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The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

Author

Listed:
  • Andreas S. Biebricher

    (LaserLaB Amsterdam, VU University Amsterdam)

  • Iddo Heller

    (LaserLaB Amsterdam, VU University Amsterdam)

  • Roel F. H. Roijmans

    (LaserLaB Amsterdam, VU University Amsterdam)

  • Tjalle P. Hoekstra

    (LaserLaB Amsterdam, VU University Amsterdam)

  • Erwin J. G. Peterman

    (LaserLaB Amsterdam, VU University Amsterdam)

  • Gijs J. L. Wuite

    (LaserLaB Amsterdam, VU University Amsterdam)

Abstract

DNA intercalators are widely used as fluorescent probes to visualize DNA and DNA transactions in vivo and in vitro. It is well known that they perturb DNA structure and stability, which can in turn influence DNA-processing by proteins. Here we elucidate this perturbation by combining single-dye fluorescence microscopy with force spectroscopy and measuring the kinetics of DNA intercalation by the mono- and bis-intercalating cyanine dyes SYTOX Orange, SYTOX Green, SYBR Gold, YO-PRO-1, YOYO-1 and POPO-3. We show that their DNA-binding affinity is mainly governed by a strongly tension-dependent dissociation rate. These rates can be tuned over a range of seven orders of magnitude by changing DNA tension, intercalating species and ionic strength. We show that optimizing these rates minimizes the impact of intercalators on strand separation and enzymatic activity. These new insights provide handles for the improved use of intercalators as DNA probes with minimal perturbation and maximal efficacy.

Suggested Citation

  • Andreas S. Biebricher & Iddo Heller & Roel F. H. Roijmans & Tjalle P. Hoekstra & Erwin J. G. Peterman & Gijs J. L. Wuite, 2015. "The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics," Nature Communications, Nature, vol. 6(1), pages 1-12, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms8304
    DOI: 10.1038/ncomms8304
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    Cited by:

    1. Junpeng Xu & Guan Alex Wang & Lu Gao & Lang Wu & Qian Lei & Hui Deng & Feng Li, 2023. "Enabling programmable dynamic DNA chemistry using small-molecule DNA binders," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Christiaan N. Hulleman & Rasmus Ø. Thorsen & Eugene Kim & Cees Dekker & Sjoerd Stallinga & Bernd Rieger, 2021. "Simultaneous orientation and 3D localization microscopy with a Vortex point spread function," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    3. Tuan Nguyen & Sai Li & Jeremy T-H Chang & John W. Watters & Htet Ng & Adewola Osunsade & Yael David & Shixin Liu, 2022. "Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Yin-Wei Kuo & Mohammed Mahamdeh & Yazgan Tuna & Jonathon Howard, 2022. "The force required to remove tubulin from the microtubule lattice by pulling on its α-tubulin C-terminal tail," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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