Functional instability allows access to DNA in longer Transcription Activator-Like Effector (TALE) arrays

Abstract
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Abstract

Transcription activator-like effectors (TALEs) bind DNA through an array of tandem 34-residue repeats. How TALE repeat domains wrap around DNA, often extending more than 1.5 helical turns, without using external energy is not well understood. Here, we examine the kinetics of DNA binding of TALE arrays with varying numbers of identical repeats. Single molecule fluorescence analysis and deterministic modeling reveal conformational heterogeneity in both the free- and DNA-bound TALE arrays. Our findings, combined with previously identified partly folded states, indicate a TALE instability that is functionally important for DNA binding. For TALEs forming less than one superhelical turn around DNA, partly folded states inhibit DNA binding. In contrast, for TALEs forming more than one turn, partly folded states facilitate DNA binding, demonstrating a mode of 'functional instability' that facilitates macromolecular assembly. Increasing repeat number slows down interconversion between the various DNA-free and DNA-bound states.

Data availability

Source data files have been provided for Figure 3. Source code and data files related to Figure 6 are publicly available and can be found at https://github.com/kgeigers/DeMASK.

The following data sets were generated

(2019) Source code for DeMASK: Deterministic Modeling for Analysis of complex Single molecule Kinetics
Github, doi:10.5281/zenodo.2538666.

https://github.com/kgeigers/DeMASK

Article and author information

Author details

Kathryn Geiger-Schuller

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-6705-0681
Jaba Mitra

Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, United States

Competing interests
No competing interests declared.
Taekjip Ha

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States

Competing interests
Taekjip Ha, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0003-2195-6258
Doug Barrick

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States

For correspondence
barrick@jhu.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-7291-1389

Funding

National Institute of General Medical Sciences (T32-GM008403)

Kathryn Geiger-Schuller

National Institute of General Medical Sciences (R01-GM068462)

Doug Barrick

National Institute of General Medical Sciences (GM1129659)

Taekjip Ha

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.