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Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA

DNA structural transitions facilitate genomic processes, mediate drug-DNA interactions, and inform the development of emerging DNA-based biotechnology such as programmable materials and DNA origami. While some features of DNA conformational changes are well characterized, fundamental information suc...

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Autores principales: Backer, Adam S., Biebricher, Andreas S., King, Graeme A., Wuite, Gijs J. L., Heller, Iddo, Peterman, Erwin J. G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6430628/
https://www.ncbi.nlm.nih.gov/pubmed/30915395
http://dx.doi.org/10.1126/sciadv.aav1083
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author Backer, Adam S.
Biebricher, Andreas S.
King, Graeme A.
Wuite, Gijs J. L.
Heller, Iddo
Peterman, Erwin J. G.
author_facet Backer, Adam S.
Biebricher, Andreas S.
King, Graeme A.
Wuite, Gijs J. L.
Heller, Iddo
Peterman, Erwin J. G.
author_sort Backer, Adam S.
collection PubMed
description DNA structural transitions facilitate genomic processes, mediate drug-DNA interactions, and inform the development of emerging DNA-based biotechnology such as programmable materials and DNA origami. While some features of DNA conformational changes are well characterized, fundamental information such as the orientations of the DNA base pairs is unknown. Here, we use concurrent fluorescence polarization imaging and DNA manipulation experiments to probe the structure of S-DNA, an elusive, elongated conformation that can be accessed by mechanical overstretching. To this end, we directly quantify the orientations and rotational dynamics of fluorescent DNA-intercalated dyes. At extensions beyond the DNA overstretching transition, intercalators adopt a tilted (θ ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (θ ~ 90°) normally assumed at lower extensions. These results provide the first experimental evidence that S-DNA has substantially inclined base pairs relative to those of the standard (Watson-Crick) B-DNA conformation.
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spelling pubmed-64306282019-03-26 Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA Backer, Adam S. Biebricher, Andreas S. King, Graeme A. Wuite, Gijs J. L. Heller, Iddo Peterman, Erwin J. G. Sci Adv Research Articles DNA structural transitions facilitate genomic processes, mediate drug-DNA interactions, and inform the development of emerging DNA-based biotechnology such as programmable materials and DNA origami. While some features of DNA conformational changes are well characterized, fundamental information such as the orientations of the DNA base pairs is unknown. Here, we use concurrent fluorescence polarization imaging and DNA manipulation experiments to probe the structure of S-DNA, an elusive, elongated conformation that can be accessed by mechanical overstretching. To this end, we directly quantify the orientations and rotational dynamics of fluorescent DNA-intercalated dyes. At extensions beyond the DNA overstretching transition, intercalators adopt a tilted (θ ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (θ ~ 90°) normally assumed at lower extensions. These results provide the first experimental evidence that S-DNA has substantially inclined base pairs relative to those of the standard (Watson-Crick) B-DNA conformation. American Association for the Advancement of Science 2019-03-22 /pmc/articles/PMC6430628/ /pubmed/30915395 http://dx.doi.org/10.1126/sciadv.aav1083 Text en Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (http://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Research Articles
Backer, Adam S.
Biebricher, Andreas S.
King, Graeme A.
Wuite, Gijs J. L.
Heller, Iddo
Peterman, Erwin J. G.
Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title_full Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title_fullStr Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title_full_unstemmed Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title_short Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA
title_sort single-molecule polarization microscopy of dna intercalators sheds light on the structure of s-dna
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6430628/
https://www.ncbi.nlm.nih.gov/pubmed/30915395
http://dx.doi.org/10.1126/sciadv.aav1083
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