Cas9の標的探索及び認識機構の生物物理学的モデリング

• Material Type: 博士論文
• Title: Cas9の標的探索及び認識機構の生物物理学的モデリング
• Author/Editor: Lu, Qiao
• Author Heading: Lu, Qiao
• Publication Date: 2023-10-31
• Publication Date (W3CDTF): 2023-10-31
• Alternative Title: Biophysical Modeling of Cas9 Target-searching and Recognition
• Degree grantor/type: Okinawa Institute of Science and Technology Graduate University
• Date Granted: 2023-10-31
• Date Granted (W3CDTF): 2023-10-31
• Dissertation Number: 甲第134号
• Degree Type: Doctor of Philosophy
• Text Language Code: eng
• Target Audience: 一般
• Note (General): In this thesis, I model the 1D diffusion and unbinding of Cas9 on/from DNA. Cas9 plays a key role in the CRISPR/Cas (CRISPR-associated protein) system. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) are regions of a prokaryote DNA in which palindromic sequences are interspaced by sequences of foreign origins. These foreign sequences can be transcribed into guide RNAs. Cas9 is an enzyme that combines with guide RNA and afterwards can recognize and cleave DNA strands that are complementary to the guide RNA. However, it is not clear how does Cas9 identify its target. The protospacer adjacent motif (PAM) is a “NGG” segment on DNA. The recognition of PAM is the initial stage of the target searching mechanism. Experiments suggest that Cas9 uses 3D diffusion combined with 1D diffusion along the DNA, a mechanism termed facilitated diffusion. My model explains the distribution of binding events observed in experiments and predicts biophysically relevant parameters. I then analyze the behavior of Cas9 on a generic DNA with disordered assortment of PAMs by using an analogy with Anderson localization in condensed matter physics. I then propose a model of the off-target behavior (specificity) of Cas9. From the measured rates, I determine the energy landscapes of on-target and off-target DNA sequences, and the thermodynamic parameters in double strand DNA and DNA-RNA hybrids. Finally, from a perspective of two-mode target recognition strategy, I investigate the effect of PAM and its binding energy on the efficiency of Cas9 in the facilitated diffusion process.
• DOI: 10.15102/0002000211; https://doi.org/10.15102/0002000211
• Persistent ID (NDL): info:ndljp/pid/13122558; https://dl.ndl.go.jp/pid/13122558
• Collection: 障害者向け資料
• Collection (Materials For Handicapped People:1): テキストデータ
• Collection (particular): 国立国会図書館デジタルコレクション > デジタル化資料 > 博士論文; https://dl.ndl.go.jp/collections/A00014
• Acquisition Basis: 博士論文（自動収集）
• Date Accepted (W3CDTF): 2023-12-15T22:13:24+09:00
• Format (IMT): application/pdf
• Access Restrictions: 国立国会図書館内限定公開
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• Periodical Title (URI): http://dx.doi.org/10.15102/0002000211; https://oist.repo.nii.ac.jp/records/2000211
• Data Provider (Database): 国立国会図書館 : 国立国会図書館デジタルコレクション; https://dl.ndl.go.jp

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