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

Adam S. Backer; Andreas S. Biebricher; Graeme A. King; Gijs J.L. Wuite; Iddo Heller; Erwin J.G. Peterman

doi:10.1126/sciadv.aav1083

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

Adam S. Backer^*, Andreas S. Biebricher, Graeme A. King, Gijs J.L. Wuite, Iddo Heller, Erwin J.G. Peterman

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-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.

Original language	English
Article number	eaav1083
Pages (from-to)	1-11
Number of pages	11
Journal	Science advances
Volume	5
Issue number	3
DOIs	https://doi.org/10.1126/sciadv.aav1083
Publication status	Published - 22 Mar 2019

Funding

A.S.Ba. acknowledges research funding and support from the Harry S. Truman Fellowship. I.H. acknowledges research funding from an NWO VIDI award. A.S.Bi. and E.J.G.P. acknowledge research funding from the Human Frontier Science Program. G.A.K., G.J.L.W., and E.J.G.P. acknowledge research funding from the Netherlands Organization for Scientific Research (NWO; “Catching PICH in the Act,” project number 741.015.002). The research leading to these results has received funding from LASERLAB-EUROPE (grant agreement no. 654148, European Union’s Horizon 2020 Research and Innovation Programme). This work was supported by the Laboratory Directed Research and Development program at Sandia National Laboratories, a multimission laboratory managed and operated by the National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract no. DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the U.S. government.

Funders	Funder number
U.S. Department of Energy	DE-NA0003525
Sandia National Laboratories
Horizon 2020 Framework Programme	654148
Instituto Nacional de Ciência e Tecnologia para Engenharia de Software

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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.",

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

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