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

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

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 (q ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (q ~ 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.

LanguageEnglish
Article numbereaav1083
Pages1-11
Number of pages11
JournalScience advances
Volume5
Issue number3
DOIs
Publication statusPublished - 22 Mar 2019

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deoxyribonucleic acid
microscopy
polarization
molecules
biotechnology
manipulators
emerging
drugs
dyes
fluorescence
probes

Cite this

@article{19ff518db6194ada8d0f808e63a80ff3,
title = "Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA",
abstract = "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 (q ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (q ~ 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.",
author = "Backer, {Adam S.} and Biebricher, {Andreas S.} and King, {Graeme A.} and Wuite, {Gijs J.L.} and Iddo Heller and Peterman, {Erwin J.G.}",
year = "2019",
month = "3",
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doi = "10.1126/sciadv.aav1083",
language = "English",
volume = "5",
pages = "1--11",
journal = "Science advances",
issn = "2375-2548",
publisher = "American Association for the Advancement of Science",
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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.

In: Science advances, Vol. 5, No. 3, eaav1083, 22.03.2019, p. 1-11.

Research output: Contribution to JournalArticleAcademicpeer-review

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AU - Backer, Adam S.

AU - Biebricher, Andreas S.

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AU - Heller, Iddo

AU - Peterman, Erwin J.G.

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AB - 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 (q ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (q ~ 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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