CRISPR-Cas Arxiv:1712.09865V1 [Q-Bio.PE] 28 Dec 2017
The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas Melia E. Bonomo1;3 and Michael W. Deem1;2;3 1Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA 2Department of Bioengineering, Rice University, Houston, TX 77005, USA 3Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR- associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, as well as non- defensive CRISPR functions that boost host cell robustness. Physical understanding of the CRISPR-Cas system will advance applications, such as efficient and specific genetic engineering, cell labeling and information storage, and combating antibiotic resistance. 1 Introduction In 1987, Ishino and colleagues had set out to identify the encoded protein and primary structure of a particular gene in Escherichia coli by analyzing its chromosomal DNA seg- arXiv:1712.09865v1 [q-bio.PE] 28 Dec 2017 ment and flanking regions [1]. They found an interesting sequence structure at the gene's 3'-end flanking region, in which five homologous sequences of 29 nucleotides were arranged as direct repeats with 32-nucleotide sequences spaced between them.
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