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. 2013 May 7;104(9):2058–2067. doi: 10.1016/j.bpj.2013.03.032

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© 2013 by the Biophysical Society.

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Molecular dynamics model of atomic DNA structure highly bent and under extreme compression. (A and B) Front and top views of all-atom initial condition of a 33-bp toroid with helical axis predicted by rod model inside the constraints of the cavity. The DNA sequence is the first 75 bps from the ϕ29 genome. (C and D) Same views of final conformations after MD equilibration within the constraints of the cavity show that basepairing is preserved. (Magenta) Hydrogen bonds. All atomistic DNA graphics generated with UCSF CHIMERA (36).