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 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.

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.

Formation of heteroduplex DNA during mammalian intrachromosomal gene conversion

1992 ◽  
Vol 12 (4) ◽  
pp. 1546-1552
Author(s):  
R J Bollag ◽  
D R Elwood ◽  
E D Tobin ◽  
A R Godwin ◽  
R M Liskay
Keyword(s):  
Gene Conversion ◽  
Mammalian Cells ◽  
Restriction Site ◽  
Genetic Evidence ◽  
Heteroduplex Dna ◽  
Daughter Cells ◽  
Single Colony ◽  
Selection For ◽  
Restriction Site Polymorphisms ◽  
Selection Of

We have studied intrachromosomal gene conversion in mouse Ltk- cells with a substrate designed to provide genetic evidence for heteroduplex DNA. Our recombination substrate consists of two defective chicken thymidine kinase genes arranged so as to favor the selection of gene conversion products. The gene intended to serve as the recipient in gene conversion differs from the donor sequence by virtue of a palindromic insertion that creates silent restriction site polymorphisms between the two genes. While selection for gene conversion at a XhoI linker insertion within the recipient gene results in coconversion of the nearby palindromic site in more than half of the convertants, 4% of convertant colonies show both parental and nonparental genotypes at the polymorphic site. We consider these mixed colonies to be the result of genotypic sectoring and interpret this sectoring to be a consequence of unrepaired heteroduplex DNA at the polymorphic palindromic site. DNA replication through the heteroduplex recombination intermediate generates genetically distinct daughter cells that comprise a single colony. We believe that the data provide the first compelling genetic evidence for the presence of heteroduplex DNA during chromosomal gene conversion in mammalian cells.

Emulsion PCR Significantly Improves Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures-Based Aptamer Selection: Allowing for Efficient and Rapid Selection of Aptamer to Unmodified ABH2 Protein

2014 ◽  
Vol 87 (2) ◽  
pp. 1411-1419 ◽  
Author(s):  
Roman Yufa ◽  
Svetlana M. Krylova ◽  
Christine Bruce ◽  
Eleanor A. Bagg ◽  
Christopher J. Schofield ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Aptamer Selection ◽  
Emulsion Pcr ◽  
Selection Of

Starters and Bacteriophages in Lactic Acid Casein Manufacture

1975 ◽  
Vol 38 (5) ◽  
pp. 275-278 ◽  
Author(s):  
T. D. THOMAS ◽  
R. J. LOWRIE
Keyword(s):  
Lactic Acid ◽  
New Zealand ◽  
Acid Production ◽  
Continuous Selection ◽  
Streptococcus Cremoris ◽  
Selection For ◽  
The Individual ◽  
First Time ◽  
Selection Of

A controlled starter system was used for the first time in commercial lactic acid casein manufacture in New Zealand. Multiple starters of up to four components were constructed from 18 recently derived Streptococcus cremoris isolates which were not lysed by any of the phages in the collection of the New Zealand Dairy Research Institute. During the first season of casein manufacture, phages attacking 17 isolates were detected in the casein whey. Of these, 12 prevented adequate acid production by the appropriate host even at levels below 1 phage per 10 to 1000 ml in the milk before starter addition. In contrast, the first detected phages attacking the other five isolates did not significantly influence the rate of acid development; use of these starters continued until phages which eliminated acid production appeared. An alternative starter system based on the continuous selection of “phage-tolerant” cultures was investigated. Regular addition of whey, from previous manufacture, to the individual mother cultures of each component permitted long-term use of the multiple starter. This procedure of continued selection for phage-tolerant organisms has been used successfully for a complete season in a major casein factory.

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