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Related Concept Videos

The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
DNA Damage Can Stall the Cell Cycle02:36

DNA Damage Can Stall the Cell Cycle

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...
DNA Damage can Stall the Cell Cycle02:36

DNA Damage can Stall the Cell Cycle

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...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
DNA Topoisomerases02:02

DNA Topoisomerases

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.
Types and Mechanism of action
Topoisomerases are divided into two main types.  Type I...

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Related Experiment Video

Updated: May 13, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

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

Published on: October 1, 2017

Molecular traffic jams on DNA.

Ilya J Finkelstein1, Eric C Greene

  • 1Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA. ifinkelstein@cm.utexas.edu

Annual Review of Biophysics
|March 5, 2013
PubMed
Summary

Motor enzymes navigate crowded DNA, essential for transcription, replication, and repair. This review explores how these DNA-binding motors overcome obstacles from other proteins using biophysical experiments.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • DNA metabolism (transcription, replication, repair) relies on motor enzymes moving along genomic DNA.
  • Chromosomes are densely packed with proteins, creating a crowded environment for DNA motor proteins.
  • Understanding how motor proteins navigate this crowded landscape is crucial but poorly understood.

Purpose of the Study:

  • To review recent advancements in understanding how DNA-binding motor proteins interact with and move past other proteins on DNA.
  • To elucidate the mechanisms by which motor proteins overcome obstacles in a crowded DNA environment.

Main Methods:

  • Focus on single-molecule biophysical experiments.
  • Analysis of single-molecule, ensemble biochemical, and in vivo data.

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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Related Experiment Videos

Last Updated: May 13, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

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

Published on: October 1, 2017

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
09:26

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

  • Mechanistic interpretation of experimental results.

    • Main Results:

    • Recent biophysical studies provide insights into motor protein navigation on crowded DNA.
    • Mechanistic models are emerging to explain how motor proteins interact with obstacles.
    • Data integration from various experimental approaches enhances understanding.

    Conclusions:

    • Progress has been made in understanding motor protein behavior in crowded DNA conditions.
    • Single-molecule techniques are vital for dissecting these complex interactions.
    • Further research is needed to fully comprehend in vivo motor protein dynamics.