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

29 Scopus citations

Abstract

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
Volume41
Issue number1
DOIs
StatePublished - Jan 2013

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility'. Together they form a unique fingerprint.

Cite this