Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein
Name
Kundukad-2013-Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein.pdf
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16.8 MB
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Author(s)
Doyle, Patrick S.
Kundukad, Binu
Cong, Piewen
van der Maarel, Johan R. C.
Date Issued
July 2013
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Kundukad, B., P. Cong, J. R. C. van der Maarel, and P. S. Doyle. “Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein.” Nucleic Acids Research (July 4, 2013).
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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Creative Commons Attribution 3.0
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DOI of Published Version
https://doi.org/10.1093/nar/gkt593
