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Peer-reviewedCC BY 4.0Cell Reports Methods

Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution

  • Amanda L. Wacker1,2
  • Ryan J. Fantasia1,2
  • Brian Tenner2
  • Boyu Liu2
  • Jerry D. Wu2,3
  • Nicholas Monell1,2
  • Pallav Kosuri1,2
  1. 1Department of Molecular Biology, University of California, San Diego, 9500 Gillman Drive, La Jolla, CA 92093, USA
  2. 2Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
  3. 3Omenn-Darling Bioengineering Institute, Princeton University, 41 Olden Street, Princeton, NJ 08544, USA
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Abstract

Protein-DNA interactions often result in rotational movements. These movements underlie many genetic processes such as DNA transcription by RNA polymerases (RNAPs). To illuminate these movements, we previously developed origami-rotor-based imaging and tracking (ORBIT), a fluorescence-based method that enables high-speed tracking of DNA rotation. When used to track DNA rotation during transcription by E. coli RNAP, ORBIT enabled the detection of single base-pair steps. However, the duration of ORBIT experiments was limited due to fluorescence photobleaching. To overcome this limitation and extend the total possible observation time, we here introduce dye-cycling ORBIT (dcORBIT), a method that enables observation of protein-DNA interactions for over 10 min at 20 Hz while maintaining single-base-pair precision. dcORBIT thereby opens new possibilities to study the fundamental rotational movements underlying gene expression.

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Cite

BibTeXRIS
BibTeX
@article{wacker2026dyecycling,
  title = {{Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution}},
  author = {Amanda L. Wacker and Ryan J. Fantasia and Brian Tenner and Boyu Liu and Jerry D. Wu and Nicholas Monell and Pallav Kosuri},
  journal = {Cell Reports Methods},
  year = {2026},
  month = aug,
  doi = {10.1016/j.crmeth.2026.101550},
  url = {https://doi.org/10.1016/j.crmeth.2026.101550},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution
AU  - Amanda L. Wacker
AU  - Ryan J. Fantasia
AU  - Brian Tenner
AU  - Boyu Liu
AU  - Jerry D. Wu
AU  - Nicholas Monell
AU  - Pallav Kosuri
PY  - 2026
DA  - 2026/08/13
JO  - Cell Reports Methods
DO  - 10.1016/j.crmeth.2026.101550
UR  - https://doi.org/10.1016/j.crmeth.2026.101550
AB  - Protein-DNA interactions often result in rotational movements. These movements underlie many genetic processes such as DNA transcription by RNA polymerases (RNAPs). To illuminate these movements, we previously developed origami-rotor-based imaging and tracking (ORBIT), a fluorescence-based method that enables high-speed tracking of DNA rotation. When used to track DNA rotation during transcription by E. coli RNAP, ORBIT enabled the detection of single base-pair steps. However, the duration of ORBIT experiments was limited due to fluorescence photobleaching. To overcome this limitation and extend the total possible observation time, we here introduce dye-cycling ORBIT (dcORBIT), a method that enables observation of protein-DNA interactions for over 10 min at 20 Hz while maintaining single-base-pair precision. dcORBIT thereby opens new possibilities to study the fundamental rotational movements underlying gene expression.
SN  - 2667-2375
ER  -