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Nucleic Acids Research Advance Access published online on January 7, 2009
Nucleic Acids Research, doi:10.1093/nar/gkn1011
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Mechanism of DNA flexibility enhancement by HMGB proteins

Jingyun Zhang1, Micah J. McCauley1, L. James Maher, III2, Mark C. Williams1,3,* and N. E. Israeloff1,3,*

1Department of Physics, Northeastern University, Boston, MA 02115, 2Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905 and 3Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 617 373 2917; Fax: +1 617 373 2943; Email: n.israeloff{at}neu.edu

Correspondence may also be addressed to Mark C. Williams. Tel: +1 617 373 7323; Fax: +1 617 373 2943; Email: mark{at}neu.edu

Received October 21, 2008. Revised December 2, 2008. Accepted December 4, 2008.

The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78°, with a standard error of 1.3° and a SD of 23°, while HMGB1 (Box A+B) binding gives a mean bend angle of 67°, with a standard error of 1.3° and a SD of 21°. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.


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