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. Author manuscript; available in PMC: 2016 May 13.
Published in final edited form as: Q Rev Biophys. 2012 Jul 31;45(3):257–299. doi: 10.1017/S0033583512000054

Fig. 6.

Fig. 6

Representative structure from an MD simulation of a highly overwound (σ=0.391) DNA duplex (Randall et al. 2009). The very high torsional strain is relieved by the formation of a 5 bp region of P-DNA, allowing the remainder of the helix to relax back to B-DNA (bottom). Counterion densities are contoured in dark blue showing the expected signatures in the grooves of the B-DNA region. In the region of P-DNA, counterions are highly concentrated near the intertwined negatively charged backbones.