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Related Concept Videos

Transcription Initiation01:47

Transcription Initiation

16.7K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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The Replisome03:01

The Replisome

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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...
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Translesion DNA Polymerases02:10

Translesion DNA Polymerases

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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...
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Proofreading01:31

Proofreading

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Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
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Related Experiment Video

Updated: Sep 2, 2025

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

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Theoretical study of RNA-polymerase behavior considering the backtracking state.

Razieh Kor1, Farshid Mohammad-Rafiee1

  • 1Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran. farshid@iasbs.ac.ir.

Soft Matter
|August 3, 2022
PubMed
Summary
This summary is machine-generated.

RNA polymerase backtracking during transcription can be rescued or arrested by external forces. This process resembles a Brownian ratchet mechanism, offering insights into gene regulation.

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Last Updated: Sep 2, 2025

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
10:59

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Theoretical Biology

Background:

  • RNA polymerase dynamics are crucial for gene expression.
  • The enzyme can enter a 'backtracked' state where RNA dislocates from the active site.
  • Understanding this state is key to comprehending transcription regulation.

Purpose of the Study:

  • To develop a theoretical model for RNA polymerase transcription, incorporating the backtracking state.
  • To investigate the enzyme's behavior under external force in the backtracking state.
  • To analyze the probabilities and rates of rescuing and arresting from backtracking.

Main Methods:

  • Theoretical modeling of RNA polymerase transcription.
  • Analysis of enzyme behavior under applied external force.
  • Investigation of backtracking state dynamics.

Main Results:

  • The model describes RNA polymerase behavior in the backtracking state under external force.
  • Two outcomes are identified: rescue from backtracking and enzyme arrest.
  • The rate and probability of these outcomes were studied.
  • Entering the backtracking state was found to mimic the Brownian ratchet mechanism.

Conclusions:

  • The developed model provides insights into RNA polymerase backtracking during transcription.
  • External forces can influence the enzyme's ability to overcome backtracking.
  • The Brownian ratchet analogy offers a new perspective on transcription dynamics and gene regulation.