Opposite effect of counterions on the persistence length of nicked and non-nicked DNA.
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.
Furrer
P
P
Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Switzerland.
Bednar
J
J
Stasiak
A Z
AZ
Katritch
V
V
Michoud
D
D
Stasiak
A
A
Dubochet
J
J
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*
D015636:Magnesium Chloride; D012965:Sodium Chloride; D004247:DNA; D015719:Single-Strand Specific DNA and RNA Endonucleases