Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies
Identifieur interne : 001C71 ( Istex/Corpus ); précédent : 001C70; suivant : 001C72Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies
Auteurs : Pierre Murat ; Romaric Bonnet ; Angéline Van Er Eyden ; Nicolas Spinelli ; Pierre Labbé ; David Monchaud ; Marie-Paule Teulade-Fichou ; Pascal Dumy ; Eric DefrancqSource :
- Chemistry – A European Journal [ 0947-6539 ] ; 2010-05-25.
English descriptors
Abstract
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2. The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=KDintra/KDinter, where KDintra is the dissociation constant for intramolecular G‐quadruplex 2 and KDinter is the dissociation constant for intermolecular G‐quadruplex 1. In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.
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DOI: 10.1002/chem.200903456
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<front><div type="abstract">A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2. The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=KDintra/KDinter, where KDintra is the dissociation constant for intramolecular G‐quadruplex 2 and KDinter is the dissociation constant for intermolecular G‐quadruplex 1. In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.</div>
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<title>Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies</title>
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<title>It should be noted that the affinity of distamycin A for duplex DNA is underestimated. Indeed, distamycin A is expected to bind with higher affinity to the AT duplex sequence. Consequently, the selectivity for G‐quadruplex versus duplex is lower than that specified (Table 2).</title>
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<genre><json:string>article</json:string>
</genre>
<host><volume>16</volume>
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<pages><total>9</total>
<last>6114</last>
<first>6106</first>
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<istex:fulltextTEI uri="https://api.istex.fr/document/78C181816C70A97B7E3F071E8A69245F28ECF106/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies</title>
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<availability><p>Copyright © 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim</p>
</availability>
<date>2010</date>
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<notesStmt><note>Centre National de la Recherche Scientifique (CNRS)</note>
<note>Ministère de la Recherche</note>
<note>Cluster de Recherche Chimie de la Région Rhône‐Alpes</note>
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<sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies</title>
<author xml:id="author-1"><persName><forename type="first">Pierre</forename>
<surname>Murat</surname>
</persName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-2"><persName><forename type="first">Romaric</forename>
<surname>Bonnet</surname>
</persName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-3"><persName><forename type="first">Angéline</forename>
<surname>Van der Heyden</surname>
</persName>
<roleName type="degree">Dr.</roleName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-4"><persName><forename type="first">Nicolas</forename>
<surname>Spinelli</surname>
</persName>
<roleName type="degree">Dr.</roleName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-5"><persName><forename type="first">Pierre</forename>
<surname>Labbé</surname>
</persName>
<roleName type="degree">Prof. Dr.</roleName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-6"><persName><forename type="first">David</forename>
<surname>Monchaud</surname>
</persName>
<roleName type="degree">Dr.</roleName>
<affiliation>Institut Curie, CNRS, UMR 176, Centre Universitaire Paris XI, 91405 Orsay (France)</affiliation>
<affiliation>Current address: Institut de Chimie Moléculaire, CNRS UMR 5260, Université de Bourgogne, 21000 Dijon (France)</affiliation>
</author>
<author xml:id="author-7"><persName><forename type="first">Marie‐Paule</forename>
<surname>Teulade‐Fichou</surname>
</persName>
<roleName type="degree">Dr.</roleName>
<affiliation>Institut Curie, CNRS, UMR 176, Centre Universitaire Paris XI, 91405 Orsay (France)</affiliation>
</author>
<author xml:id="author-8"><persName><forename type="first">Pascal</forename>
<surname>Dumy</surname>
</persName>
<roleName type="degree">Prof. Dr.</roleName>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
</author>
<author xml:id="author-9"><persName><forename type="first">Eric</forename>
<surname>Defrancq</surname>
</persName>
<roleName type="degree">Prof. Dr.</roleName>
<email>Eric.Defrancq@ujf‐grenoble.fr</email>
<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
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<monogr><title level="j">Chemistry – A European Journal</title>
<title level="j" type="abbrev">Chemistry – A European Journal</title>
<idno type="pISSN">0947-6539</idno>
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<abstract><p>A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2. The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=KDintra/KDinter, where KDintra is the dissociation constant for intramolecular G‐quadruplex 2 and KDinter is the dissociation constant for intermolecular G‐quadruplex 1. In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.</p>
</abstract>
<abstract><p>New biomolecular tool: A new biomolecular system for investigating the interactions of ligands with G‐quadruplex conformations of DNA, using surface plasmon resonance (SPR), is described (see graphic). The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), which allows precise control of the parallel G‐quadruplex conformation.</p>
</abstract>
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<item><term>quadruplex</term>
</item>
<item><term>recognition</term>
</item>
<item><term>surface plasmon resonance</term>
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<title type="tocHeading2">DNA Ligation</title>
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<copyright ownership="publisher">Copyright © 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim</copyright>
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<titleGroup><title type="main" xml:lang="en">Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies</title>
</titleGroup>
<creators><creator xml:id="au1" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Pierre</givenNames>
<familyName>Murat</familyName>
</personName>
</creator>
<creator xml:id="au2" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Romaric</givenNames>
<familyName>Bonnet</familyName>
</personName>
</creator>
<creator xml:id="au3" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Angéline</givenNames>
<familyName>Van der Heyden</familyName>
<degrees>Dr.</degrees>
</personName>
</creator>
<creator xml:id="au4" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Nicolas</givenNames>
<familyName>Spinelli</familyName>
<degrees>Dr.</degrees>
</personName>
</creator>
<creator xml:id="au5" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Pierre</givenNames>
<familyName>Labbé</familyName>
<degrees>Prof. Dr.</degrees>
</personName>
</creator>
<creator xml:id="au6" creatorRole="author" affiliationRef="#ab #ac"><personName><givenNames>David</givenNames>
<familyName>Monchaud</familyName>
<degrees>Dr.</degrees>
</personName>
</creator>
<creator xml:id="au7" creatorRole="author" affiliationRef="#ab"><personName><givenNames>Marie‐Paule</givenNames>
<familyName>Teulade‐Fichou</familyName>
<degrees>Dr.</degrees>
</personName>
</creator>
<creator xml:id="au8" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Pascal</givenNames>
<familyName>Dumy</familyName>
<degrees>Prof. Dr.</degrees>
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</creator>
<creator xml:id="au9" creatorRole="author" affiliationRef="#aa"><personName><givenNames>Eric</givenNames>
<familyName>Defrancq</familyName>
<degrees>Prof. Dr.</degrees>
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<contactDetails><email normalForm="Eric.Defrancq@ujf-grenoble.fr">Eric.Defrancq@ujf‐grenoble.fr</email>
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<affiliationGroup><affiliation xml:id="aa" countryCode="FR" type="organization"><unparsedAffiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</unparsedAffiliation>
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<affiliation xml:id="ab" countryCode="FR" type="organization"><unparsedAffiliation>Institut Curie, CNRS, UMR 176, Centre Universitaire Paris XI, 91405 Orsay (France)</unparsedAffiliation>
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<affiliation xml:id="ac" countryCode="FR" type="organization"><unparsedAffiliation>Current address: Institut de Chimie Moléculaire, CNRS UMR 5260, Université de Bourgogne, 21000 Dijon (France)</unparsedAffiliation>
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<keywordGroup xml:lang="en" type="author"><keyword xml:id="kwd1">DNA</keyword>
<keyword xml:id="kwd2">quadruplex</keyword>
<keyword xml:id="kwd3">recognition</keyword>
<keyword xml:id="kwd4">surface plasmon resonance</keyword>
<keyword xml:id="kwd5">template assembly</keyword>
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<fundingInfo><fundingAgency>Centre National de la Recherche Scientifique (CNRS)</fundingAgency>
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<fundingInfo><fundingAgency>Ministère de la Recherche</fundingAgency>
</fundingInfo>
<fundingInfo><fundingAgency>Cluster de Recherche Chimie de la Région Rhône‐Alpes</fundingAgency>
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<abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title>
<p>A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif <b>1</b>
(parallel G‐quadruplex conformation), an intramolecular G‐quadruplex <b>2</b>
, and a duplex DNA <b>3</b>
have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular <b>1</b>
and intramolecular <b>2</b>
DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes <b>1</b>
, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes <b>1</b>
or <b>2</b>
. In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex <b>1</b>
against intramolecular G‐quadruplex <b>2</b>
. The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=<i>K</i>
<sub>D</sub>
<sup>intra</sup>
/<i>K</i>
<sub>D</sub>
<sup>inter</sup>
, where <i>K</i>
<sub>D</sub>
<sup>intra</sup>
is the dissociation constant for intramolecular G‐quadruplex <b>2</b>
and <i>K</i>
<sub>D</sub>
<sup>inter</sup>
is the dissociation constant for intermolecular G‐quadruplex <b>1</b>
. In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.</p>
</abstract>
<abstract type="graphical" xml:lang="en"><p><b>New biomolecular tool</b>
: A new biomolecular system for investigating the interactions of ligands with G‐quadruplex conformations of DNA, using surface plasmon resonance (SPR), is described (see graphic). The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), which allows precise control of the parallel G‐quadruplex conformation.<blockFixed type="graphic"><mediaResourceGroup><mediaResource alt="image" eRights="yes" copyright="WILEY-VCH" href="urn:x-wiley:09476539:media:CHEM200903456:content"></mediaResource>
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<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
<role><roleTerm type="text">author</roleTerm>
</role>
</name>
<name type="personal"><namePart type="given">David</namePart>
<namePart type="family">Monchaud</namePart>
<namePart type="termsOfAddress">Dr.</namePart>
<affiliation>Institut Curie, CNRS, UMR 176, Centre Universitaire Paris XI, 91405 Orsay (France)</affiliation>
<affiliation>Current address: Institut de Chimie Moléculaire, CNRS UMR 5260, Université de Bourgogne, 21000 Dijon (France)</affiliation>
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</role>
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<name type="personal"><namePart type="given">Pascal</namePart>
<namePart type="family">Dumy</namePart>
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<affiliation>Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9 (France), Fax: (+33) 476‐51‐49‐46</affiliation>
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<abstract>A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2. The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=KDintra/KDinter, where KDintra is the dissociation constant for intramolecular G‐quadruplex 2 and KDinter is the dissociation constant for intermolecular G‐quadruplex 1. In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.</abstract>
<abstract>New biomolecular tool: A new biomolecular system for investigating the interactions of ligands with G‐quadruplex conformations of DNA, using surface plasmon resonance (SPR), is described (see graphic). The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), which allows precise control of the parallel G‐quadruplex conformation.</abstract>
<note type="funding">Centre National de la Recherche Scientifique (CNRS)</note>
<note type="funding">Ministère de la Recherche</note>
<note type="funding">Cluster de Recherche Chimie de la Région Rhône‐Alpes</note>
<subject lang="en"><genre>keywords</genre>
<topic>DNA</topic>
<topic>quadruplex</topic>
<topic>recognition</topic>
<topic>surface plasmon resonance</topic>
<topic>template assembly</topic>
</subject>
<relatedItem type="host"><titleInfo><title>Chemistry – A European Journal</title>
</titleInfo>
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</titleInfo>
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<note type="content"> Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer‐reviewed, but not copy‐edited or typeset. They are made available as submitted by the authors.Supporting Info Item: miscellaneous_information - </note>
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<identifier type="ISSN">0947-6539</identifier>
<identifier type="eISSN">1521-3765</identifier>
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<part><date>2010</date>
<detail type="volume"><caption>vol.</caption>
<number>16</number>
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