Zutao YU - Artificial Assemblies with Cooperative DNA Recognition

Aims and Scope

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Synthetic DNA binder is a long-lasting attractive topic, but few progresses achieved. In this thesis by Dr. Zutao YU, the author makes an endeavor to understand the crucial limitations of synthetic DNA binding systems and construct novel cooperative DNA binding assemblies.

In Chap., the author systematically reviews the engineering of synthetic PIPs-based DNA binding assembly. The author first separately describes the design of three structural domains (DBD, CID, and FD) and then summarizes the representative artificial assemblies from a combination of these domains. The author also points out the long-standing limitations of PIPs and provides thoughtful comments for future study.

Chaptersintroduce two exemplary cooperative DNA binding systems PIP-HoGu and PIP-NaCo, respectively, in order to overcome the issues of off-target rate and un-flexible binding mode. The CID assures the synergistic binding of two PIPs at the nearby DNA sites and with a flexible gap distance between two PIPs. PIP-NaCo system utilizes left-handed PNA as CID that exhibits orthogonality to cellular nucleic acids and tunability of cooperation. In the in vitro and cell study, both PIP-HoGu and PIP-NaCo systems demonstrate advancement in sequence selectivity and flexible binding.

In Chap., the author takes a brave step forward to construct an advanced genetic switch termed ePIP-HoGu, by installing epigenetic functionality into cooperative DNA binding system and demonstrates its effectiveness in an in vitro HAT assay.

This thesis clarifies the engineering of synthetic DNA binding systems and advanced genetic switches. Significantly, the sequential development of cooperative DNA binding system and epigenetic advanced DNA binding system will fast track the exploration and optimization of the biological study of synthetic DNA binding systems.

First and foremost, I would like to express my sincere admiration to my supervisor, Prof. Hiroshi Sugiyama. His deep insights trained me at various stages of my research and make my work productive and stimulating. I am indebted toward him for his generosity, selfless support and especially for the excellent example and patience that he has provided to me.