Right place, Right Time: Modeling the search time and specificity of Cas9 and Argonaute

Misha Klein

Research output: ThesisDissertation (TU Delft)

144 Downloads (Pure)


The past decade has witnessed a revolution in genome-engineering. Using CRISPR-Cas9 DNA sequences can be marked, detected and cleaved. Rewriting life’s instructions in such a fashion paves the way towards numerous scientific, agricultural and medical applications. Without proper quantfication of the associated risks we face the danger of applying treatments without knowing its consequences. Most notable concern lies in Cas9’s specificity. Although Cas9 targets DNA complementary to any designed 20nt guide RNA, it notoriously also acts on non-fully matching sequences. This thesis describes work towards a physical understanding of how Cas9 and similar RNA/DNA guided systems locate and recognize their target. Chapter 1 introduces the reader to life’s most important molecules (DNA, RNA and protein) as well as to the RNA guided CRISPR and Argonaute (Ago) systems. The chapter also provides an introduction to the main modeling techniques used in subsequent chapters.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Delft University of Technology
  • Joo, C., Supervisor
  • Depken, S.M., Advisor
Award date13 Dec 2019
Print ISBNs978-90-8593-420-2
Publication statusPublished - 2019


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