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Related Concept Videos

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...
Bacterial Transcription01:53

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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...
Transcription Initiation01:47

Transcription Initiation

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...
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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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Related Experiment Video

Updated: Jun 27, 2026

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

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

Published on: May 13, 2019

Bridge helix and trigger loop perturbations generate superactive RNA polymerases.

Lin Tan1, Simone Wiesler, Dominika Trzaska

  • 1Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, UK.

Journal of Biology
|December 6, 2008
PubMed
Summary

A novel robotic approach revealed that specific mutations in the bridge helix and trigger loop can enhance RNA polymerase activity. These findings support a kinked bridge helix model for the nucleotide addition cycle.

Related Experiment Videos

Last Updated: Jun 27, 2026

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

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

Published on: May 13, 2019

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Enzymology

Background:

  • Cellular RNA polymerases are crucial enzymes for nucleic acid processing.
  • The bridge helix and trigger loop domains are key to RNA polymerase function, undergoing conformational changes during the nucleotide addition cycle.
  • Assessing the functional impact of these structural changes is limited by the scarcity of static crystal structures.

Purpose of the Study:

  • To investigate the functional roles of the bridge helix and trigger loop in RNA polymerase.
  • To characterize the effects of site-directed mutations on RNA polymerase activity and mechanism.

Main Methods:

  • Utilized a novel robotic approach for high-throughput screening.
  • Generated and analyzed 367 site-directed mutants of the Methanocaldococcus jannaschii RNA polymerase A' subunit.
  • Assessed in vitro phenotypes and specific activity of mutant RNA polymerases.

Main Results:

  • Characterized a wide spectrum of in vitro phenotypes for 367 RNA polymerase mutants.
  • Identified numerous single amino acid substitutions in the bridge helix that increase RNA polymerase specific activity.
  • Discovered 'superactivating' substitutions in the adjacent base helices of the trigger loop.

Conclusions:

  • Results support a model where the nucleotide addition cycle involves a kinked bridge helix conformation.
  • The RNA polymerase active center is regulated by interactions between the bridge helix and trigger loop.
  • These interactions control fundamental parameters of RNA synthesis.