FEATURES OF ORGANOPHOSPHATES IMMOBILIZATION VIA STREPTAVIDIN-BIOTIN SYSTEM FOR EXPERIMENTS ON SELECTION OF APTAMERS

2020 ◽  
pp. 12-20
Author(s):  
D. A. Belinskaya ◽  
Yu. V. Chelusnova ◽  
V. V. Abzianidze ◽  
N. V. Goncharov
Keyword(s):  
Polyethylene Glycol ◽  
Organophosphorus Compounds ◽  
Binding Energies ◽  
Rna Aptamers ◽  
Main Method ◽  
Modeling Methods ◽  
Molecular Dynamics Methods ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Poisoning with organophosphorus compounds occupy one of the leading places in exotoxicosis. At the first stage, the detoxification of organophosphates can be provided with the help of DNA or RNA aptamers that bind the poison in the bloodstream. Currently, the main method of searching for aptamers is the experimental method of systematic evolution of ligands by exponential enrichment (SELEX). In the process of aptamer selection, the target molecule must be immobilized via the streptavidin-biotin complex. Since the poison molecule is small in size, to increase its availability for binding to aptamer, it is necessary to use a spacer between organophosphorus compounds and biotin. The aim of this work was to optimize the selection of aptamers for organophosphorus compounds by increasing the availability of a poison molecule immobilized via the streptavidin-biotin complex on the example of paraoxon. For this purpose, three spacers between organophosphorus compounds and biotin were tested using molecular modeling methods: three links of polyethylene glycol (3-PEG), four links of polyethylene glycol (4-PEG) and aminohexyl. The conformation of the biotinylated paraoxon complex with streptavidin and the interaction of paraoxon with the binding fragment of the aptamer were modeled using molecular docking and molecular dynamics methods. The ability of biotinylated paraoxon to bind to the aptamer has been evaluated by analyzing the surface area of the paraoxon available to the solvent, as well as by calculating the free binding energies. It has been shown that only in the case of aminohexyl immobilized paraoxon can contact the aptamer. At the final stage, the synthesis of paraoxon bound to biotin via aminohexyl was carried out.

Systematic Evolution of Ligands by Exponential Enrichment Selection of Specific Aptamer for Sensing of Methamphetamine

2013 ◽  
Vol 11 (3) ◽  
pp. 566-570 ◽  
Author(s):  
Mohsen Ebrahimi ◽  
Hossein Hamzeiy ◽  
Jaleh Barar ◽  
Abolfazl Barzegari ◽  
Yadollah Omidi
Keyword(s):  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Selection of aptamers specific for glycated hemoglobin and total hemoglobin using on-chip SELEX

Lab on a Chip ◽  
2015 ◽  
Vol 15 (2) ◽  
pp. 486-494 ◽  
Author(s):  
Hsin-I Lin ◽  
Ching-Chu Wu ◽  
Ching-Hsuan Yang ◽  
Ko-Wei Chang ◽  
Gwo-Bin Lee ◽  
...  
Keyword(s):  
Microfluidic Chip ◽  
Glycated Hemoglobin ◽  
Dna Aptamers ◽  
Single Stranded Dna ◽  
Total Hemoglobin ◽  
Systematic Evolution ◽  
On Chip ◽  
Exponential Enrichment ◽  
Selection Of

Selection of blood glycated hemoglobin (HbA1c)- and total hemoglobin (Hb)-specific single-stranded DNA aptamers was performed on a microfluidic chip to continuously and automatically carry out multiple rounds of systematic evolution of ligands by exponential enrichment (SELEX) processes.

scholarly journals Aptamers selection for platelets using droplet digital PCR

2021 ◽  
pp. 100-103
Author(s):  
A.V. Blagodatova ◽  
◽  
K.V. Kochkina ◽  
M.A. Komarova ◽  
N.Y. Trofina ◽  
...  
Keyword(s):  
Platelet Aggregation ◽  
Anticoagulant Activity ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Platelet Glycoprotein ◽  
Systematic Evolution ◽  
Selection For ◽  
Exponential Enrichment ◽  
Selection Of

The aim of the research. To obtain aptamers-inhibitors of platelet glycoprotein IIb / IIIa receptors, blocking platelet aggregation. Material and methods. Th e selection of aptamers for IIb / IIIa receptors of platelets was carried out according to the SELEX method (Systematic Evolution of Ligands by Exponential Enrichment), modifi ed to select aptamers for a specifi c epitope. Th e method allows selection and in vitro evolution of aptamers with selectivity to a specifi c target from a large library of oligonucleotides. Th e affi nity of aptamers for platelet IIb / IIIa receptors was determined using fl ow cytometry. Results. Pools of aptamers of aptamers with high affi nity for IIb / IIIa platelet receptors were obtained. Th e study of the antiaggregation properties of the pools with the best binding showed that platelet aggregation was minimal when using the aptamers from the pool of the 5th round of selection. Th us, the aptamers of this pool have the greatest potential to be used as an analogue of a synthetic peptide that blocks thromboaggregation. Aptamers from this pool were taken for sequencing in order to obtain sequences of aptamers with the best antiaggregatory properties. Conclusion. Pools of aptamers with high affi nity for IIb / IIIa receptors of platelets and anticoagulant activity were obtained.

scholarly journals In Silico Selection of Gp120 ssDNA Aptamer to HIV-1

2020 ◽  
Vol 25 (9) ◽  
pp. 1087-1093
Author(s):  
Hamideh Sepehri Zarandi ◽  
Mandana Behbahani ◽  
Hassan Mohabatkar
Keyword(s):  
In Silico ◽  
Dna Aptamer ◽  
Surface Glycoprotein ◽  
Aptamer Selection ◽  
Glycoprotein Gp120 ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Hiv 1 ◽  
Aptamer Sequence ◽  
Selection Of

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.

scholarly journals Magnetic Beads in Marine Toxin Detection: A Review

2019 ◽  
Vol 5 (4) ◽  
pp. 62 ◽  
Author(s):  
Greta Gaiani ◽  
Ciara K. O’Sullivan ◽  
Mònica Campàs
Keyword(s):  
Human Health ◽  
Magnetic Beads ◽  
Marine Toxins ◽  
Marine Toxin ◽  
Efficient Detection ◽  
Fish Samples ◽  
Systematic Evolution ◽  
Potential Impact ◽  
Exponential Enrichment ◽  
Selection Of

Due to the expanding occurrence of marine toxins, and their potential impact on human health, there is an increased need for tools for their rapid and efficient detection. We give an overview of the use of magnetic beads (MBs) for the detection of marine toxins in shellfish and fish samples, with an emphasis on their incorporation into electrochemical biosensors. The use of MBs as supports for the immobilization of toxins or antibodies, as signal amplifiers as well as for target pre-concentration, is reviewed. In addition, the exploitation of MBs in Systematic Evolution of Ligands by Exponential enrichment (SELEX) for the selection of aptamers is presented. These MB-based strategies have led to the development of sensitive, simple, reliable and robust analytical systems for the detection of toxins in natural samples, with applicability in seafood safety and human health protection.

scholarly journals Aptamer-iRNAs as Therapeutics for Cancer Treatment

2018 ◽  
Vol 11 (4) ◽  
pp. 108 ◽  
Author(s):  
Mario Soldevilla ◽  
Daniel Meraviglia-Crivelli de Caso ◽  
Ashwathi Menon ◽  
Fernando Pastor
Keyword(s):  
Cancer Therapy ◽  
Cancer Treatment ◽  
Antisense Oligonucleotides ◽  
Tertiary Structure ◽  
Potential Treatment ◽  
High Affinity ◽  
Different Types ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Aptamers are single-stranded oligonucleotides (ssDNA or ssRNA) that bind and recognize their targets with high affinity and specificity due to their complex tertiary structure. Aptamers are selected by a method called SELEX (Systematic Evolution of Ligands by EXponential enrichment). This method has allowed the selection of aptamers to different types of molecules. Since then, many aptamers have been described for the potential treatment of several diseases including cancer. It has been described over the last few years that aptamers represent a very useful tool as therapeutics, especially for cancer therapy. Aptamers, thanks to their intrinsic oligonucleotide nature, present inherent advantages over other molecules, such as cell-based products. Owing to their higher tissue penetrability, safer profile, and targeting capacity, aptamers are likely to become a novel platform for the delivery of many different types of therapeutic cargos. Here we focus the review on interfering RNAs (iRNAs) as aptamer-based targeting delivered agents. We have gathered the most reliable information on aptamers as targeting and carrier agents for the specific delivery of siRNAs, shRNA, microRNAs, and antisense oligonucleotides (ASOs) published in the last few years in the context of cancer therapy.

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