BY W.XU, D. DUNLAP, & L. FINZI
(Pictured Left to Right: D. Dunlap, W. XU, L. Finzi)
Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to LDNA transition, followed by a discussion of the energetics associated with the the transition to Z-form DNA.
Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNAprotein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.
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