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In response to DNA damage, cells can pause the cell cycle to assess and repair the breaks. However, the cell must check the DNA at certain critical stages during the cell cycle. If the cell cycle pauses before DNA replication, the cells will contain twice the amount of DNA. On the other hand, if cells arrest after DNA replication but before mitosis, they will contain four times the normal amount of DNA. With a host of specialized proteins at their disposal,cells must use the right protein at...

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Related Experiment Video

Updated: May 18, 2026

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

Sequence-dependent sliding kinetics of p53.

Jason S Leith¹, Anahita Tafvizi, Fang Huang

¹Program in Biophysics, Harvard University, Cambridge, MA 02138, USA.

Proceedings of the National Academy of Sciences of the United States of America

|September 27, 2012

Summary

Transcription factors (TFs) use DNA sliding to find targets, with p53 exhibiting sequence-dependent mobility. A two-mode binding model accurately predicts p53

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A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

Area of Science:

Molecular Biology
Biophysics
Genetics

Background:

Transcription factors (TFs) must efficiently locate target DNA sites for gene expression timing.
1D sliding along DNA is a proposed mechanism to accelerate TF target recognition.
Recent theories suggest TFs need multiple DNA-binding modes for simultaneous reading and sliding.

Purpose of the Study:

To investigate the sequence-dependent mobility of the tumor suppressor p53 on DNA.
To test the applicability of a two-mode DNA-binding model for p53's sliding behavior.
To determine the sequence-specific binding energy model for p53.

Main Methods:

Single-molecule microscopy to measure p53's local diffusivity on noncognate DNA.
Comparison of a two-mode binding model against a single-mode model for predicting diffusivity.
Analysis of sequence-specific binding energy, including hemi-specific binding terms.

Main Results:

p53's local diffusivity on noncognate DNA is sequence-dependent, confirming theoretical predictions.
A two-mode binding model accurately predicts the observed variations in p53's diffusivity.
A model incorporating hemi-specific binding best explains p53's sequence-specific binding energy.

Conclusions:

p53's target recognition and timing depend on its noncognate binding properties and multi-mode binding capabilities.
The study supports a two-mode model for p53, where binding to DNA is sequence-dependent.
Noncognate DNA interactions significantly influence p53's dynamic behavior and target search efficiency.