title: Opposite effect of counterions on the persistence length of nicked and non-nicked DNA.
abstract: Using cryo-electron microscopy we reconstructed the three-dimensional trajectories adopted in cryovitrified solutions by double-stranded DNA molecules in which the backbone of one strand lacked a phosphate at regular intervals of 20 nucleotides. The shape of such nicked DNA molecules was compared with that of DNA molecules with exactly the same sequence but without any single-stranded scissions. Upon changing the salt concentration we observed opposite effects of charge neutralization on nicked and non-nicked DNA. In low salt solutions (10 mM Tris-HCl, 10 mM NaCl) the applied dense nicking caused ca 3.5-fold reduction of the DNA persistence length as compared with non-nicked DNA. Upon increasing the salt concentration (to 150 mM NaCl and 10 mM MgCl2) the persistence length of non-nicked DNA appreciably decreased while that of nicked DNA molecules increased by a factor of 2.
authors.affiliation: Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Switzerland.
authors.forename: P
authors.initials: P
authors.lastname: Furrer
authors.forename: J
authors.initials: J
authors.lastname: Bednar
authors.forename: A Z
authors.initials: AZ
authors.lastname: Stasiak
authors.forename: V
authors.initials: V
authors.lastname: Katritch
authors.forename: D
authors.initials: D
authors.lastname: Michoud
authors.forename: A
authors.initials: A
authors.lastname: Stasiak
authors.forename: J
authors.initials: J
authors.lastname: Dubochet
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004249:DNA Damage; D005615:Freezing; D007091:Image Processing, Computer-Assisted; D015636:Magnesium Chloride / Q000494:pharmacology*; D008854:Microscopy, Electron; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism; D012965:Sodium Chloride / Q000494:pharmacology*
chemical_list: D015636:Magnesium Chloride; D012965:Sodium Chloride; D004247:DNA; D015719:Single-Strand Specific DNA and RNA Endonucleases