Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA
Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. Controlling the affinity and selectivity of synthetic receptors to target desired nucleotides or short sequences is a highly challenging task. Herein,...
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| Veröffentlicht in: | Chemistry : a European journal 2024-10, Vol.30 (58), p.e202402106-n/a |
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| creator | Basaran, Ismet Agafontsev, Aleksandr M. Morozov, Boris S. Oshchepkov, Alexander S. Imhof, Petra Kataev, Evgeny A. |
| description | Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. Controlling the affinity and selectivity of synthetic receptors to target desired nucleotides or short sequences is a highly challenging task. Herein, we elucidate the effect of substituents in the phenyl ring of the anthracene‐benzene azacyclophane on the recognition of nucleoside triphosphates (NTPs) and double‐stranded DNA. We show that introducing phenyl rings increases the affinity for NTPs 10‐fold and implements groove and intercalation binding modes with double‐stranded DNA. NMR studies and molecular modeling calculations support the ability of cyclophanes to encapsulate nucleobases as part of nucleotides.
Cyclophanes with different substitution patterns were prepared and studied for binding of nucleoside triphosphates and double‐stranded DNA. While the ortho‐phenyl derivative showed high affinity for nucleoside triphosphates, the meta‐derivative demonstrated GC‐selectivity and an intercalation binding mode with DNA. |
| doi_str_mv | 10.1002/chem.202402106 |
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Cyclophanes with different substitution patterns were prepared and studied for binding of nucleoside triphosphates and double‐stranded DNA. While the ortho‐phenyl derivative showed high affinity for nucleoside triphosphates, the meta‐derivative demonstrated GC‐selectivity and an intercalation binding mode with DNA.</description><identifier>ISSN: 0947-6539</identifier><identifier>ISSN: 1521-3765</identifier><identifier>EISSN: 1521-3765</identifier><identifier>DOI: 10.1002/chem.202402106</identifier><identifier>PMID: 39110145</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Affinity ; Anthracene ; Bases (nucleic acids) ; Benzene ; Binding ; Cyclophanes ; Deoxyribonucleic acid ; DNA ; Fluorescence sensing ; Gene sequencing ; Grooves ; Molecular modelling ; NMR ; Nuclear magnetic resonance ; Nucleoside triphosphates ; Nucleotide ; Nucleotide sequence ; Nucleotides ; Receptor mechanisms ; Recognition ; π–π interaction</subject><ispartof>Chemistry : a European journal, 2024-10, Vol.30 (58), p.e202402106-n/a</ispartof><rights>2024 The Author(s). Chemistry - A European Journal published by Wiley-VCH GmbH</rights><rights>2024 The Author(s). Chemistry - A European Journal published by Wiley-VCH GmbH.</rights><rights>2024. This article is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2586-a35e45451e6769a5f8001def881da7e5f8f4ac9688e600198047efe175b3c9533</cites><orcidid>0000-0002-1321-8485 ; 0000-0003-4007-8489 ; 0000-0001-9820-4578</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%2Fchem.202402106$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fchem.202402106$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39110145$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Basaran, Ismet</creatorcontrib><creatorcontrib>Agafontsev, Aleksandr M.</creatorcontrib><creatorcontrib>Morozov, Boris S.</creatorcontrib><creatorcontrib>Oshchepkov, Alexander S.</creatorcontrib><creatorcontrib>Imhof, Petra</creatorcontrib><creatorcontrib>Kataev, Evgeny A.</creatorcontrib><title>Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA</title><title>Chemistry : a European journal</title><addtitle>Chemistry</addtitle><description>Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. Controlling the affinity and selectivity of synthetic receptors to target desired nucleotides or short sequences is a highly challenging task. Herein, we elucidate the effect of substituents in the phenyl ring of the anthracene‐benzene azacyclophane on the recognition of nucleoside triphosphates (NTPs) and double‐stranded DNA. We show that introducing phenyl rings increases the affinity for NTPs 10‐fold and implements groove and intercalation binding modes with double‐stranded DNA. NMR studies and molecular modeling calculations support the ability of cyclophanes to encapsulate nucleobases as part of nucleotides.
Cyclophanes with different substitution patterns were prepared and studied for binding of nucleoside triphosphates and double‐stranded DNA. While the ortho‐phenyl derivative showed high affinity for nucleoside triphosphates, the meta‐derivative demonstrated GC‐selectivity and an intercalation binding mode with DNA.</description><subject>Affinity</subject><subject>Anthracene</subject><subject>Bases (nucleic acids)</subject><subject>Benzene</subject><subject>Binding</subject><subject>Cyclophanes</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Fluorescence sensing</subject><subject>Gene sequencing</subject><subject>Grooves</subject><subject>Molecular modelling</subject><subject>NMR</subject><subject>Nuclear magnetic resonance</subject><subject>Nucleoside triphosphates</subject><subject>Nucleotide</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Receptor mechanisms</subject><subject>Recognition</subject><subject>π–π interaction</subject><issn>0947-6539</issn><issn>1521-3765</issn><issn>1521-3765</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><recordid>eNqFkc9OGzEQh60KVMKfa4_IUi9cNrXXa699DCGUSkArBOeV8Y6J0cZO7V2l6YlH6DPyJDgKpVIvnDz2fPPJmh9CnygZU0LKL2YOi3FJyoqUlIgPaER5SQtWC76DRkRVdSE4U3toP6VHQogSjH1Ee0xRSmjFR-jXzFowfcLB4hvnH_D54E3vgted-603BXYeT3w_j9qAh-enP6c6QYuna9OF5Vx7yLMe93PAp863G8WPGJYQe5c7t2GlY4uvB9NB6F2bn7Rv8dn15BDtWt0lOHo9D9Dd-ex2elFcfv_6bTq5LEzJpSg041DxilMQtVCaW0kIbcFKSVtdQ77bShslpASRO0qSqgYLtOb3zCjO2AE62XqXMfwcIPXNwiUDXZd_HobUMCKVlCXnPKOf_0MfwxDzJjJFqcp6KkSmxlvKxJBSBNsso1vouG4oaTaZNJtMmrdM8sDxq3a4X0D7hv8NIQNqC6xcB-t3dM30Ynb1T_4CuCqYtQ</recordid><startdate>20241017</startdate><enddate>20241017</enddate><creator>Basaran, Ismet</creator><creator>Agafontsev, Aleksandr M.</creator><creator>Morozov, Boris S.</creator><creator>Oshchepkov, Alexander S.</creator><creator>Imhof, Petra</creator><creator>Kataev, Evgeny A.</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>K9.</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1321-8485</orcidid><orcidid>https://orcid.org/0000-0003-4007-8489</orcidid><orcidid>https://orcid.org/0000-0001-9820-4578</orcidid></search><sort><creationdate>20241017</creationdate><title>Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA</title><author>Basaran, Ismet ; Agafontsev, Aleksandr M. ; Morozov, Boris S. ; Oshchepkov, Alexander S. ; Imhof, Petra ; Kataev, Evgeny A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2586-a35e45451e6769a5f8001def881da7e5f8f4ac9688e600198047efe175b3c9533</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Affinity</topic><topic>Anthracene</topic><topic>Bases (nucleic acids)</topic><topic>Benzene</topic><topic>Binding</topic><topic>Cyclophanes</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Fluorescence sensing</topic><topic>Gene sequencing</topic><topic>Grooves</topic><topic>Molecular modelling</topic><topic>NMR</topic><topic>Nuclear magnetic resonance</topic><topic>Nucleoside triphosphates</topic><topic>Nucleotide</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Receptor mechanisms</topic><topic>Recognition</topic><topic>π–π interaction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Basaran, Ismet</creatorcontrib><creatorcontrib>Agafontsev, Aleksandr M.</creatorcontrib><creatorcontrib>Morozov, Boris S.</creatorcontrib><creatorcontrib>Oshchepkov, Alexander S.</creatorcontrib><creatorcontrib>Imhof, Petra</creatorcontrib><creatorcontrib>Kataev, Evgeny A.</creatorcontrib><collection>Wiley-Blackwell Open Access Titles</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><jtitle>Chemistry : a European journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Basaran, Ismet</au><au>Agafontsev, Aleksandr M.</au><au>Morozov, Boris S.</au><au>Oshchepkov, Alexander S.</au><au>Imhof, Petra</au><au>Kataev, Evgeny A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA</atitle><jtitle>Chemistry : a European journal</jtitle><addtitle>Chemistry</addtitle><date>2024-10-17</date><risdate>2024</risdate><volume>30</volume><issue>58</issue><spage>e202402106</spage><epage>n/a</epage><pages>e202402106-n/a</pages><issn>0947-6539</issn><issn>1521-3765</issn><eissn>1521-3765</eissn><abstract>Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. 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Cyclophanes with different substitution patterns were prepared and studied for binding of nucleoside triphosphates and double‐stranded DNA. While the ortho‐phenyl derivative showed high affinity for nucleoside triphosphates, the meta‐derivative demonstrated GC‐selectivity and an intercalation binding mode with DNA.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>39110145</pmid><doi>10.1002/chem.202402106</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-1321-8485</orcidid><orcidid>https://orcid.org/0000-0003-4007-8489</orcidid><orcidid>https://orcid.org/0000-0001-9820-4578</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Affinity Anthracene Bases (nucleic acids) Benzene Binding Cyclophanes Deoxyribonucleic acid DNA Fluorescence sensing Gene sequencing Grooves Molecular modelling NMR Nuclear magnetic resonance Nucleoside triphosphates Nucleotide Nucleotide sequence Nucleotides Receptor mechanisms Recognition π–π interaction |
| title | Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA |
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