title: Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace.
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.
authors.affiliation: Department of Physics, National University of Singapore, Singapore 117542.
authors.forename: Ce
authors.initials: C
authors.lastname: Zhang
authors.forename: Durgarao
authors.initials: D
authors.lastname: Guttula
authors.forename: Fan
authors.initials: F
authors.lastname: Liu
authors.forename: Piravi P
authors.initials: PP
authors.lastname: Malar
authors.forename: Siow Yee
authors.initials: SY
authors.lastname: Ng
authors.forename: Liang
authors.initials: L
authors.lastname: Dai
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
authors.forename: Jeroen A
authors.initials: JA
authors.lastname: van Kan
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
mesh_terms: D002876:Chromosomes, Bacterial / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D020868:Gene Silencing; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C116822:hns protein, E coli; D004247:DNA