Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain
•DNA aptamers were generated against the norovirus GII.4 P domain.•Aptamers showed broad reactivity with majority of a 14 strain capsid panel.•One aptamer showed at least low to moderate binding to all strains tested.•Aptamers bound dilutions of partially purified virus from clinical isolates.•Aptam...
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| Veröffentlicht in: | Journal of biotechnology 2015-09, Vol.209, p.41-49 |
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| creator | Moore, Matthew D. Escudero-Abarca, Blanca I. Suh, Soo Hwan Jaykus, Lee-Ann |
| description | •DNA aptamers were generated against the norovirus GII.4 P domain.•Aptamers showed broad reactivity with majority of a 14 strain capsid panel.•One aptamer showed at least low to moderate binding to all strains tested.•Aptamers bound dilutions of partially purified virus from clinical isolates.•Aptamers could concentrate norovirus from stool using magnetic capture.
Human noroviruses (NoV) are the leading cause of acute viral gastroenteritis worldwide. Significant antigenic diversity of NoV strains has limited the availability of broadly reactive ligands for design of detection assays. The purpose of this work was to produce and characterize single stranded (ss)DNA aptamers with binding specificity to human NoV using an easily produced NoV target—the P domain protein. Aptamer selection was done using SELEX (Systematic Evolution of Ligands by EXponential enrichment) directed against an Escherichia coli-expressed and purified epidemic NoV GII.4 strain P domain. Two of six unique aptamers (designated M1 and M6-2) were chosen for characterization. Inclusivity testing using an enzyme-linked aptamer sorbent assay (ELASA) against a panel of 14 virus-like particles (VLPs) showed these aptamers had broad reactivity and exhibited strong binding to GI.7, GII.2, two GII.4 strains, and GII.7 VLPs. Aptamer M6-2 exhibited at least low to moderate binding to all VLPs tested. Aptamers significantly (p |
| doi_str_mv | 10.1016/j.jbiotec.2015.06.389 |
| format | Article |
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Human noroviruses (NoV) are the leading cause of acute viral gastroenteritis worldwide. Significant antigenic diversity of NoV strains has limited the availability of broadly reactive ligands for design of detection assays. The purpose of this work was to produce and characterize single stranded (ss)DNA aptamers with binding specificity to human NoV using an easily produced NoV target—the P domain protein. Aptamer selection was done using SELEX (Systematic Evolution of Ligands by EXponential enrichment) directed against an Escherichia coli-expressed and purified epidemic NoV GII.4 strain P domain. Two of six unique aptamers (designated M1 and M6-2) were chosen for characterization. Inclusivity testing using an enzyme-linked aptamer sorbent assay (ELASA) against a panel of 14 virus-like particles (VLPs) showed these aptamers had broad reactivity and exhibited strong binding to GI.7, GII.2, two GII.4 strains, and GII.7 VLPs. Aptamer M6-2 exhibited at least low to moderate binding to all VLPs tested. Aptamers significantly (p<0.05) bound virus in partially purified GII.4 New Orleans outbreak stool specimens as demonstrated by ELASA and aptamer magnetic capture (AMC) followed by RT-qPCR. This is the first demonstration of human NoV P domain protein as a functional target for the selection of nucleic acid aptamers that specifically bind and broadly recognize diverse human NoV strains.</description><identifier>ISSN: 0168-1656</identifier><identifier>EISSN: 1873-4863</identifier><identifier>DOI: 10.1016/j.jbiotec.2015.06.389</identifier><identifier>PMID: 26080079</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Aptamer ; Aptamers, Nucleotide - chemistry ; Aptamers, Nucleotide - metabolism ; Assaying ; Binding ; Capsid Proteins - genetics ; Capsid Proteins - metabolism ; Escherichia ; Feces - virology ; Human ; Humans ; Ligands ; Molecular detection ; Norovirus ; Norovirus - classification ; Norovirus - genetics ; Norovirus - isolation & purification ; Nucleic acids ; Panels ; Proteins ; SELEX ; SELEX Aptamer Technique - methods ; Sensitivity and Specificity ; Strain ; Viral diagnostics</subject><ispartof>Journal of biotechnology, 2015-09, Vol.209, p.41-49</ispartof><rights>2015 The Authors</rights><rights>Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c581t-fd3aab486d4abc3980014cb0b1531c258c4b1b213692a364f5b0d4819a1050be3</citedby><cites>FETCH-LOGICAL-c581t-fd3aab486d4abc3980014cb0b1531c258c4b1b213692a364f5b0d4819a1050be3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jbiotec.2015.06.389$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26080079$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Moore, Matthew D.</creatorcontrib><creatorcontrib>Escudero-Abarca, Blanca I.</creatorcontrib><creatorcontrib>Suh, Soo Hwan</creatorcontrib><creatorcontrib>Jaykus, Lee-Ann</creatorcontrib><title>Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain</title><title>Journal of biotechnology</title><addtitle>J Biotechnol</addtitle><description>•DNA aptamers were generated against the norovirus GII.4 P domain.•Aptamers showed broad reactivity with majority of a 14 strain capsid panel.•One aptamer showed at least low to moderate binding to all strains tested.•Aptamers bound dilutions of partially purified virus from clinical isolates.•Aptamers could concentrate norovirus from stool using magnetic capture.
Human noroviruses (NoV) are the leading cause of acute viral gastroenteritis worldwide. Significant antigenic diversity of NoV strains has limited the availability of broadly reactive ligands for design of detection assays. The purpose of this work was to produce and characterize single stranded (ss)DNA aptamers with binding specificity to human NoV using an easily produced NoV target—the P domain protein. Aptamer selection was done using SELEX (Systematic Evolution of Ligands by EXponential enrichment) directed against an Escherichia coli-expressed and purified epidemic NoV GII.4 strain P domain. Two of six unique aptamers (designated M1 and M6-2) were chosen for characterization. Inclusivity testing using an enzyme-linked aptamer sorbent assay (ELASA) against a panel of 14 virus-like particles (VLPs) showed these aptamers had broad reactivity and exhibited strong binding to GI.7, GII.2, two GII.4 strains, and GII.7 VLPs. Aptamer M6-2 exhibited at least low to moderate binding to all VLPs tested. Aptamers significantly (p<0.05) bound virus in partially purified GII.4 New Orleans outbreak stool specimens as demonstrated by ELASA and aptamer magnetic capture (AMC) followed by RT-qPCR. This is the first demonstration of human NoV P domain protein as a functional target for the selection of nucleic acid aptamers that specifically bind and broadly recognize diverse human NoV strains.</description><subject>Aptamer</subject><subject>Aptamers, Nucleotide - chemistry</subject><subject>Aptamers, Nucleotide - metabolism</subject><subject>Assaying</subject><subject>Binding</subject><subject>Capsid Proteins - genetics</subject><subject>Capsid Proteins - metabolism</subject><subject>Escherichia</subject><subject>Feces - virology</subject><subject>Human</subject><subject>Humans</subject><subject>Ligands</subject><subject>Molecular detection</subject><subject>Norovirus</subject><subject>Norovirus - classification</subject><subject>Norovirus - genetics</subject><subject>Norovirus - isolation & purification</subject><subject>Nucleic acids</subject><subject>Panels</subject><subject>Proteins</subject><subject>SELEX</subject><subject>SELEX Aptamer Technique - methods</subject><subject>Sensitivity and Specificity</subject><subject>Strain</subject><subject>Viral diagnostics</subject><issn>0168-1656</issn><issn>1873-4863</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFu1DAQhi0EokvhEUA-cknwxLHXOSFU0WWlSnCAszVxJl2vNvFiO1Xh6XG7C1d6sjT-_pmxP8begqhBgP6wr_e9D5lc3QhQtdC1NN0ztgKzllVrtHzOVoUzFWilL9irlPZCiLZT8JJdNFoYIdbdit1vaKaI2YeZ4zxwt8OILlP0v0_FMPJ5cQfyjqPzA8djxoli4hnjLWU_3_K8I-7wmMrtNz6ECf1jDPlumXDmc4jhzscl8c12W7c85ViI1-zFiIdEb87nJftx_fn71Zfq5utme_XppnLKQK7GQSL25T1Di72TXVkbWteLHpQE1yjj2h76BqTuGpS6HVUvhtZAhyCU6ElesvenvscYfi6Usp18cnQ44ExhSRbWYDrVibV-Aio60LqR5iloo5UUCgqqTqiLIaVIoz1GP2H8ZUHYB5V2b88q7YNKK7QtKkvu3XnE0k80_Ev9dVeAjyeAyvfdeYo2OU-zo8FHctkOwf9nxB91MrHU</recordid><startdate>20150901</startdate><enddate>20150901</enddate><creator>Moore, Matthew D.</creator><creator>Escudero-Abarca, Blanca I.</creator><creator>Suh, Soo Hwan</creator><creator>Jaykus, Lee-Ann</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7QO</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>7U5</scope><scope>L7M</scope></search><sort><creationdate>20150901</creationdate><title>Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain</title><author>Moore, Matthew D. ; Escudero-Abarca, Blanca I. ; Suh, Soo Hwan ; Jaykus, Lee-Ann</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c581t-fd3aab486d4abc3980014cb0b1531c258c4b1b213692a364f5b0d4819a1050be3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Aptamer</topic><topic>Aptamers, Nucleotide - chemistry</topic><topic>Aptamers, Nucleotide - metabolism</topic><topic>Assaying</topic><topic>Binding</topic><topic>Capsid Proteins - genetics</topic><topic>Capsid Proteins - metabolism</topic><topic>Escherichia</topic><topic>Feces - virology</topic><topic>Human</topic><topic>Humans</topic><topic>Ligands</topic><topic>Molecular detection</topic><topic>Norovirus</topic><topic>Norovirus - classification</topic><topic>Norovirus - genetics</topic><topic>Norovirus - isolation & purification</topic><topic>Nucleic acids</topic><topic>Panels</topic><topic>Proteins</topic><topic>SELEX</topic><topic>SELEX Aptamer Technique - methods</topic><topic>Sensitivity and Specificity</topic><topic>Strain</topic><topic>Viral diagnostics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Moore, Matthew D.</creatorcontrib><creatorcontrib>Escudero-Abarca, Blanca I.</creatorcontrib><creatorcontrib>Suh, Soo Hwan</creatorcontrib><creatorcontrib>Jaykus, Lee-Ann</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><jtitle>Journal of biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Moore, Matthew D.</au><au>Escudero-Abarca, Blanca I.</au><au>Suh, Soo Hwan</au><au>Jaykus, Lee-Ann</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain</atitle><jtitle>Journal of biotechnology</jtitle><addtitle>J Biotechnol</addtitle><date>2015-09-01</date><risdate>2015</risdate><volume>209</volume><spage>41</spage><epage>49</epage><pages>41-49</pages><issn>0168-1656</issn><eissn>1873-4863</eissn><abstract>•DNA aptamers were generated against the norovirus GII.4 P domain.•Aptamers showed broad reactivity with majority of a 14 strain capsid panel.•One aptamer showed at least low to moderate binding to all strains tested.•Aptamers bound dilutions of partially purified virus from clinical isolates.•Aptamers could concentrate norovirus from stool using magnetic capture.
Human noroviruses (NoV) are the leading cause of acute viral gastroenteritis worldwide. Significant antigenic diversity of NoV strains has limited the availability of broadly reactive ligands for design of detection assays. The purpose of this work was to produce and characterize single stranded (ss)DNA aptamers with binding specificity to human NoV using an easily produced NoV target—the P domain protein. Aptamer selection was done using SELEX (Systematic Evolution of Ligands by EXponential enrichment) directed against an Escherichia coli-expressed and purified epidemic NoV GII.4 strain P domain. Two of six unique aptamers (designated M1 and M6-2) were chosen for characterization. Inclusivity testing using an enzyme-linked aptamer sorbent assay (ELASA) against a panel of 14 virus-like particles (VLPs) showed these aptamers had broad reactivity and exhibited strong binding to GI.7, GII.2, two GII.4 strains, and GII.7 VLPs. Aptamer M6-2 exhibited at least low to moderate binding to all VLPs tested. Aptamers significantly (p<0.05) bound virus in partially purified GII.4 New Orleans outbreak stool specimens as demonstrated by ELASA and aptamer magnetic capture (AMC) followed by RT-qPCR. This is the first demonstration of human NoV P domain protein as a functional target for the selection of nucleic acid aptamers that specifically bind and broadly recognize diverse human NoV strains.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>26080079</pmid><doi>10.1016/j.jbiotec.2015.06.389</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Aptamer Aptamers, Nucleotide - chemistry Aptamers, Nucleotide - metabolism Assaying Binding Capsid Proteins - genetics Capsid Proteins - metabolism Escherichia Feces - virology Human Humans Ligands Molecular detection Norovirus Norovirus - classification Norovirus - genetics Norovirus - isolation & purification Nucleic acids Panels Proteins SELEX SELEX Aptamer Technique - methods Sensitivity and Specificity Strain Viral diagnostics |
| title | Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain |
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