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Detection of single DNA molecules by multicolor quantum-dot end-labeling

Identifieur interne : 000990 ( Istex/Corpus ); précédent : 000989; suivant : 000991

Detection of single DNA molecules by multicolor quantum-dot end-labeling

Auteurs : Aure Lien Crut ; Be Ne Dicte Ge Ron-Landre ; Isabelle Bonnet ; Ste Phane Bonneau ; Pierre Desbiolles ; Christophe Escude

Source :

RBID : ISTEX:6CDC46285C7526CA1CB86DD6590969430BEB01F4

Abstract

Observation of DNA–protein interactions by single molecule fluorescence microscopy is usually performed by using fluorescent DNA binding agents. However, such dyes have been shown to induce cleavage of the DNA molecule and perturb its interactions with proteins. A new method for the detection of surface-attached DNA molecules by fluorescence microscopy is introduced in this paper. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both extremities of a DNA molecule via sequence-specific hybridization and ligation. After the modified DNA molecules have been stretched on a glass surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots (QD). We demonstrate that under carefully selected conditions, the position and orientation of individual DNA molecules can be inferred with good efficiency from the QD fluorescence signals alone. This is achieved by selecting QD pairs that have the distance and direction expected for the combed DNA molecules. Direct observation of single DNA molecules in the absence of DNA staining agent opens new possibilities in the fundamental study of DNA–protein interactions. This work also documents new possibilities regarding the use of QD for nucleic acid detection and analysis.

Url:
DOI: 10.1093/nar/gni097

Links to Exploration step

ISTEX:6CDC46285C7526CA1CB86DD6590969430BEB01F4

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<subject>4</subject>
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<article-title>Detection of single DNA molecules by multicolor quantum-dot end-labeling</article-title>
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<contrib contrib-type="author">
<name>
<surname>Crut</surname>
<given-names>Aurélien</given-names>
</name>
<xref rid="AU1">1</xref>
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<given-names>Bénédicte</given-names>
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<xref rid="AU2">2</xref>
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<name>
<surname>Bonnet</surname>
<given-names>Isabelle</given-names>
</name>
<xref rid="AU1">1</xref>
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<contrib contrib-type="author">
<name>
<surname>Bonneau</surname>
<given-names>Stéphane</given-names>
</name>
<xref rid="AU1">1</xref>
<xref rid="AU3">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Desbiolles</surname>
<given-names>Pierre</given-names>
</name>
<xref rid="AU1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Escudé</surname>
<given-names>Christophe</given-names>
</name>
<xref rid="AU2">2</xref>
<xref rid="COR1">*</xref>
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<aff id="AU1">
<sup>1</sup>
Laboratoire Kastler Brossel, Unité de Recherche de l'Ecole Normale Supérieure et de l'Université Pierre et Marie Curie, associée au CNRS, Département de Physique 24 rue Lhomond, F-75005 Paris, France</aff>
<aff id="AU2">
<sup>2</sup>
Laboratoire ‘Régulation et Dynamique des Génomes’, Département ‘Régulations, Développement et Diversité Moléculaire’, USM 0503 Muséum National d'Histoire Naturelle, CNRS UMR5153, INSERM U565 Case Postale 26, 43 rue Cuvier, F-75231 Paris Cedex 05, France</aff>
<aff id="AU3">
<sup>3</sup>
CEREMADE, Université Paris IX -Dauphine F-75775 Paris, France</aff>
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<sup>*</sup>
To whom correspondence should be addressed. Tel: +33 1 40793774; Fax: +33 1 40793705; Email:
<ext-link xlink:href="escude@mnhn.fr" ext-link-type="email">escude@mnhn.fr</ext-link>
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<pub-date pub-type="ppub">
<year>2005</year>
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<volume>33</volume>
<issue>11</issue>
<fpage>e98</fpage>
<lpage>e98</lpage>
<history>
<date date-type="accepted">
<day>31</day>
<month>5</month>
<year>2005</year>
</date>
<date date-type="received">
<day>13</day>
<month>4</month>
<year>2005</year>
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<date date-type="rev-recd">
<day>31</day>
<month>5</month>
<year>2005</year>
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<copyright-statement>© The Author 2005. Published by Oxford University Press. All rights reserved
 The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact
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<p>Observation of DNA–protein interactions by single molecule fluorescence microscopy is usually performed by using fluorescent DNA binding agents. However, such dyes have been shown to induce cleavage of the DNA molecule and perturb its interactions with proteins. A new method for the detection of surface-attached DNA molecules by fluorescence microscopy is introduced in this paper. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both extremities of a DNA molecule via sequence-specific hybridization and ligation. After the modified DNA molecules have been stretched on a glass surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots (QD). We demonstrate that under carefully selected conditions, the position and orientation of individual DNA molecules can be inferred with good efficiency from the QD fluorescence signals alone. This is achieved by selecting QD pairs that have the distance and direction expected for the combed DNA molecules. Direct observation of single DNA molecules in the absence of DNA staining agent opens new possibilities in the fundamental study of DNA–protein interactions. This work also documents new possibilities regarding the use of QD for nucleic acid detection and analysis.</p>
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