title: Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein.
abstract: HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA-HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ∼2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.
authors.affiliation: BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore-Massachusetts Institute of Technology Alliance, National University of Singapore, Singapore 117576, Department of Physics, National University of Singapore, Singapore 117542 and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Binu
authors.initials: B
authors.lastname: Kundukad
authors.forename: Piewen
authors.initials: P
authors.lastname: Cong
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D004270:DNA, Circular / Q000648:ultrastructure; D004278:DNA, Superhelical / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000378:metabolism*; D018625:Microscopy, Atomic Force
chemical_list: D001426:Bacterial Proteins; D004270:DNA, Circular; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; C040330:histone-like protein HU, bacteria; D004247:DNA