Computational design of sequence-specific DNA-binding proteins

• DOI: 10.1101/2023.09.20.558720
• Publication Date: 2023-09-22T04:25:13Z
• Authors: Cameron J. Glasscock; Robert Pecoraro; Ryan McHugh; Lindsey A. Doyle; Wei Chen; Olivier Boivin; Beau Lonnquist; Emily Na; Yuliya Politanska; Hugh K. Haddox; David Cox; Christoffer Norn; Brian Coventry; Inna Goreshnik; Dionne Vafeados; Gyu Rie Lee; Raluca Gordan; Barry L. Stoddard; Frank DiMaio; David Baker
• Keywords: Synthetic Biology; Sequence (biology); Sequence space

Abstract Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, there has been considerable interest the engineering of DBPs with new or altered specificities for genome editing other applications. While some success reprogramming naturally occurring using selection methods, computational design that recognize arbitrary target sites remains an outstanding challenge. We describe a method small specific sequences through interactions bases major groove, employ this conjunction experimental screening to generate binders 5 distinct DNA targets. These exhibit specificity closely matching models at as many 6 base positions affinities low 30–100 nM. The crystal structure designed DBP-target site complex is close agreement model, highlighting accuracy method. function both Escherichia coli mammalian cells repress activate transcription neighboring genes. Our substantial step towards general route hence readily deliverable sequence-specific gene regulation editing.