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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 Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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...
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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Updated: Jun 3, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Nonequilibrium phase transitions associated with DNA replication.

Hyung-June Woo1, Anders Wallqvist

  • 1Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Dietrick, Maryland 21702, USA. woo@bioanalysis.org

Physical Review Letters
|March 17, 2011
PubMed
Summary
This summary is machine-generated.

This study reveals a nonequilibrium phase transition in DNA/RNA synthesis, driven by polymerase fidelity. High fidelity leads to distinct states with faster synthesis and fewer errors, mimicking liquid-vapor transitions.

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Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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Last Updated: Jun 3, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
07:27

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Published on: April 29, 2010

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

Area of Science:

  • Biophysics
  • Chemical kinetics
  • Theoretical biology

Background:

  • Understanding the thermodynamics of template-directed nucleic acid synthesis is crucial for origins of life research.
  • Replicator dynamics are often modeled using simplified fitness landscapes.

Purpose of the Study:

  • To analytically investigate the thermodynamics of DNA/RNA synthesis under template control.
  • To apply these thermodynamic principles to the population dynamics of competing replicators.
  • To identify and characterize phase transitions in replicator systems.

Main Methods:

  • Analytical treatment of thermodynamics for template-directed synthesis.
  • Modeling population dynamics of self-replicating macromolecules.
  • Analysis of nonequilibrium phase transitions and critical phenomena.

Main Results:

  • A nonequilibrium phase transition is identified for high polymerase fidelity in single replicators.
  • Two distinct stationary states emerge: one with high elongation velocity and low error rate.
  • The system's behavior parallels equilibrium liquid-vapor phase transitions, with diverging susceptibility at the critical point.
  • Eigen's error catastrophe precedes this thermodynamic transition in competing replicator populations during starvation.

Conclusions:

  • Polymerase fidelity plays a critical role in driving phase transitions in replicator systems.
  • Thermodynamic forces can enhance replicator fitness, particularly above a fidelity threshold.
  • These findings offer insights into the physical limits of molecular replication and the evolution of early life.