Competing B-Z and helix-coil conformational transitions in supercoiled plasmid DNA

Aboul-ela, Fareed, Bowater, Richard P. and Lilley, David M.J. (1992) Competing B-Z and helix-coil conformational transitions in supercoiled plasmid DNA. Journal of Biological Chemistry, 267 (3). pp. 1776-1785. ISSN 0021-9258

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Abstract

The formation of melted regions from A + T-rich sequences and left-handed Z-DNA by alternating purine-pyrimidine sequences will both be facilitated by negative supercoiling, and thus if the sequences are present within the same plasmid molecule they will compete for the free energy of supercoiling. We have studied a series of plasmids that contain either (CG)8 or (TG)12 sequences in either G + C or A + T-rich contexts, by means of two-dimensional gel electrophoresis and chemical modification. We observe both B-Z and helix-coil transitions in all plasmids at elevated temperatures and low ionic strength. The plasmids fall into a number of different classes, in terms of the conformational behavior. As the superhelix density is increased, pCG8/vec ((CG)8 in G + C-rich context) undergoes an initial B-Z transition, followed by melting transitions in sequences remote from the (CG)8 sequence. The two transitions are coupled through the topology of the molecule but are otherwise independent. When the (CG)8 sequence was placed in an A + T-rich context (pCG8/col), the helix-coil transition was perturbed by the presence of the Z-DNA segment. Replacement of the (CG)8 tracts by (TG)12 sequences resulted in a further level of interaction between the transitions. Statistical mechanical modeling of the transitions suggested that at intermediate levels of negative supercoiling the Z-DNA formed by the (TG)12 sequence has a lowered probability due to the helixcoil transition in the A + T-rich sequences. These studies illustrate the complexities of competing conformational equilibria in supercoiled DNA molecules.

Item Type:	Article
Uncontrolled Keywords:	biochemistry,molecular biology,cell biology ,/dk/atira/pure/subjectarea/asjc/1300/1303
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	26 May 2026 13:30
Last Modified:	31 May 2026 05:28
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103155
DOI:

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