Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers
Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spi...
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Veröffentlicht in: | Analytical chemistry (Washington) 2023-10, Vol.95 (39), p.14651-14658 |
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description | Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release ( |
doi_str_mv | 10.1021/acs.analchem.3c02477 |
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In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/acs.analchem.3c02477</identifier><language>eng</language><publisher>Washington: American Chemical Society</publisher><subject>Adenosine ; Aptamers ; Deoxyribonucleic acid ; DNA ; Enrichment ; Gold ; Immobilization ; Libraries ; Nanoparticles</subject><ispartof>Analytical chemistry (Washington), 2023-10, Vol.95 (39), p.14651-14658</ispartof><rights>2023 American Chemical Society</rights><rights>Copyright American Chemical Society Oct 3, 2023</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a353t-add26bedb38c47a6aeb7eee52355dd02e45f11db5c52c1b8ac774b91acdffa6a3</citedby><cites>FETCH-LOGICAL-a353t-add26bedb38c47a6aeb7eee52355dd02e45f11db5c52c1b8ac774b91acdffa6a3</cites><orcidid>0000-0001-5918-9336</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.analchem.3c02477$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.analchem.3c02477$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2752,27053,27901,27902,56713,56763</link.rule.ids></links><search><creatorcontrib>Ding, Yuzhe</creatorcontrib><creatorcontrib>Liu, Juewen</creatorcontrib><title>Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.</description><subject>Adenosine</subject><subject>Aptamers</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Enrichment</subject><subject>Gold</subject><subject>Immobilization</subject><subject>Libraries</subject><subject>Nanoparticles</subject><issn>0003-2700</issn><issn>1520-6882</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp9kMFKw0AQhhdRsFbfwEPAiwdTZzfZ3fRYQqxCoYgKXiRMdjc0JcnG3UTw7U1p68GDp5lhvv8_fIRcU5hRYPQelZ9hi7XamGYWKWCxlCdkQjmDUCQJOyUTAIhCJgHOyYX3WwBKgYoJ-XgesO2rHvvqywSpbTp0lbdtYMsgxa4fnAlfslX2fhcs18cNWx0sba33d1BaF2Stq9SmMW2_Sy66Hhvj_CU5K7H25uowp-TtIXtNH8PVevmULlYhRjzqQ9SaicLoIkpULFGgKaQxhrOIc62BmZiXlOqCK84ULRJUUsbFnKLSZTni0ZTc7ns7Zz8H4_u8qbwydY2tsYPPWSJEJKUAMaI3f9CtHdwob0dJIZI5BzZS8Z5SznrvTJl3rmrQfecU8p3zfHSeH53nB-djDPax3fe399_ID_u3h8g</recordid><startdate>20231003</startdate><enddate>20231003</enddate><creator>Ding, Yuzhe</creator><creator>Liu, Juewen</creator><general>American Chemical Society</general><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>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7U5</scope><scope>7U7</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</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/0000-0001-5918-9336</orcidid></search><sort><creationdate>20231003</creationdate><title>Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers</title><author>Ding, Yuzhe ; Liu, Juewen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a353t-add26bedb38c47a6aeb7eee52355dd02e45f11db5c52c1b8ac774b91acdffa6a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Adenosine</topic><topic>Aptamers</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Enrichment</topic><topic>Gold</topic><topic>Immobilization</topic><topic>Libraries</topic><topic>Nanoparticles</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ding, Yuzhe</creatorcontrib><creatorcontrib>Liu, Juewen</creatorcontrib><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>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS 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>AIDS and Cancer Research Abstracts</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>Analytical chemistry (Washington)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ding, Yuzhe</au><au>Liu, Juewen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers</atitle><jtitle>Analytical chemistry (Washington)</jtitle><addtitle>Anal. Chem</addtitle><date>2023-10-03</date><risdate>2023</risdate><volume>95</volume><issue>39</issue><spage>14651</spage><epage>14658</epage><pages>14651-14658</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><abstract>Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.</abstract><cop>Washington</cop><pub>American Chemical Society</pub><doi>10.1021/acs.analchem.3c02477</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0001-5918-9336</orcidid></addata></record> |
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subjects | Adenosine Aptamers Deoxyribonucleic acid DNA Enrichment Gold Immobilization Libraries Nanoparticles |
title | Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers |
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