical modifications, such as 5′ amine modification and Cy5-labeling, as well as the stability of aptamers, make them attractive agents [ 18 ]. Due to these advantages, aptamers are used in various fields, including imaging, drug delivery, and as biosensors [ 19 , 20 , 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection

Park

Cha

et al. 2020

Biosensors

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Aptamers are biomaterials that bind to a target molecule through a unique structure, and have high applicability in the diagnostic and medical fields. To effectively utilize aptamers, it is important to analyze the structure of the aptamer binding to the target molecule; however, there are difficulties in experimentally identifying this structure. In the modern pharmaceutical industry, computer-driven docking simulations that predict intermolecular binding models are used to select candidates that effectively bind target molecules. Botulinum toxin (BoNT) is the most poisonous neurotoxin produced from the Clostridium botulinum bacteria, and BoNT/C, one of the eight serotypes, causes paralysis in livestock. In this study, the aptamers that bound to BoNT/C were screened via the systematic evolution of ligands by exponential enrichment, and the binding affinity analysis and binding model were evaluated to select optimal aptamers. Based on surface plasmon resonance analysis and molecular operating environment docking simulation, a pair of aptamers that had high binding affinity to BoNT/C and were bound to different BoNT/C sites were selected. A sandwich assay based on this aptamer pair detected the BoNT/C protein to a concentration as low as ~0.2 ng Ml−1. These results show that docking simulations are a useful strategy for screening aptamers that bind to specific targets.

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Defining the copper binding aptamotif and aptamer integrated recovery platform (AIRP)

Cited by 34 publications

References 43 publications

Detecting and Discriminating Shigella sonnei Using an Aptamer-Based Fluorescent Biosensor Platform

Detecting and Discriminating Shigella sonnei Using an Aptamer-Based Fluorescent Biosensor Platform

Novel Approach to Overcome Defects of Cell-SELEX in Developing Aptamers against Aspartate β-Hydroxylase

Docking Simulation and Sandwich Assay for Aptamer-Based Botulinum Neurotoxin Type C Detection

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