The techniques of molecular and harmonic dynamics are used to study the internal mobility of three double-stranded DNA hexamers. A 60 ps molecular dynamics simulation and a normal mode description of d(CpGpCpGpCpG)2 in the B conformation characterize the atomic fluctuations of this structure. A comparison between the two approaches validates the harmonic results at room temperature. Detailed examination of the normal modes indicates that only the low-frequency modes are needed to determine atomic fluctuations. A harmonic analysis is made of d(CpGpCpGpCpG)2 in the Z conformation and of d(TpApTpApTpA)2 in the B conformation using only the low-frequency modes. The atomic fluctuations of the three alternating pyrimidine-purine helices are compared and the dependence on conformation and sequence are discussed. The insights which theoretical calculations can provide for the interpretation of experimental results are explored.