Homology sensing via non-linear amplification of sequence dependent pausing by RecQ helicase
- National Heart, Lung and Blood Institute, National Institutes of Health, United States
- Eötvös Loránd University, Hungary
Abstract
RecQ helicases promote genomic stability through their unique ability to suppress illegitimate recombination and resolve recombination intermediates. These DNA structure-specific activities of RecQ helicases are mediated by the helicase-and-RNAseD like C-terminal (HRDC) domain, via unknown mechanisms. Here, employing single-molecule magnetic tweezers and rapid kinetic approaches we establish that the HRDC domain stabilizes intrinsic, sequence-dependent, pauses of the core helicase (lacking the HRDC) in a DNA geometry-dependent manner. We elucidate the core unwinding mechanism in which the unwinding rate depends on the stability of the duplex DNA leading to transient sequence-dependent pauses. We further demonstrate a non-linear amplification of these transient pauses by the controlled binding of the HRDC domain. The resulting DNA sequence- and geometry-dependent pausing may underlie a homology sensing mechanism that allows rapid disruption of unstable (illegitimate) and stabilization of stable (legitimate) DNA strand invasions, which suggests an intrinsic mechanism of recombination quality control by RecQ helicases.
Data availability
The single molecule experimental data analysis codes in this study were previously published and referenced in the manuscript. The Kerssemakers step-finder routine (J. W. J. Kerssemakers et. al., (2006) Nature, 442:709-712) is available from the authors. Alternative step-finding routines (Wiggins, P. A. (2015). Biophys J 109: 346-354; Hill, F. R., et al. (2018) J Chem Phys 148: 123317) are available here (http://mtshasta.phys.washington.edu/website/steppi/, or here https://github.com/duderstadt-lab/Julia_KCP_Notebooks). Source data for all of the figures and graphs are provided in the main and supplemental data.
Article and author information
Author details
Funding
Human Frontier Science Program (RGY0072/2010)
- Yeonee Seol
- Gábor M Harami
- Mihály Kovács
- Keir C Neuman
National Institutes of Health (HL001056-12)
- Yeonee Seol
- Keir C Neuman
Hungarian Academy of Sciences (LP2011-006/2011)
- Gábor M Harami
- Mihály Kovács
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Homology sensing via non-linear amplification of sequence dependent pausing by RecQ helicase
eLife 8:e45909.
https://doi.org/10.7554/eLife.45909
