Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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Author(s)

  • Ce Zhang
  • Durgarao Guttula
  • Fan Liu
  • Piravi P. Malar
  • Siow Yee Ng
  • Patrick S. Doyle
  • Jeroen A. van Kan
  • Johan R. C. van der Maarel

Detail(s)

Original languageEnglish
Pages (from-to)9593-9601
Journal / PublicationSoft Matter
Volume9
Issue number40
Online published14 Aug 2013
Publication statusPublished - 28 Oct 2013
Externally publishedYes

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. © 2013 The Royal Society of Chemistry.

Citation Format(s)

Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace. / Zhang, Ce; Guttula, Durgarao; Liu, Fan; Malar, Piravi P.; Ng, Siow Yee; Dai, Liang; Doyle, Patrick S.; van Kan, Jeroen A.; van der Maarel, Johan R. C.

In: Soft Matter, Vol. 9, No. 40, 28.10.2013, p. 9593-9601.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review