A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin
•We identified a family of eight G-quadruplex-based DNA aptamers specific to thrombin.•Aptamers vary based on duplex region length (from two to eight base pairs).•Duplex region length influences kinetic and equilibrium constants.•Increasing duplex region length increases affinity to thrombin and pro...
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| Veröffentlicht in: | FEBS letters 2015-07, Vol.589 (16), p.2043-2049 |
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| creator | Spiridonova, V.A. Barinova, K.V. Glinkina, K.A. Melnichuk, A.V. Gainutdynov, A.A. Safenkova, I.V. Dzantiev, B.B. |
| description | •We identified a family of eight G-quadruplex-based DNA aptamers specific to thrombin.•Aptamers vary based on duplex region length (from two to eight base pairs).•Duplex region length influences kinetic and equilibrium constants.•Increasing duplex region length increases affinity to thrombin and prothrombin.•The duplex, which is not the main binding domain, greatly influences the interaction.
Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10−8M to 5.6×10−10M and from 1.8×10−5M to 7.1×10−9M) with an increase in the number of nucleotide pairs in the duplex region. |
| doi_str_mv | 10.1016/j.febslet.2015.06.020 |
| format | Article |
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Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10−8M to 5.6×10−10M and from 1.8×10−5M to 7.1×10−9M) with an increase in the number of nucleotide pairs in the duplex region.</description><identifier>ISSN: 0014-5793</identifier><identifier>EISSN: 1873-3468</identifier><identifier>DOI: 10.1016/j.febslet.2015.06.020</identifier><identifier>PMID: 26143256</identifier><language>eng</language><publisher>England: Elsevier B.V</publisher><subject>Aptamer ; Aptamers, Nucleotide - chemistry ; Aptamers, Nucleotide - metabolism ; Base Pairing ; Circular Dichroism ; Equilibrium constant ; Humans ; Kinetic constant ; Kinetics ; Ligands ; Models, Molecular ; Molecular Weight ; Nucleic Acid Denaturation ; Nucleotide Motifs ; Prothrombin ; Prothrombin - chemistry ; Prothrombin - metabolism ; Surface Plasmon Resonance ; Thrombin ; Thrombin - chemistry ; Thrombin - metabolism ; Transition Temperature</subject><ispartof>FEBS letters, 2015-07, Vol.589 (16), p.2043-2049</ispartof><rights>2015 Federation of European Biochemical Societies</rights><rights>FEBS Letters 589 (2015) 1873-3468 © 2015 Federation of European Biochemical Societies</rights><rights>Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5800-653832c71fddf7ee83f10e8592beefd4dc3fbc35d726b0983a169e75240440393</citedby><cites>FETCH-LOGICAL-c5800-653832c71fddf7ee83f10e8592beefd4dc3fbc35d726b0983a169e75240440393</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1016%2Fj.febslet.2015.06.020$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0014579315005530$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,1411,1427,3537,27901,27902,45550,45551,46384,46808,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26143256$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Spiridonova, V.A.</creatorcontrib><creatorcontrib>Barinova, K.V.</creatorcontrib><creatorcontrib>Glinkina, K.A.</creatorcontrib><creatorcontrib>Melnichuk, A.V.</creatorcontrib><creatorcontrib>Gainutdynov, A.A.</creatorcontrib><creatorcontrib>Safenkova, I.V.</creatorcontrib><creatorcontrib>Dzantiev, B.B.</creatorcontrib><title>A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin</title><title>FEBS letters</title><addtitle>FEBS Lett</addtitle><description>•We identified a family of eight G-quadruplex-based DNA aptamers specific to thrombin.•Aptamers vary based on duplex region length (from two to eight base pairs).•Duplex region length influences kinetic and equilibrium constants.•Increasing duplex region length increases affinity to thrombin and prothrombin.•The duplex, which is not the main binding domain, greatly influences the interaction.
Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10−8M to 5.6×10−10M and from 1.8×10−5M to 7.1×10−9M) with an increase in the number of nucleotide pairs in the duplex region.</description><subject>Aptamer</subject><subject>Aptamers, Nucleotide - chemistry</subject><subject>Aptamers, Nucleotide - metabolism</subject><subject>Base Pairing</subject><subject>Circular Dichroism</subject><subject>Equilibrium constant</subject><subject>Humans</subject><subject>Kinetic constant</subject><subject>Kinetics</subject><subject>Ligands</subject><subject>Models, Molecular</subject><subject>Molecular Weight</subject><subject>Nucleic Acid Denaturation</subject><subject>Nucleotide Motifs</subject><subject>Prothrombin</subject><subject>Prothrombin - chemistry</subject><subject>Prothrombin - metabolism</subject><subject>Surface Plasmon Resonance</subject><subject>Thrombin</subject><subject>Thrombin - chemistry</subject><subject>Thrombin - metabolism</subject><subject>Transition Temperature</subject><issn>0014-5793</issn><issn>1873-3468</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkctu1DAUhi0EokPhEUBeskk4jmPHWaGhtLRSBQtgbTn2ccejXAY70zJvj6OZdltW1pH_i30-Qt4zKBkw-WlbeuxSj3NZARMlyBIqeEFWTDW84LVUL8kKgNWFaFp-Rt6ktIU8K9a-JmeVZDWvhFyRfk29GUJ_oJOnX7-vqdnNZsCY6EOYN_TexICOuv2ux7804l2YRtrjeJfv5o2ZqZ_ikKidhkWAJ9e8idPQhZGa0dFdnB7nt-SVN33Cd6fznPy-uvx1cV3c_vh2c7G-LaxQAIUUXPHKNsw75xtExT0DVKKtOkTvame57ywXrqlkB63ihskWG1HVUNfAW35OPh5zc_efPaZZDyFZ7Hsz4rRPmjWCLVuD5nmpzPmqFQyyVBylNk4pRfR6F8Ng4kEz0AsTvdUnJnpJ1yB1ZpJ9H04V-25A9-R6hJAF10fBQ-jx8H-p-uryS_VzAbzwzV8BIfjS9fkYhXm99wGjTjbgaNGFiHbWbgrPvPYfwh-1cQ</recordid><startdate>20150722</startdate><enddate>20150722</enddate><creator>Spiridonova, V.A.</creator><creator>Barinova, K.V.</creator><creator>Glinkina, K.A.</creator><creator>Melnichuk, A.V.</creator><creator>Gainutdynov, A.A.</creator><creator>Safenkova, I.V.</creator><creator>Dzantiev, B.B.</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>8FD</scope><scope>FR3</scope><scope>P64</scope></search><sort><creationdate>20150722</creationdate><title>A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin</title><author>Spiridonova, V.A. ; Barinova, K.V. ; Glinkina, K.A. ; Melnichuk, A.V. ; Gainutdynov, A.A. ; Safenkova, I.V. ; Dzantiev, B.B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5800-653832c71fddf7ee83f10e8592beefd4dc3fbc35d726b0983a169e75240440393</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>Base Pairing</topic><topic>Circular Dichroism</topic><topic>Equilibrium constant</topic><topic>Humans</topic><topic>Kinetic constant</topic><topic>Kinetics</topic><topic>Ligands</topic><topic>Models, Molecular</topic><topic>Molecular Weight</topic><topic>Nucleic Acid Denaturation</topic><topic>Nucleotide Motifs</topic><topic>Prothrombin</topic><topic>Prothrombin - chemistry</topic><topic>Prothrombin - metabolism</topic><topic>Surface Plasmon Resonance</topic><topic>Thrombin</topic><topic>Thrombin - chemistry</topic><topic>Thrombin - metabolism</topic><topic>Transition Temperature</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Spiridonova, V.A.</creatorcontrib><creatorcontrib>Barinova, K.V.</creatorcontrib><creatorcontrib>Glinkina, K.A.</creatorcontrib><creatorcontrib>Melnichuk, A.V.</creatorcontrib><creatorcontrib>Gainutdynov, A.A.</creatorcontrib><creatorcontrib>Safenkova, I.V.</creatorcontrib><creatorcontrib>Dzantiev, B.B.</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>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>FEBS letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Spiridonova, V.A.</au><au>Barinova, K.V.</au><au>Glinkina, K.A.</au><au>Melnichuk, A.V.</au><au>Gainutdynov, A.A.</au><au>Safenkova, I.V.</au><au>Dzantiev, B.B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin</atitle><jtitle>FEBS letters</jtitle><addtitle>FEBS Lett</addtitle><date>2015-07-22</date><risdate>2015</risdate><volume>589</volume><issue>16</issue><spage>2043</spage><epage>2049</epage><pages>2043-2049</pages><issn>0014-5793</issn><eissn>1873-3468</eissn><abstract>•We identified a family of eight G-quadruplex-based DNA aptamers specific to thrombin.•Aptamers vary based on duplex region length (from two to eight base pairs).•Duplex region length influences kinetic and equilibrium constants.•Increasing duplex region length increases affinity to thrombin and prothrombin.•The duplex, which is not the main binding domain, greatly influences the interaction.
Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10−8M to 5.6×10−10M and from 1.8×10−5M to 7.1×10−9M) with an increase in the number of nucleotide pairs in the duplex region.</abstract><cop>England</cop><pub>Elsevier B.V</pub><pmid>26143256</pmid><doi>10.1016/j.febslet.2015.06.020</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| source | Wiley Free Content; MEDLINE; Wiley Online Library Journals Frontfile Complete; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Alma/SFX Local Collection |
| subjects | Aptamer Aptamers, Nucleotide - chemistry Aptamers, Nucleotide - metabolism Base Pairing Circular Dichroism Equilibrium constant Humans Kinetic constant Kinetics Ligands Models, Molecular Molecular Weight Nucleic Acid Denaturation Nucleotide Motifs Prothrombin Prothrombin - chemistry Prothrombin - metabolism Surface Plasmon Resonance Thrombin Thrombin - chemistry Thrombin - metabolism Transition Temperature |
| title | A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin |
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