scholarly journals Rapid acquisition of high-affinity DNA aptamer motifs recognizing microbial cell surfaces using polymer-enhanced capillary transient isotachophoresis

2016 ◽  
Vol 52 (3) ◽  
pp. 461-464 ◽  
Author(s):  
Shingo Saito ◽  
Kazuki Hirose ◽  
Maho Tsuchida ◽  
Koji Wakui ◽  
Keitaro Yoshimoto ◽  
...  

A polymer-enhanced capillary transient isotachophoresis selection methodology was developed for rapid acquisition of high affinity DNA aptamers recognizing microbial cell surfaces.

The Analyst ◽  
2017 ◽  
Vol 142 (21) ◽  
pp. 4030-4038 ◽  
Author(s):  
Kazuki Hirose ◽  
Maho Tsuchida ◽  
Hinako Asakura ◽  
Koji Wakui ◽  
Keitaro Yoshimoto ◽  
...  

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


Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1213 ◽  
Author(s):  
Miguel Moreno ◽  
María Fernández-Algar ◽  
Javier Fernández-Chamorro ◽  
Jorge Ramajo ◽  
Encarnación Martínez-Salas ◽  
...  

Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.


2019 ◽  
Vol 34 (1) ◽  
pp. 365-385 ◽  
Author(s):  
Carolina O. Matos ◽  
Yulli M. Passos ◽  
Mariana J. Amaral ◽  
Bruno Macedo ◽  
Matheus H. Tempone ◽  
...  

1997 ◽  
Vol 11 (4) ◽  
pp. 388-394 ◽  
Author(s):  
H.C. Van Der Mei ◽  
H.J. Busscher

Physicochemical and structural properties of microbial cell surfaces play an important role in their adhesion to surfaces and are determined by the chemical composition of the outermost cell surface. Many traditional methods used to determine microbial cell wall composition require fractionation of the organisms and consequently do not yield information about the composition of the outermost cell surface. X-ray photoelectron spectroscopy (XPS) measures the elemental composition of the outermost cell surfaces of micro-organisms. The technique requires freeze-drying of the organisms, but, nevertheless, elemental surface concentration ratios of oral streptococcal cell surfaces with peritrichously arranged surface structures showed good relationships with physicochemical properties measured under physiological conditions, such as zeta potentials. Isoelectric points ap-peared to be governed by the relative abundance of oxygen- and nitrogen-containing groups on the cell surfaces. Also, the intrinsic microbial cell-surface hydrophobicity by water contact angles related to the cell-surface composition as by XPS and was highest for strains with an elevated isoelectric point. Inclusion of elemental surface compositions for tufted streptococcal strains caused deterioration of the relationships found. Interestingly, hierarchical cluster analysis on the basis of the elemental surface compositions revealed that, of 36 different streptococcal strains, only four S. rattus as well as nine S. mitis strains were located in distinct groups, well separated from the other streptococcal strains, which were all more or less mixed in one group.


RSC Advances ◽  
2019 ◽  
Vol 9 (66) ◽  
pp. 38867-38876 ◽  
Author(s):  
Kun Li ◽  
Liqing Qi ◽  
LiMing Gao ◽  
Ming Shi ◽  
Jian Li ◽  
...  

Aptamer Seq-2 with high affinity and selectivity was screened against colorectal cancer serum directly for clinical application.


2020 ◽  
Vol 30 (3) ◽  
pp. 175-187 ◽  
Author(s):  
Elena Zavyalova ◽  
Askar Turashev ◽  
Anastasia Novoseltseva ◽  
Valeriia Legatova ◽  
Olga Antipova ◽  
...  

2020 ◽  
Vol 2 ◽  
pp. 116-129 ◽  
Author(s):  
Steve Tuske ◽  
Jie Zheng ◽  
Erik D. Olson ◽  
Francesc X. Ruiz ◽  
Bruce D. Pascal ◽  
...  

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