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Low complexity channel estimation for single-carrier block transmission systems over multiple-input multiple-output time varying frequency-selective channels is investigated. A time slot structure that uses Golay complementary sequences with perfect periodic autocorrelations as two-sided pilot blocks is presented. Employing this structure, optimal least square estimate in the minimum mean square error (MMSE) sense is achieved. Furthermore, a computationally efficient algorithm which is named as fast periodic Golay correlation is proposed based on the specific generator and the properties related to circulant matrices. Finally, the simulation results show the MMSE performance of the proposed scheme and algorithm.