Physical manipulation of single-molecule DNA using microbead and its application to analysis of DNA–protein interaction

2009 ◽  
Vol 321 (7) ◽  
pp. 655-658
Author(s):  
Hirofumi Kurita ◽  
Hachiro Yasuda ◽  
Kazunori Takashima ◽  
Shinji Katsura ◽  
Akira Mizuno
Keyword(s):  
Single Molecule ◽  
Protein Interaction ◽  
Dna Protein Interaction ◽  
Physical Manipulation

scholarly journals 1P327 Development of a novel mechano-fluorescence microscope for measurement of DNA/protein interaction at single molecule level II

2005 ◽  
Vol 45 (supplement) ◽  
pp. S113
Author(s):  
H. Yokota ◽  
YW. Han ◽  
Jean-Francois Allemand ◽  
Xueuang Xi ◽  
Vincent Croquette ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Interaction ◽  
Fluorescence Microscope ◽  
Single Molecule Level ◽  
Level Ii ◽  
Dna Protein Interaction

scholarly journals Probing protein - DNA interaction by single molecule and structural analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C198-C198
Author(s):  
Jianshi Jin ◽  
Tengfei Lian ◽  
Chan Gu ◽  
Yiqin Gao ◽  
Yujie Sun ◽  
...  
Keyword(s):  
Conformational Change ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Fundamental Property ◽  
Dna Interaction ◽  
Allosteric Effect ◽  
Dna Protein Interaction ◽  
Fine Tune

In proteins, conformational change impacting their function has been well investigated in the past decades, and was named `allosteric effect'. However, in DNA-protein interaction, the concept of DNA conformational change caused by DNA-protein binding will affect another nearby DNA-binding protein has not been well investigated and understood. Combined with structural biology and Single Molecule Assays, we can now probe and study allosteric propagation through DNA which exists as a fundamental property in DNA-protein interaction, and this allosteric effect through DNA can fine tune gene expression. Therefore, DNA conformational changes should be seriously considered and analyzed for DNA –protein interactions in general.

scholarly journals Mapping protein binding stability on nucleosomal DNA by single-molecule approach

2014 ◽  
Vol 70 (a1) ◽  
pp. C111-C111
Author(s):  
Jianshi Jin ◽  
Teng-fei Lian ◽  
Xiaoliang Xie ◽  
Xiao-Dong Su
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Conformational Changes ◽  
Protein Interaction ◽  
Binding Sites ◽  
Binding Domain ◽  
Shielding Effect ◽  
Dna Binding Domain ◽  
Nucleosomal Dna ◽  
Dna Protein Interaction

The conformation of nucleosomal DNA is significantly different from that of a canonical B-form double stranded DNA (dsDNA), and is generally regarded to be less flexible and less accessible than free dsDNA due to the tight association of histone cores. Previous studies have demonstrated that the key mechanism involved in nucleosomal DNA-protein interaction is the protein accessibility to the DNA binding site. In this work, we used single molecule assays to measure the stability of two transcriptional factors (glucocorticoid receptor DNA binding domain (GRDBD) and estrogen receptor DNA-binding domain (ERDBD)) bound to their binding sites on different positions of the nucleosomal DNA. Interestingly, the results demonstrated that the nucleosomal DNA-GRDBD binding is not always consistent with the histone shielding effect, but adjusted by additional structural changes. Furthermore, the changes of these DNA-GRDBD interaction profiles were confirmed using molecular modeling and docking approaches based on their crystal structures. Very differently, ERDBD essentially is unable to bind to the nucleosomal DNA anywhere including the unblocked positions. We thus have concluded that the nucleosomal DNA-protein interaction is regulated not only by the histone shielding of the DNA binding sites, but also by the conformational changes of the nucleosomal DNA.

scholarly journals 2P287 Development of a novel mechano-fluorescence microscope for measurement of DNA/protein interaction at single molecule level

2004 ◽  
Vol 44 (supplement) ◽  
pp. S181
Author(s):  
H. Yokota ◽  
Jean-Francois Allemand ◽  
Xuguang Xi ◽  
Vincent Croquette ◽  
David Bensimon
Keyword(s):  
Single Molecule ◽  
Protein Interaction ◽  
Fluorescence Microscope ◽  
Single Molecule Level ◽  
Dna Protein Interaction

Weakening of DNA-protein interaction in cultured human fibroblasts induced by chemical mutagens

1987 ◽  
Vol 104 (6) ◽  
pp. 1730-1732
Author(s):  
A. I. Gorin ◽  
N. S. Bogomolova ◽  
A. V. Ermakov ◽  
M. I. Freidin ◽  
V. A. Chernov ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Human Fibroblasts ◽  
Chemical Mutagens ◽  
Cultured Human Fibroblasts ◽  
Dna Protein Interaction
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