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Related Concept Videos

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...
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...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

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Related Experiment Video

Updated: Jun 13, 2026

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

Polynucleotide Phosphorylase Stops Replication Restart by Degrading the RNA within R-loops during

Oyku Sensoy1, Juan Carvajal-Garcia1, Shahin Boumi1

  • 1Department of Biochemistry, Vanderbilt University School of Medicine. Nashville, TN 37232, USA.

Biorxiv : the Preprint Server for Biology
|June 12, 2026
PubMed
Summary

Polynucleotide phosphorylase (PNPase) prevents replication restart from RNA:DNA hybrids, which form during DNA replication-transcription conflicts. This prevents potentially mutagenic restarts, safeguarding genome stability.

Keywords:
GeneticsR-loopsRNA:DNA HybridsRNA:DNA hybridsReplication-transcription conflictsmutagenesispolynucleotide phosphorylasereplication restartreplication-transcription conflicts

Related Experiment Videos

Last Updated: Jun 13, 2026

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

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • DNA replication and transcription can conflict, leading to R-loop formation (RNA:DNA hybrids).
  • R-loop accumulation causes replication fork stalling and cell death.
  • Replication restart mechanisms normally resolve stalled forks but are inhibited during conflicts.

Purpose of the Study:

  • To investigate the role of Polynucleotide Phosphorylase (PNPase) in resolving conflicts between DNA replication and transcription.
  • To determine if PNPase affects replication restart from RNA:DNA hybrids.

Main Methods:

  • In vitro biochemical assays to assess PNPase activity on RNA:DNA hybrids.
  • In vivo studies in *Bacillus subtilis* to examine PNPase localization and R-loop levels.
  • Analysis of replication restart and mutation rates in the presence and absence of PNPase.

Main Results:

  • PNPase binds to RNA:DNA hybrids and digests the RNA component.
  • PNPase localizes to conflict regions in vivo and reduces R-loop levels.
  • PNPase inhibits replication restart from RNA:DNA hybrids, and its absence promotes restart.
  • PNPase activity reduces mutations, indicating mutagenic potential of replication restart from R-loops.

Conclusions:

  • PNPase acts as an exonuclease that resolves RNA:DNA hybrids, similar to RNase H.
  • PNPase prevents mutagenic replication restart from R-loops by degrading the RNA strand.
  • PNPase functions as a crucial safeguard for genome integrity during replication-transcription conflicts.