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Related Concept Videos

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...
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:
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into 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...

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Related Experiment Video

Updated: Jul 8, 2026

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

DNA bending in transcription initiation.

Vladimir Tchernaenko1, Monika Radlinska, Lucyna Lubkowska

  • 1Molecular Biology Section, Bone and Joint Center, Henry Ford Hospital, Detroit, Michigan 48202, USA.

Biochemistry
|January 22, 2008
PubMed
Summary

DNA bending in bacteriophage lambda PR promoter initiation complexes was analyzed. Both open and abortive complexes exhibit similar DNA bending, challenging previous models and revealing insights into transcription initiation.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Bacteriophage lambda PR promoter is crucial for viral gene expression.
  • Understanding DNA structure in transcription initiation complexes is key to elucidating regulatory mechanisms.

Purpose of the Study:

  • To characterize the DNA structure, specifically bending and bubble formation, in bacteriophage lambda PR promoter initiation complexes.
  • To investigate the role of DNA topology in transcription initiation.

Main Methods:

  • Electrophoretic mobility shift (bandshift) phasing analysis.
  • Rotational variant topological analysis.
  • Analysis of constructs with tandemly repeated PR promoter sequences.

Main Results:

  • Both open and +3 abortive initiation complexes exhibit significant DNA bending (approx. 47-49 degrees).
  • The DNA bending is consistent between the two complexes, contradicting models of extensive superhelical wrapping.
  • Transcription bubble sizes differ: 10.4 bp for the open complex and 12.2 bp for the +3 complex, supporting DNA scrunching.
  • A model for DNA path in the open complex consistent with measured bend angle was proposed.

Conclusions:

  • DNA bending is a key feature of bacteriophage lambda PR promoter initiation complexes.
  • The observed DNA structure challenges previous models and provides a more accurate description of solution structures.
  • Findings complement crystal structures, offering a comprehensive understanding of initiation complex dynamics.