A Novel in silico SELEX Method to Screen and Identify Aptamers against Vibrio cholerae
Copyright© Bentham Science Publishers; For any queries, please email at epubbenthamscience.net..
BACKGROUND: Vibrio cholerae, the causative agent of cholera, has been responsible for global epidemics and many other problems over the centuries. It is one of the main public health issues in less-developed and developing countries and is considered one of the deadliest infectious agents. Therefore, precise and susceptible detection of V. cholerae</i> from environmental and biological samples is critical. Aptamers provide a rapid, sensitive, highly specific, and inexpensive alternative to traditional methods.
OBJECTIVE: The present study develops a new protocol inspired by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to implement an in silico</i> aptamer selection against V. cholerae</i>, which can also be employed in the case of other pathogenic microorganisms.
METHODS: First, we built an oligonucleotide pool and screened it based on the secondary structure. Following that, we modeled the tertiary structures of filtered sequences and performed RNAprotein dockings to assess binding affinities between RNA sequences and Outer Membrane Protein U (OmpU), an effective marker in distinguishing epidemic strains of V. cholerae</i>, which constitute up to 60% of the total outer membrane protein. Finally, we used molecular dynamics simulation to validate the results.
RESULTS: Three sequences (ChOmpUapta) were proposed as final aptameric candidates. Analysis of the top-ranked docking results revealed that these candidate aptamers bound to all subunits of OmpU at the extracellular side with high affinity. Moreover, ChOmpUapta-3 and ChOmpUapta-2 were fully stable and formed strong bonds under dynamic conditions.
CONCLUSION: We propose incorporating these candidate sequences into aptasensors for V. cholerae</i> detection.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:19 |
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| Enthalten in: |
Current computer-aided drug design - 19(2023), 6 vom: 26., Seite 416-424 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Rasouli Jazi, Hamid Reza [VerfasserIn] |
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| Links: |
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| Themen: |
Detection |
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| Anmerkungen: |
Date Completed 17.05.2023 Date Revised 18.05.2023 published: Print Citation Status MEDLINE |
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| doi: |
10.2174/1573409919666230126101635 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 500 | |a Date Revised 18.05.2023 | ||
| 500 | |a published: Print | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright© Bentham Science Publishers; For any queries, please email at epubbenthamscience.net. | ||
| 520 | |a BACKGROUND: Vibrio cholerae, the causative agent of cholera, has been responsible for global epidemics and many other problems over the centuries. It is one of the main public health issues in less-developed and developing countries and is considered one of the deadliest infectious agents. Therefore, precise and susceptible detection of V. cholerae</i> from environmental and biological samples is critical. Aptamers provide a rapid, sensitive, highly specific, and inexpensive alternative to traditional methods | ||
| 520 | |a OBJECTIVE: The present study develops a new protocol inspired by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to implement an in silico</i> aptamer selection against V. cholerae</i>, which can also be employed in the case of other pathogenic microorganisms | ||
| 520 | |a METHODS: First, we built an oligonucleotide pool and screened it based on the secondary structure. Following that, we modeled the tertiary structures of filtered sequences and performed RNAprotein dockings to assess binding affinities between RNA sequences and Outer Membrane Protein U (OmpU), an effective marker in distinguishing epidemic strains of V. cholerae</i>, which constitute up to 60% of the total outer membrane protein. Finally, we used molecular dynamics simulation to validate the results | ||
| 520 | |a RESULTS: Three sequences (ChOmpUapta) were proposed as final aptameric candidates. Analysis of the top-ranked docking results revealed that these candidate aptamers bound to all subunits of OmpU at the extracellular side with high affinity. Moreover, ChOmpUapta-3 and ChOmpUapta-2 were fully stable and formed strong bonds under dynamic conditions | ||
| 520 | |a CONCLUSION: We propose incorporating these candidate sequences into aptasensors for V. cholerae</i> detection | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a OmpU | |
| 650 | 4 | |a RNA aptamer screening | |
| 650 | 4 | |a Vibrio cholera</i> | |
| 650 | 4 | |a detection | |
| 650 | 4 | |a highthroughput screening | |
| 650 | 4 | |a in silico</i> SELEX | |
| 650 | 4 | |a molecular dynamics simulation | |
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| 650 | 7 | |a Ligands |2 NLM | |
| 650 | 7 | |a Membrane Proteins |2 NLM | |
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| 700 | 1 | |a Arab, Seyed Shahriar |e verfasserin |4 aut | |
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