Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace
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Doyle_Effect of H-NS.pdf
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Author(s)
Zhang, Ce
Guttula, Durgarao
Liu, Fan
Malar, Piravi P.
Ng, Siow Yee
Dai, Liang
van Kan, Jeroen A.
van der Maarel, Johan R. C.
Doyle, Patrick S
Date Issued
August 2013
Journal
Soft Matter
Publisher
Royal Society of Chemistry
Citation
Zhang, Ce et al. “Effect of H-NS on the Elongation and Compaction of Single DNA Molecules in a Nanospace.” Soft Matter 9.40 (2013): 9593. © 2013 Royal Society of Chemistry
Version
Final published version
Abstract
The effect of the bacterial heat-stable nucleoid-structuring protein (H-NS) on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. With increasing concentration of H-NS, the DNA molecules either elongate or contract. The conformational response is related to filamentation of H-NS on DNA through oligomerization and H-NS mediated bridging of distal DNA segments and is controlled by the concentration and ionic composition of the buffer. Confinement in a nanochannel also facilitates compaction of DNA into a condensed form for over-threshold concentrations of H-NS. Divalent ions such as magnesium facilitate but are not required for bridging nor condensation. The time scale of the collapse after exposure to H-NS was determined to be on the order of minutes, which is much shorter than the measured time required for filamentation of around one hour. We found that the effect of H-NS is not only related to its binding properties but also the confinement is of paramount importance. The interplay between confinement, H-NS-mediated attraction, and filamentation controls the conformation and compaction of DNA. This finding might have implications for gene silencing and chromosome organisation, because the cross-sectional dimensions of the channels are comparable to those of the bacterial nucleoid.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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Creative Commons Attribution-NonCommercial 3.0 Unported
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DOI of Published Version
https://doi.org/10.1039/c3sm51214b
