Programming Protein Organization into Sequence-Encoded Architectures Using DNA

Winegar, Peter Henry

doi:https://doi.org/10.21985/n2-6vxj-m452

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Programming Protein Organization into Sequence-Encoded Architectures Using DNA

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Proteins are the nanoscale building blocks of life. Their sophisticated but well-defined architectures result in complex biological functions, including ones involved in metabolism, photosynthesis, transcription, translation, and immunity. To study and improve upon the natural functions of proteins, it is desirable to develop methodology for organizing proteins into targeted architectures. While methods exist for controlling proteins and even small collections of proteins into aggregate materials, it is still challenging to organize proteins reliably and quickly into predefined architectures. This is because the chemical structures of proteins and protein–protein interactions are highly complex. The work in this dissertation studies how complex protein–protein interactions can be replaced with well-defined DNA–DNA interactions to program the organization of proteins into sequence-encoded architectures, including single crystals and oligomers. In Chapter One, current approaches to synthesize protein architectures and their limitations are described. In Chapter Two, the impact of DNA on protein crystallization is investigated by replacing native protein–protein interactions with DNA–DNA interactions. In Chapter Three, a modular DNA scaffold is designed to explore the generalizable assembly of proteins into vast numbers of oligomers that contain exact numbers and orders of proteins. In Chapter Four, protein block co-oligomers are synthesized to study the impact of block design on assembly outcome. In Chapter Five, fundamental lessons learned from this work are summarized and future research directions are discussed. Collectively, this dissertation establishes methods to program the organization of proteins into synthetic architectures and discusses the implications of these architectures on protein function, enabling future development of protein-based materials that mimic and surpass the natural functions of proteins.

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