Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A

Authors

Manas Kumar Sarangi, University of Illinois at ChicagoFollow
Viktoriya Zvoda, University of Illinois at ChicagoFollow
Molly Nelson Holte, Mayo Clinic College of Medicine and ScienceFollow
Nicole A. Becker, Mayo Clinic College of Medicine and ScienceFollow
Justin Peters, University of Northern IowaFollow
L. James Maher III, Mayo Clinic College of Medicine and ScienceFollow
Anjum Ansari, University of Illinois at ChicagoFollow

Document Type

Article

Publication Version

Published Version

Keywords

Flexibility In-Vitro, HMG Box Interactions, Saccharomyes-Cerevisiae, Crystal-Structure, Repression Loop, Faciliated Dissociation, Conformational-Changes, Single; HU, Complex

Journal/Book/Conference Title Title

Nucleic Acids Research

Volume

47

Issue

6

First Page

2871

Last Page

2883

Abstract

The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60◦. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18- base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6Abound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45◦C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35◦C. Microseconds-resolved laser temperaturejump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 s−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.

Department

Department of Chemistry and Biochemistry

Comments

First published in Nucleic Acids Research, v.47 n.6 (April 2019), by Oxford Academic.DOI: 10.1093/nar/gkz022.

Original Publication Date

4-8-2019

DOI of published version

10.1093/nar/gkz022

Repository

UNI ScholarWorks, Rod Library, University of Northern Iowa

Copyright

©2019 Manas Kumar Sarangi, Viktoriya Zvoda, Molly Nelson Holte, Nicole A. Becker, Justin Peters, L. James Maher III, and Anjum Ansari.

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

Date Digital

2019

Language

en

File Format

application/pdf

Recommended Citation

Sarangi, Manas Kumar; Zvoda, Viktoriya; Holte, Molly Nelson; Becker, Nicole A.; Peters, Justin; Maher, L. James III; and Ansari, Anjum, "Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A" (2019). Faculty Publications. 4.
https://scholarworks.uni.edu/che_facpub/4