ApT pocket

A recent nanosecond range MD simulation on the DNA duplex d(CGCGAATTCGCG)2, based on the AMBER 4.1 force-field and the PME method, confirmed independently the stability of B-form duplexes under these simulation conditions. The authors observed an intrusion of a Na counterion in the DNA minor groove at an ApT step termed subsequently the ApT pocket . They concluded that such ion intrusion in DNA minor grooves may influence thermodynamical and structural DNA properties in a sequence-dependent manner. The dynamical properties as well as the hydration of the B-form d(CCAACGTTGG)2 decamer, shown to be stable in the nanosecond range, were investigated by Cheatham et al. ... 

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