title: Reprogramming homing endonuclease specificity through computational design and directed evolution.
abstract: Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE variants with novel DNA cleavage specificities using an integrated experimental and computational approach. Using computational modeling and an improved selection strategy, which optimizes specificity in addition to activity, we engineered an endonuclease to cleave in a gene associated with Anopheles sterility and another to cleave near a mutation that causes pyruvate kinase deficiency. In the course of this work we observed unanticipated context-dependence between bases which will need to be mechanistically understood for reprogramming of specificity to succeed more generally.
authors.affiliation: Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA, Graduate Program in Biomolecular Structure and Design, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA, Graduate Program in Molecular and Cellular Biology, University of Washington, UW Box 357275, 1959 NE Pacific St., Seattle, WA 98195, USA, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, Imperial College Road, London SW7 2AZ, UK, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB1 3QA, UK, Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA and Howard Hughes Medical Institute, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA.
authors.forename: Summer B
authors.initials: SB
authors.lastname: Thyme
authors.forename: Sandrine J S
authors.initials: SJ
authors.lastname: Boissel
authors.forename: S
authors.initials: S
authors.lastname: Arshiya Quadri
authors.forename: Tony
authors.initials: T
authors.lastname: Nolan
authors.forename: Dean A
authors.initials: DA
authors.lastname: Baker
authors.forename: Rachel U
authors.initials: RU
authors.lastname: Park
authors.forename: Lara
authors.initials: L
authors.lastname: Kusak
authors.forename: Justin
authors.initials: J
authors.lastname: Ashworth
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D019295:Computational Biology; D053837:DNA Cleavage; D019020:Directed Molecular Evolution / Q000379:methods*; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017344:Genes, Insect; D008958:Models, Molecular; D015202:Protein Engineering / Q000379:methods*; D013379:Substrate Specificity
chemical_list: D004706:Endodeoxyribonucleases