Role of Mg2+ ions in flavin recognition by RNA aptamer
[Display omitted] •Binding interactions of flavins by RNA aptamer.•Effect of conformational flexibility of FAD over aptamer recognition.•Thermodynamic insights of flavin recognition by RNA aptamer.•Effect of Mg2+ ion concentrations over flavin recognition. The role of Mg2+ ion in flavin (flavin aden...
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| Veröffentlicht in: | Journal of photochemistry and photobiology. B, Biology Biology, 2014-11, Vol.140, p.240-248 |
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| container_title | Journal of photochemistry and photobiology. B, Biology |
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| creator | Sengupta, Abhigyan Gavvala, Krishna Koninti, Raj Kumar Hazra, Partha |
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•Binding interactions of flavins by RNA aptamer.•Effect of conformational flexibility of FAD over aptamer recognition.•Thermodynamic insights of flavin recognition by RNA aptamer.•Effect of Mg2+ ion concentrations over flavin recognition.
The role of Mg2+ ion in flavin (flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)) recognition by RNA aptamer has been explored through steady state and time-resolved fluorescence, circular dichroism (CD), thermal melting (TM) and isothermal titration calorimetry (ITC) studies. A strong quenching of flavin emission is detected due to stacking interaction with the nucleobases in the mismatched region of aptamer, and it enhances manifold with increasing Mg2+ concentrations. A comparatively lower binding affinity toward FAD compared to FMN is attributed to the presence of intramolecular ‘stack’ conformer of FAD, which cannot participate in the intermolecular stacking interactions with the nucleobases. CD and TM studies predict that flavin detection causes structural reformation of RNA aptamer. ITC results indicate that flavin detection is thermodynamically feasible and highly enthalpy driven. |
| doi_str_mv | 10.1016/j.jphotobiol.2014.08.007 |
| format | Article |
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•Binding interactions of flavins by RNA aptamer.•Effect of conformational flexibility of FAD over aptamer recognition.•Thermodynamic insights of flavin recognition by RNA aptamer.•Effect of Mg2+ ion concentrations over flavin recognition.
The role of Mg2+ ion in flavin (flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)) recognition by RNA aptamer has been explored through steady state and time-resolved fluorescence, circular dichroism (CD), thermal melting (TM) and isothermal titration calorimetry (ITC) studies. A strong quenching of flavin emission is detected due to stacking interaction with the nucleobases in the mismatched region of aptamer, and it enhances manifold with increasing Mg2+ concentrations. A comparatively lower binding affinity toward FAD compared to FMN is attributed to the presence of intramolecular ‘stack’ conformer of FAD, which cannot participate in the intermolecular stacking interactions with the nucleobases. CD and TM studies predict that flavin detection causes structural reformation of RNA aptamer. ITC results indicate that flavin detection is thermodynamically feasible and highly enthalpy driven.</description><identifier>ISSN: 1011-1344</identifier><identifier>EISSN: 1873-2682</identifier><identifier>DOI: 10.1016/j.jphotobiol.2014.08.007</identifier><identifier>PMID: 25173759</identifier><language>eng</language><publisher>Switzerland: Elsevier B.V</publisher><subject>Aptamers, Nucleotide - chemistry ; Aptamers, Nucleotide - metabolism ; Flavin Mononucleotide - metabolism ; Flavins ; Flavins - metabolism ; Kinetics ; Magnesium - metabolism ; Molecular recognition ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; RNA-aptamer ; Thermodynamics parameters ; Transition Temperature</subject><ispartof>Journal of photochemistry and photobiology. B, Biology, 2014-11, Vol.140, p.240-248</ispartof><rights>2014 Elsevier B.V.</rights><rights>Copyright © 2014 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c304t-f41c5d2bf697c414910e9a59650f71ca70e1d6176fc0ed51d7026cb46aae21bb3</citedby><cites>FETCH-LOGICAL-c304t-f41c5d2bf697c414910e9a59650f71ca70e1d6176fc0ed51d7026cb46aae21bb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jphotobiol.2014.08.007$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25173759$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sengupta, Abhigyan</creatorcontrib><creatorcontrib>Gavvala, Krishna</creatorcontrib><creatorcontrib>Koninti, Raj Kumar</creatorcontrib><creatorcontrib>Hazra, Partha</creatorcontrib><title>Role of Mg2+ ions in flavin recognition by RNA aptamer</title><title>Journal of photochemistry and photobiology. B, Biology</title><addtitle>J Photochem Photobiol B</addtitle><description>[Display omitted]
•Binding interactions of flavins by RNA aptamer.•Effect of conformational flexibility of FAD over aptamer recognition.•Thermodynamic insights of flavin recognition by RNA aptamer.•Effect of Mg2+ ion concentrations over flavin recognition.
The role of Mg2+ ion in flavin (flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)) recognition by RNA aptamer has been explored through steady state and time-resolved fluorescence, circular dichroism (CD), thermal melting (TM) and isothermal titration calorimetry (ITC) studies. A strong quenching of flavin emission is detected due to stacking interaction with the nucleobases in the mismatched region of aptamer, and it enhances manifold with increasing Mg2+ concentrations. A comparatively lower binding affinity toward FAD compared to FMN is attributed to the presence of intramolecular ‘stack’ conformer of FAD, which cannot participate in the intermolecular stacking interactions with the nucleobases. CD and TM studies predict that flavin detection causes structural reformation of RNA aptamer. ITC results indicate that flavin detection is thermodynamically feasible and highly enthalpy driven.</description><subject>Aptamers, Nucleotide - chemistry</subject><subject>Aptamers, Nucleotide - metabolism</subject><subject>Flavin Mononucleotide - metabolism</subject><subject>Flavins</subject><subject>Flavins - metabolism</subject><subject>Kinetics</subject><subject>Magnesium - metabolism</subject><subject>Molecular recognition</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleic Acid Denaturation</subject><subject>RNA-aptamer</subject><subject>Thermodynamics parameters</subject><subject>Transition Temperature</subject><issn>1011-1344</issn><issn>1873-2682</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkFtLxDAQhYMo3v-C5FGQ1pk0TdpHFW_gBUSfQ5pONUu3WZvugv_eyHp5dF7OMJyZw3yMcYQcAdXpLJ8t3sIUGh_6XADKHKocQG-wXax0kQlVic3UA2KGhZQ7bC_GGaQqld5mO6JEXeiy3mXqKfTEQ8fvX8UJ92GI3A-86-0qyUguvA5-SmPefPCnhzNuF5Od03jAtjrbRzr81n32cnX5fHGT3T1e316c3WWuADllnURXtqLpVK2dRFkjUG3LWpXQaXRWA2GrUKvOAbUlthqEco1U1pLApin22fH67mIM70uKk5n76Kjv7UBhGQ2qQgotSiiStVpb3RhiHKkzi9HP7fhhEMwXNTMzf9TMFzUDlUnU0urRd8qymVP7u_iDKRnO1wZKv648jSY6T4Oj1idGk2mD_z_lEwT1gWE</recordid><startdate>201411</startdate><enddate>201411</enddate><creator>Sengupta, Abhigyan</creator><creator>Gavvala, Krishna</creator><creator>Koninti, Raj Kumar</creator><creator>Hazra, Partha</creator><general>Elsevier B.V</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>7X8</scope></search><sort><creationdate>201411</creationdate><title>Role of Mg2+ ions in flavin recognition by RNA aptamer</title><author>Sengupta, Abhigyan ; Gavvala, Krishna ; Koninti, Raj Kumar ; Hazra, Partha</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c304t-f41c5d2bf697c414910e9a59650f71ca70e1d6176fc0ed51d7026cb46aae21bb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Aptamers, Nucleotide - chemistry</topic><topic>Aptamers, Nucleotide - metabolism</topic><topic>Flavin Mononucleotide - metabolism</topic><topic>Flavins</topic><topic>Flavins - metabolism</topic><topic>Kinetics</topic><topic>Magnesium - metabolism</topic><topic>Molecular recognition</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleic Acid Denaturation</topic><topic>RNA-aptamer</topic><topic>Thermodynamics parameters</topic><topic>Transition Temperature</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sengupta, Abhigyan</creatorcontrib><creatorcontrib>Gavvala, Krishna</creatorcontrib><creatorcontrib>Koninti, Raj Kumar</creatorcontrib><creatorcontrib>Hazra, Partha</creatorcontrib><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><jtitle>Journal of photochemistry and photobiology. B, Biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sengupta, Abhigyan</au><au>Gavvala, Krishna</au><au>Koninti, Raj Kumar</au><au>Hazra, Partha</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Role of Mg2+ ions in flavin recognition by RNA aptamer</atitle><jtitle>Journal of photochemistry and photobiology. B, Biology</jtitle><addtitle>J Photochem Photobiol B</addtitle><date>2014-11</date><risdate>2014</risdate><volume>140</volume><spage>240</spage><epage>248</epage><pages>240-248</pages><issn>1011-1344</issn><eissn>1873-2682</eissn><abstract>[Display omitted]
•Binding interactions of flavins by RNA aptamer.•Effect of conformational flexibility of FAD over aptamer recognition.•Thermodynamic insights of flavin recognition by RNA aptamer.•Effect of Mg2+ ion concentrations over flavin recognition.
The role of Mg2+ ion in flavin (flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)) recognition by RNA aptamer has been explored through steady state and time-resolved fluorescence, circular dichroism (CD), thermal melting (TM) and isothermal titration calorimetry (ITC) studies. A strong quenching of flavin emission is detected due to stacking interaction with the nucleobases in the mismatched region of aptamer, and it enhances manifold with increasing Mg2+ concentrations. A comparatively lower binding affinity toward FAD compared to FMN is attributed to the presence of intramolecular ‘stack’ conformer of FAD, which cannot participate in the intermolecular stacking interactions with the nucleobases. CD and TM studies predict that flavin detection causes structural reformation of RNA aptamer. ITC results indicate that flavin detection is thermodynamically feasible and highly enthalpy driven.</abstract><cop>Switzerland</cop><pub>Elsevier B.V</pub><pmid>25173759</pmid><doi>10.1016/j.jphotobiol.2014.08.007</doi><tpages>9</tpages></addata></record> |
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| ispartof | Journal of photochemistry and photobiology. B, Biology, 2014-11, Vol.140, p.240-248 |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete |
| subjects | Aptamers, Nucleotide - chemistry Aptamers, Nucleotide - metabolism Flavin Mononucleotide - metabolism Flavins Flavins - metabolism Kinetics Magnesium - metabolism Molecular recognition Nucleic Acid Conformation Nucleic Acid Denaturation RNA-aptamer Thermodynamics parameters Transition Temperature |
| title | Role of Mg2+ ions in flavin recognition by RNA aptamer |
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