scholarly journals Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Regina Stoltenburg ◽  
Nadia Nikolaus ◽  
Beate Strehlitz
Keyword(s):  
Magnetic Beads ◽  
Selection Process ◽  
Aminoglycoside Antibiotic ◽  
Dna Aptamer ◽  
Dna Aptamers ◽  
Common Procedure ◽  
Aptamer Selection ◽  
Starting Point ◽  
Exponential Enrichment ◽  
Selection Of

Small organic molecules are challenging targets for an aptamer selection using the SELEX technology (SELEX—Systematic Evolution of Ligans by EXponential enrichment). Often they are not suitable for immobilization on solid surfaces, which is a common procedure in known aptamer selection methods. The Capture-SELEX procedure allows the selection of DNA aptamers for solute targets. A special SELEX library was constructed with the aim to immobilize this library on magnetic beads or other surfaces. For this purpose a docking sequence was incorporated into the random region of the library enabling hybridization to a complementary oligo fixed on magnetic beads. Oligonucleotides of the library which exhibit high affinity to the target and a secondary structure fitting to the target are released from the beads for binding to the target during the aptamer selection process. The oligonucleotides of these binding complexes were amplified, purified, and immobilized via the docking sequence to the magnetic beads as the starting point of the following selection round. Based on this Capture-SELEX procedure, the successful DNA aptamer selection for the aminoglycoside antibiotic kanamycin A as a small molecule target is described.

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 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.

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 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 Inside the Black Box: What Makes SELEX Better?

Molecules ◽  
2019 ◽  
Vol 24 (19) ◽  
pp. 3598 ◽  
Author(s):  
Natalia Komarova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
Selection Process ◽  
Combinatorial Libraries ◽  
Black Box ◽  
Aptamer Selection ◽  
Selection Protocol ◽  
Systematic Evolution ◽  
Exponential Enrichment

Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.

A FUZZY LOGIC AND DEFAULT REASONING MODEL OF SOCIAL NORMS AND EQUILIBRIUM SELECTION IN GAMES UNDER UNFORESEEN CONTINGENCIES

2008 ◽  
Vol 16 (01) ◽  
pp. 59-81 ◽  
Author(s):  
LORENZO SACCONI ◽  
STEFANO MORETTI
Keyword(s):  
Social Norms ◽  
Selection Process ◽  
Equilibrium Points ◽  
Equilibrium Selection ◽  
Possibility Theory ◽  
Default Reasoning ◽  
Social Conventions ◽  
Starting Point ◽  
Unforeseen Contingencies ◽  
Selection Of

This paper focuses on the role that social norms play in the selection of equilibrium points seen as social conventions under unforeseen contingencies — that is, their role in the emergence of regularities of behavior which are self-enforcing and effectively adhered to by bounded rational agents due to their self-policing incentives. Differently stated, given a set of game situations imperfectly described, we want to understand how general and abstract norms provide at least the starting point for a norm-based equilibrium selection reasoning procedure which in the end will be able to determine which equilibrium point, belonging to perfectly described games, will be played as the unique solution of each imperfectly described game. In order to solve such a problem we introduce a selection process based on the reformulation of default logic in terms of possibility theory.

Sign in / Sign up

Export Citation Format

Share Document