Competitive superhelical transitions involving cruciform extrusion
نویسندگان
چکیده
منابع مشابه
Competitive superhelical transitions involving cruciform extrusion
A DNA molecule under negative superhelical stress becomes susceptible to transitions to alternate structures. The accessible alternate conformations depend on base sequence and compete for occupancy. We have developed a method to calculate equilibrium distributions among the states available to such systems, as well as their average thermodynamic properties. Here we extend this approach to incl...
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We present a detailed study of the extrusion of an imperfect palindrome, derived from the terminal regions of vaccinia virus DNA and contained in a superhelical plasmid, into a cruciform containing bulged bases. We monitor the course of extrusion by two-dimensional gel electrophoresis experiments as a function of temperature and linking number. We find that extrusion pauses at partially extrude...
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The relative stability of the cruciform state at the large inverted repeat of plasmid pVH51 is measured. At physiological superhelical densities, the cruciform state is present in a high percentage of the plasmid molecules. Investigation of the relationship between negative superhelical density and cruciform prevalence reveals a sharp transition from an undetectable level to a relatively stable...
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Metropolis–Monte Carlo algorithms are developed to analyze the strand separation transition in circular superhelical DNA molecules. Moves that randomize the locations of unpaired regions are required in order to diminish correlations among the sampled states. This approach enables accurate simulations to be performed in reasonable computational times. Sufficient conditions to guarantee the form...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2013
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkt733