Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation
ABSTRACT We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the l...
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| Veröffentlicht in: | Biotechnology and bioengineering 2017-10, Vol.114 (10), p.2196-2203 |
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| creator | Yokoyama, Tomomi Tsukakoshi, Kaori Yoshida, Wataru Saito, Taiki Teramoto, Kentaro Savory, Nasa Abe, Koichi Ikebukuro, Kazunori |
| description | ABSTRACT
We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.
The authors have reported an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). In this study, new aptamers against Hepatocyte growth factor were developed by a combination of G4PAS and ISM, resulting in avoidance of PCR. |
| doi_str_mv | 10.1002/bit.26354 |
| format | Article |
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We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.
The authors have reported an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). In this study, new aptamers against Hepatocyte growth factor were developed by a combination of G4PAS and ISM, resulting in avoidance of PCR.</description><identifier>ISSN: 0006-3592</identifier><identifier>EISSN: 1097-0290</identifier><identifier>DOI: 10.1002/bit.26354</identifier><identifier>PMID: 28627727</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>aptamer improvement ; aptamer selection ; Aptamers ; Aptamers, Nucleotide - genetics ; Binding Sites ; Bioinformatics ; Directed evolution ; Evolution ; G-Quadruplexes ; G‐quadruplex ; Hepatocyte growth factor ; Hepatocyte Growth Factor - genetics ; High-Throughput Screening Assays - methods ; Identification methods ; in silico ; Ligands ; Maturation ; Promoter Regions, Genetic - genetics ; Protein Binding ; SELEX Aptamer Technique - methods ; Sequence Analysis, DNA</subject><ispartof>Biotechnology and bioengineering, 2017-10, Vol.114 (10), p.2196-2203</ispartof><rights>2017 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3904-b3d47807e241b9c1aa0e88711ade816d1eb350935c84e2962005cc6703b21c023</citedby><cites>FETCH-LOGICAL-c3904-b3d47807e241b9c1aa0e88711ade816d1eb350935c84e2962005cc6703b21c023</cites><orcidid>0000-0003-2838-0562</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fbit.26354$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fbit.26354$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28627727$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yokoyama, Tomomi</creatorcontrib><creatorcontrib>Tsukakoshi, Kaori</creatorcontrib><creatorcontrib>Yoshida, Wataru</creatorcontrib><creatorcontrib>Saito, Taiki</creatorcontrib><creatorcontrib>Teramoto, Kentaro</creatorcontrib><creatorcontrib>Savory, Nasa</creatorcontrib><creatorcontrib>Abe, Koichi</creatorcontrib><creatorcontrib>Ikebukuro, Kazunori</creatorcontrib><title>Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation</title><title>Biotechnology and bioengineering</title><addtitle>Biotechnol Bioeng</addtitle><description>ABSTRACT
We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.
The authors have reported an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). In this study, new aptamers against Hepatocyte growth factor were developed by a combination of G4PAS and ISM, resulting in avoidance of PCR.</description><subject>aptamer improvement</subject><subject>aptamer selection</subject><subject>Aptamers</subject><subject>Aptamers, Nucleotide - genetics</subject><subject>Binding Sites</subject><subject>Bioinformatics</subject><subject>Directed evolution</subject><subject>Evolution</subject><subject>G-Quadruplexes</subject><subject>G‐quadruplex</subject><subject>Hepatocyte growth factor</subject><subject>Hepatocyte Growth Factor - genetics</subject><subject>High-Throughput Screening Assays - methods</subject><subject>Identification methods</subject><subject>in silico</subject><subject>Ligands</subject><subject>Maturation</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Protein Binding</subject><subject>SELEX Aptamer Technique - methods</subject><subject>Sequence Analysis, DNA</subject><issn>0006-3592</issn><issn>1097-0290</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc9O3DAQhy1UBMu2h75AZamXcgiM7SS2j5Q_CxJSL_QcOc5sMUrire2AuFR9BJ6RJ8HsAgckTqPRfPNpND9CvjI4YAD8sHXpgNeiKrfIjIGWBXANn8gMAOpCVJrvkr0Yb3IrVV3vkF2uai4llzPy7wRvsferAcdE_ZKeL84e_z-0buzc-IeaVTIDhkjvXLqm6Rqp9UMemuT8-IwvSroKfvAJQ17rMLhb7F7XaMQe7Ro1Y0fdSKPrnfV0MGkKa8dnsr00fcQvL3VOfp-dXh2fF5e_FhfHR5eFFRrKohVdKRVI5CVrtWXGAColGTMdKlZ3DFtRgRaVVSVyXXOAytpagmg5s8DFnPzYePO1fyeMqRlctNj3ZkQ_xYZpxjhoyF-ck-_v0Bs_hTFflykhVKWyNlP7G8oGH2PAZbMKbjDhvmHQPIfS5FCadSiZ_fZinNoBuzfyNYUMHG6AO9fj_cem5ufF1Ub5BL9ul9I</recordid><startdate>201710</startdate><enddate>201710</enddate><creator>Yokoyama, Tomomi</creator><creator>Tsukakoshi, Kaori</creator><creator>Yoshida, Wataru</creator><creator>Saito, Taiki</creator><creator>Teramoto, Kentaro</creator><creator>Savory, Nasa</creator><creator>Abe, Koichi</creator><creator>Ikebukuro, Kazunori</creator><general>Wiley Subscription Services, Inc</general><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>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-2838-0562</orcidid></search><sort><creationdate>201710</creationdate><title>Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation</title><author>Yokoyama, Tomomi ; Tsukakoshi, Kaori ; Yoshida, Wataru ; Saito, Taiki ; Teramoto, Kentaro ; Savory, Nasa ; Abe, Koichi ; Ikebukuro, Kazunori</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3904-b3d47807e241b9c1aa0e88711ade816d1eb350935c84e2962005cc6703b21c023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>aptamer improvement</topic><topic>aptamer selection</topic><topic>Aptamers</topic><topic>Aptamers, Nucleotide - genetics</topic><topic>Binding Sites</topic><topic>Bioinformatics</topic><topic>Directed evolution</topic><topic>Evolution</topic><topic>G-Quadruplexes</topic><topic>G‐quadruplex</topic><topic>Hepatocyte growth factor</topic><topic>Hepatocyte Growth Factor - genetics</topic><topic>High-Throughput Screening Assays - methods</topic><topic>Identification methods</topic><topic>in silico</topic><topic>Ligands</topic><topic>Maturation</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Protein Binding</topic><topic>SELEX Aptamer Technique - methods</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yokoyama, Tomomi</creatorcontrib><creatorcontrib>Tsukakoshi, Kaori</creatorcontrib><creatorcontrib>Yoshida, Wataru</creatorcontrib><creatorcontrib>Saito, Taiki</creatorcontrib><creatorcontrib>Teramoto, Kentaro</creatorcontrib><creatorcontrib>Savory, Nasa</creatorcontrib><creatorcontrib>Abe, Koichi</creatorcontrib><creatorcontrib>Ikebukuro, Kazunori</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Biotechnology and bioengineering</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yokoyama, Tomomi</au><au>Tsukakoshi, Kaori</au><au>Yoshida, Wataru</au><au>Saito, Taiki</au><au>Teramoto, Kentaro</au><au>Savory, Nasa</au><au>Abe, Koichi</au><au>Ikebukuro, Kazunori</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation</atitle><jtitle>Biotechnology and bioengineering</jtitle><addtitle>Biotechnol Bioeng</addtitle><date>2017-10</date><risdate>2017</risdate><volume>114</volume><issue>10</issue><spage>2196</spage><epage>2203</epage><pages>2196-2203</pages><issn>0006-3592</issn><eissn>1097-0290</eissn><abstract>ABSTRACT
We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.
The authors have reported an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). In this study, new aptamers against Hepatocyte growth factor were developed by a combination of G4PAS and ISM, resulting in avoidance of PCR.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>28627727</pmid><doi>10.1002/bit.26354</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0003-2838-0562</orcidid></addata></record> |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | aptamer improvement aptamer selection Aptamers Aptamers, Nucleotide - genetics Binding Sites Bioinformatics Directed evolution Evolution G-Quadruplexes G‐quadruplex Hepatocyte growth factor Hepatocyte Growth Factor - genetics High-Throughput Screening Assays - methods Identification methods in silico Ligands Maturation Promoter Regions, Genetic - genetics Protein Binding SELEX Aptamer Technique - methods Sequence Analysis, DNA |
| title | Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation |
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