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As a potential alternative to CMOS technology, QCA provides an interesting paradigm in both communication and computation. However, QCA's unique four-phase clocking scheme and timing constraints present serious timing issues for interconnection and feedback. In this work, a cut-set retiming design procedure is proposed to resolve these QCA timing issues. The proposed design procedure can accommodate QCA's unique characteristics by performing delay-transfer and time-scaling to reallocate the existing delays so as to achieve efficient clocking zone assignment. Cut-set retiming makes it possible to effectively design relatively complex QCA circuits that include feedback. It utilizes the similar characteristics of synchronization, deep pipelines and local interconnections common to both QCA and systolic architectures. As a case study, a systolic Montgomery modular multiplier is designed to illustrate the procedure. Furthermore, a nonsystolic architecture, an S27 benchmark circuit, is designed and compared with previous designs. The comparison shows that the cut-set retiming method achieves a more efficient design, with a reduction of 22%, 44%, and 46% in terms of cell count, area, and latency, respectively.