Chalmers Conferences, 9th European Conference on Mathematical and Theoretical Biology

Computational Studies of B-Z transitions in DNA
Nam-Kyung Lee, Ah-Young Kwon

Last modified: 2014-03-28


Left-handed Z-DNA has drawn much attention because of its relevance to various biological processes.

Under the negative torsion, DNA adopts to the left-handed helical forms. The standard form of right-handed B-DNA unwinds to left-handed Z-DNA or L- DNA. While Z-DNA has well defined structure and localized in the specific sequence, L-DNA may form from any sequence and its structure is also dubious. The interplay between these conformations is essential to understand the thermodynamic stability of Z-form. We provide the model for the helical structural transitions in DNA as a helical worm-like chain. Using density of state method, we investigate the mechanical properties of the B-Z transition occurring in short Z-DNA forming sequences imbedded in a random sequence. The B-Z transitions in those sequences are sensitive to applied tension and torsion. Considering the relevant binding energies of base pairs and mechanical parameters, we compute the energy landscape of underwound DNA at various tensions and estimate the energy barrier and critical torque for B-Z transitions.


DNA B-Z transition; density of state methods; kinetics; energetics