Knotting of a DNA chain during ring closure.
The formation of knotted species on random ring closure of two DNAs that are 5.6 kilobase pairs (kbp) and 8.6 kbp in length was measured, and these data were used to calculate the effective DNA helix diameter as a function of sodium ion and magnesium ion concentration. In the presence of more than 50 mM magnesium ion, interactions between DNA segments appear to be attractive rather than repulsive. The free energy of formation of relaxed trefoil and figure-eight DNA knots and of supercoiled trefoil DNA knots was also evaluated.
Shaw
S Y
SY
Harvard University, Department of Biochemistry and Molecular Biology, Cambridge, MA 02138.
Wang
J C
JC
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004270:DNA, Circular / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism; D008274:Magnesium / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011336:Probability; D012965:Sodium Chloride / Q000494:pharmacology; D013816:Thermodynamics
D004270:DNA, Circular; D004277:DNA, Single-Stranded; D004278:DNA, Superhelical; D012965:Sodium Chloride; D004247:DNA; D008274:Magnesium