scholarly journals Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Davide Normanno ◽  
Lydia Boudarène ◽  
Claire Dugast-Darzacq ◽  
Jiji Chen ◽  
Christian Richter ◽  
...  
Keyword(s):  
Dna Binding ◽  
Mammalian Cells ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Target Search

scholarly journals Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

2020 ◽  
Author(s):  
Mathew Stracy ◽  
Jakob Schweizer ◽  
David J Sherratt ◽  
Achillefs N Kapanidis ◽  
Stephan Uphoff ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Proteins ◽  
Search Time ◽  
Dna Binding Proteins ◽  
Protein Diffusion ◽  
Chromosomal Dna ◽  
Dna Interactions ◽  
Target Search ◽  
Molecular Weights

ABSTRACTDespite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Towards identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions, rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid does not pose a physical barrier for protein diffusion, but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58-99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome-crowding likely has important implications for the function of all DNA-binding proteins.

scholarly journals Single stranded DNA binding proteins derive from hnRNP proteins by proteolysis in mammalian cells

1985 ◽  
Vol 13 (18) ◽  
pp. 6577-6590 ◽  
Author(s):  
Massimo Pandolfo ◽  
Omar Valentini ◽  
Giuseppe Biamonti ◽  
Carlo Morandi ◽  
Silvano Riva
Keyword(s):  
Dna Binding ◽  
Mammalian Cells ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Single Stranded Dna ◽  
Hnrnp Proteins

scholarly journals Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

2021 ◽  
Author(s):  
Mathew Stracy ◽  
Jakob Schweizer ◽  
David J. Sherratt ◽  
Achillefs N. Kapanidis ◽  
Stephan Uphoff ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Target Search ◽  
Bacterial Dna

Disparity in anomalous diffusion of proteins searching for their target DNA sites in a crowded medium is controlled by the size, shape and mobility of macromolecular crowders

Soft Matter ◽  
2019 ◽  
Vol 15 (9) ◽  
pp. 1960-1969 ◽  
Author(s):  
Pinki Dey ◽  
Arnab Bhattacherjee
Keyword(s):  
Dna Binding ◽  
Physical Properties ◽  
Computer Simulations ◽  
Anomalous Diffusion ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Molecular Crowding ◽  
Target Search ◽  
Target Dna

Using extensive computer simulations, we analyzed the role of physical properties of molecular crowding agents such as size, shape and mobility in the target search dynamics of DNA binding proteins.

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