Slow cruciform transitions in palindromic DNA.
- 1 September 1983
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 80 (18), 5545-5549
- https://doi.org/10.1073/pnas.80.18.5545
Abstract
Extrusion of cruciform structures in self-complementary regions of DNA is known to be favored by negative supercoiling of DNA. In moderately supercoiled DNA, cruciform extrusion is a very slow process. In plasmid pUC7 DNA, with a 48 base-pair palindrome, the half-time of extrusion at 50.degree. C is typically several hours; rates are even slower at lower temperature. The rates increase significantly with increasing DNA supercoiling but are only slightly faster in DNA species with much longer palindromes. The reabsorption of cruciform arms is also very slow. The equilibrium between cruciform and regular DNA structures is sensitive to changes in the linking number. Measurement of this equilibrium leads to an estimate of 18 kcal/mol (75.3 kJ/mol) for the free energy required to generate a cruciform structure. In bacterial cells, cruciform DNA may be rare, even when it is thermodynamically favored, because of its slow formation.Keywords
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