Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility

Micah J. McCauley, Emily M. Rueter, Ioulia Rouzina, L. James Maher, Mark C. Williams

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (∼10 s-1) are higher than those observed for wild-type proteins (∼0.1-1.0 s-1), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB-DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility.

Original languageEnglish (US)
Pages (from-to)167-181
Number of pages15
JournalNucleic acids research
Issue number1
StatePublished - Jan 2013

Bibliographical note

Funding Information:
National Institutes of Health [2R01GM72462 to M.C.W., 2R01GM075965 to L.J.M.]; Mayo Foundation. Funding for open access charge: NIH [GM075965].


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