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Related Concept Videos

Labeling DNA Probes03:31

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.
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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...
Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

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Related Experiment Video

Updated: Jul 13, 2026

Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

Probing ATR activation with model DNA templates.

Karlene A Cimprich1

  • 1Stanford University, Department of Chemical and Systems Biology, Stanford, California 94305-5441, USA. cimprich@stanford.edu

Cell Cycle (Georgetown, Tex.)
|August 19, 2007
PubMed
Summary

Primed single-stranded DNA (ssDNA) can activate the ATR kinase, a key component of DNA damage checkpoints. This finding clarifies the DNA structures necessary for initiating cellular responses to DNA replication stress.

Area of Science:

  • Cellular biology
  • Molecular genetics
  • Biochemistry

Background:

  • The ATR kinase pathway is crucial for responding to DNA damage and replication stress.
  • DNA replication and repair processes generate DNA structures that activate ATR signaling.
  • Single-stranded DNA (ssDNA) and double-stranded/single-stranded DNA (ds/ssDNA) junctions are known components of ATR-activating structures.

Purpose of the Study:

  • To determine if primed ssDNA alone is sufficient to activate the ATR response.
  • To investigate the roles of ds/ssDNA junctions and ssDNA in checkpoint activation using a defined DNA structure.

Main Methods:

  • Utilized Xenopus egg extracts to study ATR activation.
  • Employed a well-defined primed ssDNA structure to elicit checkpoint responses.

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  • Examined the contribution of different DNA structures to checkpoint signaling.

    • Main Results:

    • Demonstrated that primed ssDNA is sufficient to induce a bona fide checkpoint response in Xenopus egg extracts.
    • Identified primed ssDNA as the first well-defined DNA structure capable of eliciting ATR activation.
    • Showed that the context of checkpoint-activating structure generation influences signaling properties.

    Conclusions:

    • Primed ssDNA is sufficient for ATR activation, establishing a minimal requirement for checkpoint signaling.
    • The cellular context and the specific DNA structures involved in ATR activation are critical for signaling outcomes.
    • Findings advance the understanding of DNA damage and replication checkpoint mechanisms.