한빛사 논문
Sook Ho Kim1,2,3, Hae Jun Jung1,2, Il-Buem Lee1,2, Nam-Kyung Lee4,* and Seok-Cheol Hong1,2,*
1Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841 Korea,
2Department of Physics, Korea University, Seoul, 02841 Korea,
3GRI-TPC International Research Center, Sejong University, Seoul, 05006 Korea and
4Department of Physics and Astronomy, Sejong University, Seoul, 05006 Korea
*Corresponding author
Abstract
Despite recent genome-wide investigations of functional DNA elements, the mechanistic details about their actions remain elusive. One intriguing possibility is that DNA sequences with special patterns play biological roles, adopting non-B-DNA conformations. Here we investigated dynamics of thymine-guanine (TG) repeats, microsatellite sequences and recurrently found in promoters, as well as cytosine–guanine (CG) repeats, best-known Z-DNA forming sequence, in the aspect of Z-DNA formation. We measured the energy barriers of the B–Z transition with those repeats and discovered the sequence-dependent penalty for Z-DNA generates distinctive thermodynamic and kinetic features in the torque-induced transition. Due to the higher torsional stress required for Z-form in TG repeats, a bubble could be induced more easily, suppressing Z-DNA induction, but facilitate the B–Z interconversion kinetically at the transition midpoint. Thus, the Z-form by TG repeats has advantages as a torsion buffer and bubble selector while the Z-form by CG repeats likely behaves as torsion absorber. Our statistical physics model supports quantitatively the populations of Z-DNA and reveals the pivotal roles of bubbles in state dynamics. All taken together, a quantitative picture for the transition was deduced within the close interplay among bubbles, plectonemes and Z-DNA.
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