Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles
Gold nanoparticles (AuNPs) were used as colorimetric probe and fluorescence quencher for affinity analysis of DNA aptamers toward their target mucin 1 (MUC1) peptide. Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in...
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| Veröffentlicht in: | Analytical biochemistry 2012-02, Vol.421 (2), p.725-731 |
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| container_title | Analytical biochemistry |
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| creator | Tan, Lihan Neoh, Koon Gee Kang, En-Tang Choe, Woo-Seok Su, Xiaodi |
| description | Gold nanoparticles (AuNPs) were used as colorimetric probe and fluorescence quencher for affinity analysis of DNA aptamers toward their target mucin 1 (MUC1) peptide. Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in the presence of their target peptide due to the increase in steric protection conferred by the ssDNA–peptide complexes formed on the AuNPs. Based on changes in the UV–vis extinction spectrum of AuNPs (a measure of AuNPs aggregation) and fluorescence restoration of CY5-ssDNA upon ssDNA–peptide complex formation, the formation of the complexes and ssDNA sequence-dependent dissociation constant (Kd) were determined. Besides the UV–vis and fluorescence measurements, the hydrodynamic diameters, zeta potential measurements, and transmission electron microscopy (TEM) images of AuNPs after various coatings supported the assay principle. The methodology presented herein provides a rapid and sensitive alternative solution for the identification of high affinity binders from systematic evolution of ligands by exponential enrichment (SELEX). |
| doi_str_mv | 10.1016/j.ab.2011.12.007 |
| format | Article |
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Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in the presence of their target peptide due to the increase in steric protection conferred by the ssDNA–peptide complexes formed on the AuNPs. Based on changes in the UV–vis extinction spectrum of AuNPs (a measure of AuNPs aggregation) and fluorescence restoration of CY5-ssDNA upon ssDNA–peptide complex formation, the formation of the complexes and ssDNA sequence-dependent dissociation constant (Kd) were determined. Besides the UV–vis and fluorescence measurements, the hydrodynamic diameters, zeta potential measurements, and transmission electron microscopy (TEM) images of AuNPs after various coatings supported the assay principle. The methodology presented herein provides a rapid and sensitive alternative solution for the identification of high affinity binders from systematic evolution of ligands by exponential enrichment (SELEX).</description><identifier>ISSN: 0003-2697</identifier><identifier>EISSN: 1096-0309</identifier><identifier>DOI: 10.1016/j.ab.2011.12.007</identifier><identifier>PMID: 22214880</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Affinity interaction ; Aptamers, Nucleotide - chemistry ; coatings ; Colorimetric ; colorimetry ; dissociation ; DNA, Single-Stranded - chemistry ; extinction ; Fluorescence ; Gold - chemistry ; Gold nanoparticle ; Humans ; hydrodynamics ; Metal Nanoparticles ; MUC1 peptide ; Mucin-1 - chemistry ; mucins ; nanogold ; oligonucleotides ; Peptides - chemistry ; SELEX Aptamer Technique ; single-stranded DNA ; sodium chloride ; ssDNA aptamer ; systematic evolution of ligands by exponential enrichment ; transmission electron microscopy ; zeta potential</subject><ispartof>Analytical biochemistry, 2012-02, Vol.421 (2), p.725-731</ispartof><rights>2011 Elsevier Inc.</rights><rights>Copyright © 2011 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c471t-6bd6eb8c6a6fc0b4891e147cd3e9afa8e0645769f4759a93a8896d9ab675c3c53</citedby><cites>FETCH-LOGICAL-c471t-6bd6eb8c6a6fc0b4891e147cd3e9afa8e0645769f4759a93a8896d9ab675c3c53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ab.2011.12.007$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22214880$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tan, Lihan</creatorcontrib><creatorcontrib>Neoh, Koon Gee</creatorcontrib><creatorcontrib>Kang, En-Tang</creatorcontrib><creatorcontrib>Choe, Woo-Seok</creatorcontrib><creatorcontrib>Su, Xiaodi</creatorcontrib><title>Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles</title><title>Analytical biochemistry</title><addtitle>Anal Biochem</addtitle><description>Gold nanoparticles (AuNPs) were used as colorimetric probe and fluorescence quencher for affinity analysis of DNA aptamers toward their target mucin 1 (MUC1) peptide. Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in the presence of their target peptide due to the increase in steric protection conferred by the ssDNA–peptide complexes formed on the AuNPs. Based on changes in the UV–vis extinction spectrum of AuNPs (a measure of AuNPs aggregation) and fluorescence restoration of CY5-ssDNA upon ssDNA–peptide complex formation, the formation of the complexes and ssDNA sequence-dependent dissociation constant (Kd) were determined. Besides the UV–vis and fluorescence measurements, the hydrodynamic diameters, zeta potential measurements, and transmission electron microscopy (TEM) images of AuNPs after various coatings supported the assay principle. The methodology presented herein provides a rapid and sensitive alternative solution for the identification of high affinity binders from systematic evolution of ligands by exponential enrichment (SELEX).</description><subject>Affinity interaction</subject><subject>Aptamers, Nucleotide - chemistry</subject><subject>coatings</subject><subject>Colorimetric</subject><subject>colorimetry</subject><subject>dissociation</subject><subject>DNA, Single-Stranded - chemistry</subject><subject>extinction</subject><subject>Fluorescence</subject><subject>Gold - chemistry</subject><subject>Gold nanoparticle</subject><subject>Humans</subject><subject>hydrodynamics</subject><subject>Metal Nanoparticles</subject><subject>MUC1 peptide</subject><subject>Mucin-1 - chemistry</subject><subject>mucins</subject><subject>nanogold</subject><subject>oligonucleotides</subject><subject>Peptides - chemistry</subject><subject>SELEX Aptamer Technique</subject><subject>single-stranded DNA</subject><subject>sodium chloride</subject><subject>ssDNA aptamer</subject><subject>systematic evolution of ligands by exponential enrichment</subject><subject>transmission electron microscopy</subject><subject>zeta potential</subject><issn>0003-2697</issn><issn>1096-0309</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0b-O1DAQBnALgbjloKeCdFQJ4zhxbLrV8Vc6ARJcbU2c8cqrrBNsL9J2vANvyJPg0x50SFTT_OYb6RvGnnJoOHD5ct_g2LTAecPbBmC4xzYctKxBgL7PNgAg6lbq4YI9SmkPBXa9fMgu2rblnVKwYZ-3zvng86nCgPMp-VQtrnr9cVvhmvFA8dePnyut2U9U-ZApos1-Cak6Jh921W6ZpypgWFaM2duZ0mP2wOGc6MndvGQ3b998vXpfX3969-Fqe13bbuC5luMkaVRWonQWxk5pTrwb7CRIo0NFILt-kNp1Q69RC1RKy0njKIfeCtuLS_binLvG5duRUjYHnyzNMwZajsnoVioNXAz_IUFIWXyRcJY2LilFcmaN_oDxZDiY28LN3uBobgs3vDWl8LLy7C78OB5o-rvwp-ECnp-Bw8XgLvpkbr6UBFmewxUXoohXZ0Glru-eoknWU7A0-Ug2m2nx_77_G8Rlmes</recordid><startdate>20120215</startdate><enddate>20120215</enddate><creator>Tan, Lihan</creator><creator>Neoh, Koon Gee</creator><creator>Kang, En-Tang</creator><creator>Choe, Woo-Seok</creator><creator>Su, Xiaodi</creator><general>Elsevier Inc</general><scope>FBQ</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>7TM</scope></search><sort><creationdate>20120215</creationdate><title>Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles</title><author>Tan, Lihan ; Neoh, Koon Gee ; Kang, En-Tang ; Choe, Woo-Seok ; Su, Xiaodi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c471t-6bd6eb8c6a6fc0b4891e147cd3e9afa8e0645769f4759a93a8896d9ab675c3c53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Affinity interaction</topic><topic>Aptamers, Nucleotide - chemistry</topic><topic>coatings</topic><topic>Colorimetric</topic><topic>colorimetry</topic><topic>dissociation</topic><topic>DNA, Single-Stranded - chemistry</topic><topic>extinction</topic><topic>Fluorescence</topic><topic>Gold - chemistry</topic><topic>Gold nanoparticle</topic><topic>Humans</topic><topic>hydrodynamics</topic><topic>Metal Nanoparticles</topic><topic>MUC1 peptide</topic><topic>Mucin-1 - chemistry</topic><topic>mucins</topic><topic>nanogold</topic><topic>oligonucleotides</topic><topic>Peptides - chemistry</topic><topic>SELEX Aptamer Technique</topic><topic>single-stranded DNA</topic><topic>sodium chloride</topic><topic>ssDNA aptamer</topic><topic>systematic evolution of ligands by exponential enrichment</topic><topic>transmission electron microscopy</topic><topic>zeta potential</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tan, Lihan</creatorcontrib><creatorcontrib>Neoh, Koon Gee</creatorcontrib><creatorcontrib>Kang, En-Tang</creatorcontrib><creatorcontrib>Choe, Woo-Seok</creatorcontrib><creatorcontrib>Su, Xiaodi</creatorcontrib><collection>AGRIS</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>Nucleic Acids Abstracts</collection><jtitle>Analytical biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tan, Lihan</au><au>Neoh, Koon Gee</au><au>Kang, En-Tang</au><au>Choe, Woo-Seok</au><au>Su, Xiaodi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles</atitle><jtitle>Analytical biochemistry</jtitle><addtitle>Anal Biochem</addtitle><date>2012-02-15</date><risdate>2012</risdate><volume>421</volume><issue>2</issue><spage>725</spage><epage>731</epage><pages>725-731</pages><issn>0003-2697</issn><eissn>1096-0309</eissn><abstract>Gold nanoparticles (AuNPs) were used as colorimetric probe and fluorescence quencher for affinity analysis of DNA aptamers toward their target mucin 1 (MUC1) peptide. Single-stranded DNA (ssDNA) aptamer-coated AuNPs showed increased stability (i.e., more resistant to aggregation induced by NaCl) in the presence of their target peptide due to the increase in steric protection conferred by the ssDNA–peptide complexes formed on the AuNPs. Based on changes in the UV–vis extinction spectrum of AuNPs (a measure of AuNPs aggregation) and fluorescence restoration of CY5-ssDNA upon ssDNA–peptide complex formation, the formation of the complexes and ssDNA sequence-dependent dissociation constant (Kd) were determined. Besides the UV–vis and fluorescence measurements, the hydrodynamic diameters, zeta potential measurements, and transmission electron microscopy (TEM) images of AuNPs after various coatings supported the assay principle. The methodology presented herein provides a rapid and sensitive alternative solution for the identification of high affinity binders from systematic evolution of ligands by exponential enrichment (SELEX).</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>22214880</pmid><doi>10.1016/j.ab.2011.12.007</doi><tpages>7</tpages></addata></record> |
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| subjects | Affinity interaction Aptamers, Nucleotide - chemistry coatings Colorimetric colorimetry dissociation DNA, Single-Stranded - chemistry extinction Fluorescence Gold - chemistry Gold nanoparticle Humans hydrodynamics Metal Nanoparticles MUC1 peptide Mucin-1 - chemistry mucins nanogold oligonucleotides Peptides - chemistry SELEX Aptamer Technique single-stranded DNA sodium chloride ssDNA aptamer systematic evolution of ligands by exponential enrichment transmission electron microscopy zeta potential |
| title | Affinity analysis of DNA aptamer–peptide interactions using gold nanoparticles |
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