Dynamics of the B-to-Z transition in supercoiled DNA.
The sequence (dC-dG)16, inserted into the polylinker of plasmid pUC8, adopts a left-handed Z-DNA conformation at "natural" supercoil density. The radioactively labeled monoclonal antibody Z-D11, which has a very high affinity for this DNA conformation, provides a convenient sensitive tool to measure selectively the amount of Z-DNA. Chloroquine reversibly changes the supercoil density of plasmid DNA and thereby the equilibrium between right- and left-handed double-helical DNA. The time-dependent formation or disappearance of Z-DNA was measured by using the antibody either as a fast indicator of Z-DNA or as an additional effector of the B-to-Z equilibrium. In the middle of the transition, a relaxation time of about 1 hr is observed in 0.1 M NaCl at 22 degrees C. The kinetic data are compatible with an all-or-none transition between the two conformations. The overall rate constant for Z-DNA formation, kBZ, decreases with the square of the chloroquine concentration, while the reverse one, kZB, increases with about the fourth power.
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D000911:Antibodies, Monoclonal / Q000276:immunology; D000918:Antibody Specificity; D002738:Chloroquine / Q000494:pharmacology; D004247:DNA / Q000032:analysis / Q000276:immunology; D004269:DNA, Bacterial / Q000032:analysis / Q000276:immunology; D004278:DNA, Superhelical / Q000032:analysis* / Q000276:immunology; D007700:Kinetics; D009690:Nucleic Acid Conformation / Q000187:drug effects; D010957:Plasmids; D012965:Sodium Chloride / Q000494:pharmacology
D000911:Antibodies, Monoclonal; D004269:DNA, Bacterial; D004278:DNA, Superhelical; D012965:Sodium Chloride; D002738:Chloroquine; D004247:DNA