DNA aptamer identification and characterization for E. coli O157 detection using cell based SELEX method

Amraee, Masoum; Oloomi, Mana; Yavari, Afsaneh; Bouzari, Saeid

doi:10.1016/j.ab.2017.08.005

Cited by 54 publications

(19 citation statements)

References 31 publications

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“…Secondary structure of the Hp4 aptamer revealed that there are four loops in its backbone, which may improve its stability . However, it is important to consider that the structure prediction may not reflect the structure of the aptamer's natural folding pattern; therefore, point mutations and protein truncation may be used to verify the core‐binding site of the aptamer …”

Section: Discussionmentioning

confidence: 99%

“…40 However, it is important to consider that the structure prediction may not reflect the structure of the aptamer's natural folding pattern; therefore, point mutations and protein truncation may be used to verify the core-binding site of the aptamer. 41,42 During the screening process, we maintained the temperature at 37°C to allow the aptamers to detect H pylori in humans, which was optimized to be the most suitable temperature condition. The identified aptamer Hp4 was designed to target the specific protein on the surface of H pylori, so as to increase the specificity of the aptamer compared to the screening process with only the intact thallus.…”

Section: Discussionmentioning

confidence: 99%

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Recognition of Helicobacter pylori by protein‐targeting aptamers

Yan

Ren

et al. 2019

Helicobacter

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Background Helicobacter pylori (H pylori) is a disease‐causing pathogen capable of surviving under acidic conditions of the human stomach. Almost half of the world's population is infected with H pylori, with gastric cancer being the most unsatisfactory prognosis. Although H pylori has been discovered 30 years ago, the effective treatment and elimination of H pylori continue to be problematic. Materials and methods In our study, we screened nucleic acid aptamers using H pylori surface recombinant antigens as targets. Trypsin was used for separating aptamers that were bound to proteins. Following nine rounds of screening, we performed sequence similarity analyses to assess whether the aptamers can recognize the target protein. Two sequences with desirable recognition ability were selected for affinity detection. Aptamer Hp4 with the strongest binding ability to the H pylori surface recombinant antigen was chosen. After optimization of the binding conditions, we conducted specificity tests for Hp4 using Escherichia coli, Staphylococcus aureus, Vibrioanguillarum, and H pylori. Results The data indicated that the aptamer Hp4 had an equilibrium dissociation constant (Kd) of 26.48 ± 5.72 nmol/L to the target protein. This aptamer was capable of exclusively detecting H pylori cells, without displaying any specificity for other bacteria. Conclusions We obtained a high‐affinity aptamer for H pylori, which is expected to serve as a new molecular probe for detection of H pylori.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Recognition of Helicobacter pylori by protein‐targeting aptamers

Yan

Ren

et al. 2019

Helicobacter

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“…Masoum et al isolated an aptamer specific for E. coli O157:H7, a pathogenic strain that causes foodborne illnesses in humans [ 24 ]. Following nine rounds of positive selection and a final tenth round of negative selection, the author reported a highly specific aptamer with a Kd of 107.6 ± 67.8 pM.…”

Section: In Vitro Selection Of Ssdna Aptamersmentioning

confidence: 99%

Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications

Trunzo

Hong

2020

IJMS

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Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.

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“…Amraee et al selected ssDNA aptamer AM-6 with higher sensitivity and specificity for recognition of whole-cell E. coli O157:H7 and reported that the binding affinity of aptamer AM-6 for the target bacteria is 107.6 ± 67.8 pM. 63 An ssDNA aptamer library specific for E. coli K88 whole cells was enriched by Peng et al . for E. coli detection.…”

Section: E Colimentioning

confidence: 99%

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

Pan

Liu

Zhang

2018

Journal of Infection

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The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.

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DNA aptamer identification and characterization for E. coli O157 detection using cell based SELEX method

Cited by 54 publications

References 31 publications

Recognition of Helicobacter pylori by protein‐targeting aptamers

Recognition of Helicobacter pylori by protein‐targeting aptamers

Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

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