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Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer

Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated us...

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Autores principales: Williams, Sarah L., Parkhurst, Laura K., Parkhurst, Lawrence J.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369283/
https://www.ncbi.nlm.nih.gov/pubmed/16481311
http://dx.doi.org/10.1093/nar/gkj498
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author Williams, Sarah L.
Parkhurst, Laura K.
Parkhurst, Lawrence J.
author_facet Williams, Sarah L.
Parkhurst, Laura K.
Parkhurst, Lawrence J.
author_sort Williams, Sarah L.
collection PubMed
description Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′–3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′–3′ distance while neighboring aminopropynyl groups lengthen the helix.
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spelling pubmed-13692832006-02-16 Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer Williams, Sarah L. Parkhurst, Laura K. Parkhurst, Lawrence J. Nucleic Acids Res Article Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′–3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′–3′ distance while neighboring aminopropynyl groups lengthen the helix. Oxford University Press 2006 2006-02-14 /pmc/articles/PMC1369283/ /pubmed/16481311 http://dx.doi.org/10.1093/nar/gkj498 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Williams, Sarah L.
Parkhurst, Laura K.
Parkhurst, Lawrence J.
Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title_full Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title_fullStr Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title_full_unstemmed Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title_short Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
title_sort changes in dna bending and flexing due to tethered cations detected by fluorescence resonance energy transfer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369283/
https://www.ncbi.nlm.nih.gov/pubmed/16481311
http://dx.doi.org/10.1093/nar/gkj498
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AT parkhurstlawrencej changesindnabendingandflexingduetotetheredcationsdetectedbyfluorescenceresonanceenergytransfer