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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Cooperative Binding of Transcription Regulators

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Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

Nonspecifically bound proteins spin while diffusing along DNA.

Paul C Blainey1, Guobin Luo, S C Kou

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Nature Structural & Molecular Biology
|November 10, 2009
PubMed
Summary
This summary is machine-generated.

DNA-binding proteins slide along DNA via rotation-coupled motion, not just simple translation. This mechanism, observed across various protein sizes, facilitates efficient DNA site searching with low energy barriers.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Protein Dynamics

Background:

  • DNA-binding proteins search for specific sites by moving along the DNA helix.
  • The precise mechanism of protein motion (pure translation vs. rotation-coupled sliding) has been unclear.

Purpose of the Study:

  • To elucidate the motion dynamics of DNA-binding proteins along the DNA helix.
  • To differentiate between one-dimensional (1D) translational diffusion and rotation-coupled sliding.

Main Methods:

  • Measured 1D diffusion constants of proteins as a function of protein size.
  • Employed bootstrap analysis of single-molecule diffusion data.
  • Compared experimental results with theoretical models of pure translation and rotation-coupled sliding.

Main Results:

  • DNA-binding proteins exhibit rotation-coupled sliding along the DNA helix.
  • This motion is consistent with diffusion on a rugged free-energy landscape.
  • Rotation-coupled sliding is a general phenomenon observed for proteins of varying sizes.

Conclusions:

  • DNA-binding proteins utilize rotation-coupled sliding for efficient search along DNA.
  • The average free-energy barrier for sliding is low (1.1 +/- 0.2 k(B)T).
  • These low barriers enable rapid target site identification.