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Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Protein Diffusion in the Membrane01:24

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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Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking
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Diffusion-based DNA target colocalization by thermodynamic mechanisms.

Antonio Scialdone1, Mario Nicodemi

  • 1Dipartimento di Scienze Fisiche, Università di Napoli "Federico II" and INFN, Napoli, 80126, Italy. antonio.scialdone@na.infn.it

Development (Cambridge, England)
|October 28, 2010
PubMed
Summary
This summary is machine-generated.

DNA interactions in cell nuclei rely on bridging molecules. Stable contacts form via a thermodynamic switch, requiring sufficient binder concentration and affinity for DNA target recognition.

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Area of Science:

  • Cell Biology
  • Biophysics
  • Genomics

Background:

  • Eukaryotic cell nuclei feature complex DNA interactions and 3D architecture.
  • These interactions are shaped by intra- and inter-chromosomal cross-talks.
  • Mechanisms for DNA loci recognition and transport by Brownian diffusion remain unclear.

Purpose of the Study:

  • To investigate the physics of DNA loci recognition and colocalization.
  • To model the role of diffusing bridging molecules in mediating DNA interactions.
  • To understand the conditions necessary for stable DNA contacts.

Main Methods:

  • Developed a physics model incorporating diffusing bridging molecules.
  • Analyzed the thermodynamic switch-like process for target recognition.
  • Examined the kinetics of passive shuttling via random diffusion.

Main Results:

  • DNA target recognition and colocalization occur via a thermodynamic switch-like process.
  • Stable contacts require binding molecules above a specific concentration and affinity threshold.
  • The model predicts outcomes based on genomic modifications and deletions.

Conclusions:

  • Bridging molecules are crucial for DNA loci recognition and stable contact formation.
  • A thermodynamic phase transition governs DNA colocalization in a passive diffusion model.
  • The findings offer insights into nuclear architecture and genome organization.