WEKO3
アイテム
Cas9の標的探索及び認識機構の生物物理学的モデリング
https://doi.org/10.15102/0002000211
https://doi.org/10.15102/0002000211b10cebbc-131a-44f0-98bc-6082fe8a0e61
名前 / ファイル | ライセンス | アクション |
---|---|---|
LuQiaoFulltext.pdf (3.1 MB)
|
|
|
LuQiaoExamAbstract.pdf (48 KB)
|
|
Item type | 学位論文 / Thesis or Dissertation(1) | |||||||
---|---|---|---|---|---|---|---|---|
公開日 | 2023-11-15 | |||||||
タイトル | ||||||||
タイトル | Cas9の標的探索及び認識機構の生物物理学的モデリング | |||||||
言語 | ja | |||||||
タイトル | ||||||||
タイトル | Biophysical Modeling of Cas9 Target-searching and Recognition | |||||||
言語 | en | |||||||
言語 | ||||||||
言語 | eng | |||||||
資源タイプ | ||||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_db06 | |||||||
資源タイプ | doctoral thesis | |||||||
ID登録 | ||||||||
ID登録 | 10.15102/0002000211 | |||||||
ID登録タイプ | JaLC | |||||||
アクセス権 | ||||||||
アクセス権 | open access | |||||||
アクセス権URI | http://purl.org/coar/access_right/c_abf2 | |||||||
著者 (英) |
Lu, Qiao
× Lu, Qiao
|
|||||||
抄録 | ||||||||
内容記述タイプ | Abstract | |||||||
内容記述 | 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. | |||||||
言語 | en | |||||||
口頭試問日 | ||||||||
値 | 2023-09-11 | |||||||
学位授与年月日 | ||||||||
学位授与年月日 | 2023-10-31 | |||||||
学位名 | ||||||||
学位名 | Doctor of Philosophy | |||||||
学位授与番号 | ||||||||
学位授与番号 | 甲第134号 | |||||||
学位授与機関 | ||||||||
学位授与機関識別子Scheme | kakenhi | |||||||
学位授与機関識別子 | 38005 | |||||||
学位授与機関名 | Okinawa Institute of Science and Technology Graduate University | |||||||
著者版フラグ | ||||||||
出版タイプ | VoR | |||||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||||
権利 | ||||||||
権利情報 | © 2023 The Author. |