A Study of p53 Action on DNA at the Single Molecule Level

Kamagata, Kiyoto

doi:10.5772/intechopen.96163

Cited by 2 publications

(2 citation statements)

References 60 publications

(72 reference statements)

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“…It forms a tetramer and utilizes a folded core domain and a disordered C-terminal (CT) domain for DNA binding in a specific and nonspecific manner, respectively (Anderson et al, 1997). Fifty percent of gene mutations in tumor cells were found in p53, and (Itoh et al, 2018;Subekti et al, 2020;Kamagata et al, 2021b;Kamagata, 2021) with some modifications. Panel (E) was reprinted with permission from (Takada et al, 2015) Copyright 2015 American Chemical Society with some modifications.…”

Section: Action Of Dna-binding Proteins Along Dnamentioning

confidence: 99%

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Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

Kamagata

2021

Front. Mol. Biosci.

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DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.

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Section: Action Of Dna-binding Proteins Along Dnamentioning

confidence: 99%

“…A p53 molecule transferred at the intersection between two DNA molecules. Panels (A-D, F) are adapted from various references(Itoh et al, 2018;Subekti et al, 2020;Kamagata et al, 2021b;Kamagata, 2021) with some modifications. Panel (E) was reprinted with permission from(Takada et al, 2015) Copyright 2015 American Chemical Society with some modifications.…”

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confidence: 99%

Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

Kamagata

2021

Front. Mol. Biosci.

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Engineering of the genome editing protein Cas9 to slide along DNA

Banerjee

Takahashi

Subekti

et al. 2021

Sci Rep

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The genome editing protein Cas9 faces engineering challenges in improving off–target DNA cleavage and low editing efficiency. In this study, we aimed to engineer Cas9 to be able to slide along DNA, which might facilitate genome editing and reduce off-target cleavage. We used two approaches to achieve this: reducing the sliding friction along DNA by removing the interactions of Cas9 residues with DNA and facilitating sliding by introducing the sliding-promoting tail of Nhp6A. Seven engineered mutants of Cas9 were prepared, and their performance was tested using single-molecule fluorescence microscopy. Comparison of the mutations enabled the identification of key residues of Cas9 to enhance the sliding along DNA in the presence and absence of single guide RNA (sgRNA). The attachment of the tail to Cas9 mutants enhanced sliding along DNA, particularly in the presence of sgRNA. Together, using the proposed approaches, the sliding ability of Cas9 was improved up to eightfold in the presence of sgRNA. A sliding model of Cas9 and its engineering action are discussed herein.

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A Study of p53 Action on DNA at the Single Molecule Level

Cited by 2 publications

References 60 publications

Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

Engineering of the genome editing protein Cas9 to slide along DNA

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