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Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation

BACKGROUND AND OBJECTIVES: This study aimed to investigate the accessible regions of the fimH mRNA using computational prediction and dot-blot hybridization to increase the effectiveness of antisense anti-virulence therapeutics against Uropathogenic Escherichia coli. MATERIALS AND METHODS: We predic...

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Autores principales: Mood, Elnaz Harifi, Japoni-Nejad, Alireza, Karam, Mohammadreza Asadi, Pooya, Mohammad, Bouzari, Saeid, Shahrokhi, Nader
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Tehran University of Medical Sciences 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8629811/
https://www.ncbi.nlm.nih.gov/pubmed/34900163
http://dx.doi.org/10.18502/ijm.v13i5.7430
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author Mood, Elnaz Harifi
Japoni-Nejad, Alireza
Karam, Mohammadreza Asadi
Pooya, Mohammad
Bouzari, Saeid
Shahrokhi, Nader
author_facet Mood, Elnaz Harifi
Japoni-Nejad, Alireza
Karam, Mohammadreza Asadi
Pooya, Mohammad
Bouzari, Saeid
Shahrokhi, Nader
author_sort Mood, Elnaz Harifi
collection PubMed
description BACKGROUND AND OBJECTIVES: This study aimed to investigate the accessible regions of the fimH mRNA using computational prediction and dot-blot hybridization to increase the effectiveness of antisense anti-virulence therapeutics against Uropathogenic Escherichia coli. MATERIALS AND METHODS: We predicted the secondary structure of the E. coli fimH mRNA using the Sfold and Mfold Web servers and RNA structure 5.5 program. Considering the predicted secondary structure, accessible regions in mRNA of fimH were determined and oligonucleotides complementary to these regions were synthesized and hybridization activity of those oligonucleotides to the fimH Digoxigenin (DIG) labeled mRNA was assessed with dot-blot hybridization. RESULTS: When searching the fimH gene in the GenBank database, two lengths for this gene was discovered in different strains of E. coli. The difference was related to the nine bases in the first part of the gene utilizing either of two translation initiation sites. Based on the bioinformatics analyses, five regions lacking obvious stable secondary structures were selected in mRNA of fimH. The result of dot-blot hybridization exhibited strongest hybridization signal between the antisense oligonucleotide number one and fimH labeled mRNA, whereas hybridization signals were not seen for the negative control. CONCLUSION: The results obtained here demonstrate that the region contains start codon of fimH mRNA could act as the potential mRNA target site for anti-fimH antisense therapeutics. It is recommended in the future both of utilizing translation initiation sites be targeted with antisense oligomers compounds.
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spelling pubmed-86298112021-12-10 Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation Mood, Elnaz Harifi Japoni-Nejad, Alireza Karam, Mohammadreza Asadi Pooya, Mohammad Bouzari, Saeid Shahrokhi, Nader Iran J Microbiol Original Article BACKGROUND AND OBJECTIVES: This study aimed to investigate the accessible regions of the fimH mRNA using computational prediction and dot-blot hybridization to increase the effectiveness of antisense anti-virulence therapeutics against Uropathogenic Escherichia coli. MATERIALS AND METHODS: We predicted the secondary structure of the E. coli fimH mRNA using the Sfold and Mfold Web servers and RNA structure 5.5 program. Considering the predicted secondary structure, accessible regions in mRNA of fimH were determined and oligonucleotides complementary to these regions were synthesized and hybridization activity of those oligonucleotides to the fimH Digoxigenin (DIG) labeled mRNA was assessed with dot-blot hybridization. RESULTS: When searching the fimH gene in the GenBank database, two lengths for this gene was discovered in different strains of E. coli. The difference was related to the nine bases in the first part of the gene utilizing either of two translation initiation sites. Based on the bioinformatics analyses, five regions lacking obvious stable secondary structures were selected in mRNA of fimH. The result of dot-blot hybridization exhibited strongest hybridization signal between the antisense oligonucleotide number one and fimH labeled mRNA, whereas hybridization signals were not seen for the negative control. CONCLUSION: The results obtained here demonstrate that the region contains start codon of fimH mRNA could act as the potential mRNA target site for anti-fimH antisense therapeutics. It is recommended in the future both of utilizing translation initiation sites be targeted with antisense oligomers compounds. Tehran University of Medical Sciences 2021-10 /pmc/articles/PMC8629811/ /pubmed/34900163 http://dx.doi.org/10.18502/ijm.v13i5.7430 Text en Copyright © 2021 The Authors. Published by Tehran University of Medical Sciences https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International license (https://creativecommons.org/licenses/by-nc/4.0/). Non-commercial uses of the work are permitted, provided the original work is properly cited.
spellingShingle Original Article
Mood, Elnaz Harifi
Japoni-Nejad, Alireza
Karam, Mohammadreza Asadi
Pooya, Mohammad
Bouzari, Saeid
Shahrokhi, Nader
Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title_full Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title_fullStr Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title_full_unstemmed Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title_short Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation
title_sort evaluation of accessible regions of escherichia coli fimh mrna through computational prediction and experimental investigation
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8629811/
https://www.ncbi.nlm.nih.gov/pubmed/34900163
http://dx.doi.org/10.18502/ijm.v13i5.7430
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