Escherichia coli-aptamer

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Description

 In 2012, Lee et al. identified a RNA aptamer-based ligand which can specifically distinguish the pathogen E. coli O157:H7 from others was developed by a subtractive cell-SELEX method. The isolated RNA aptamer that distinguishes between the virulent serotype and the nonpathogenic strain specifically bound to an O157:H7-specific lipopolysaccharide which includes the O antigen[1].

SELEX

In 2012, Lee et al. identified a RNA aptamer-based ligand which can specifically distinguish the pathogen E. coli O157:H7 from others was developed by a subtractive cell-SELEX method. An RNA library was first incubated with the E. coli K12 strain, and the RNAs binding to the strain were discarded. The precluded RNAs were then used for the selection of O157:H7-specific aptamers. After 6 rounds of the subtractive cell-SELEX process, the selected aptamer was found to specifically bind to the O157:H7 serotype, but not to the K12 strain[1].
Detailed information are accessible on SELEX page.



Structure

I-1 was the aptamer sequence mainly studied in the article, which had a high affinity with Escherichia coli O157H7. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].

5'-UGAUUCCAUCUUCCUGGACUGUCGAAAAUUCAGUAUCGGGAGGUUACGUAUUUGGUUUAU-3'

 drawing


Ligand information

SELEX ligand

Escherichia coli O157:H7 is a serotype of the bacterial species Escherichia coli and is one of the Shiga-like toxin–producing types of E. coli. It is a cause of disease, typically foodborne illness, through consumption of contaminated and raw food, including raw milk and undercooked ground beef. Infection with this type of pathogenic bacteria may lead to hemorrhagic diarrhea, and to kidney failure; these have been reported to cause the deaths of children younger than five years of age, of elderly patients, and of patients whose immune systems are otherwise compromised.-----From Wiki

Name GenBase gene GenBase protein NCBI ID
Escherichia coli O157:H7 AB011548.2 ACT76084.1 83334

Some isolated sequences bind to the affinity of the protein.

Name Sequence Ligand Affinity
I-1 aptamer 5'-UGAUUCCAUCUUCCUGGACUGUCGAAAAUUCAGUAUCGGGAGGUUACGUAUUUGGUUUAU-3' Escherichia coli O157:H7 110 nM
drawing


References

[1] In vitro selection of Escherichia coli O157:H7-specific RNA aptamer.
Lee, YJ., Han, SR., Maeng, JS., Cho, YJ., & Lee, SW.
Biochemical and Biophysical Research Communications,417(1):414-20. (2012)