Capillary Electrophoresis–Systematic Evolution of Ligands by Exponential Enrichment Selection of Base- and Sugar-Modified DNA Aptamers: Target Binding Dominated by 2′-O,4′-C-Methylene-Bridged/Locked Nucleic Acid Primer

2013 ◽  
Vol 85 (10) ◽  
pp. 4961-4967 ◽  
Author(s):  
Yuuya Kasahara ◽  
Yuuta Irisawa ◽  
Hiroto Fujita ◽  
Aiko Yahara ◽  
Hiroaki Ozaki ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Dna Aptamers ◽  
Modified Dna ◽  
Systematic Evolution ◽  
Target Binding ◽  
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.

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.

A single-round selection of selective DNA aptamers for mammalian cells by polymer-enhanced capillary transient isotachophoresis

The Analyst ◽  
2017 ◽  
Vol 142 (21) ◽  
pp. 4030-4038 ◽  
Author(s):  
Kazuki Hirose ◽  
Maho Tsuchida ◽  
Hinako Asakura ◽  
Koji Wakui ◽  
Keitaro Yoshimoto ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Mammalian Cells ◽  
Dna Aptamer ◽  
Dna Aptamers ◽  
Aptamer Selection ◽  
Selection For ◽  
First Time ◽  
Selection Of

A single-round DNA aptamer selection for mammalian cells was successfully achieved for the first time using a capillary electrophoresis (CE)-based methodology.

scholarly journals G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3781 ◽  
Author(s):  
Carolina Roxo ◽  
Weronika Kotkowiak ◽  
Anna Pasternak
Keyword(s):  
Nucleic Acid ◽  
Production Costs ◽  
Biological Processes ◽  
Disease Treatment ◽  
Diagnostic Potential ◽  
G Quadruplex ◽  
Fast Development ◽  
Systematic Evolution ◽  
Nucleic Acid Structures ◽  
Exponential Enrichment

G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

scholarly journals Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

2020 ◽  
Vol 21 (22) ◽  
pp. 8774
Author(s):  
Natalia Komarova ◽  
Daria Barkova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Combinatorial Libraries ◽  
Structure And Function ◽  
Huge Number ◽  
Systematic Evolution ◽  
And Function ◽  
Exponential Enrichment

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.

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

scholarly journals Selection of DNA aptamers with two modified bases

2017 ◽  
Vol 114 (11) ◽  
pp. 2898-2903 ◽  
Author(s):  
Bharat N. Gawande ◽  
John C. Rohloff ◽  
Jeffrey D. Carter ◽  
Ira von Carlowitz ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Chemical Diversity ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
Dramatic Improvement ◽  
Protein Targets ◽  
Dna And Rna ◽  
Modified Dna ◽  
Pyrimidine Bases ◽  
Representative Protein ◽  
Selection Of

The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid–like modifications on both pyrimidine bases. Using proprotein convertase subtilisin/kexin type 9 as a representative protein target, we identify specific pairwise combinations of modifications that result in higher affinity, metabolic stability, and inhibitory potency compared with aptamers with single modifications. Such doubly modified aptamers are also more likely to be encoded in shorter sequences and occupy nonoverlapping epitopes more frequently than aptamers with single modifications. These highly modified DNA aptamers have broad utility in research, diagnostic, and therapeutic applications.

Sign in / Sign up

Export Citation Format

Share Document