Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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 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...
Transcription in Prokaryotes01:28

Transcription in Prokaryotes

Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.Initiation of TranscriptionIn bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow box)...
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...
Replication in Eukaryotes01:29

Replication in Eukaryotes

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
Many Proteins Orchestrate Replication at the Origin
Eukaryotic replication follows many of the same...
Replication in Eukaryotes02:31

Replication in Eukaryotes

Overview

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Chromatin buffers torsional stress during transcription.

Science (New York, N.Y.)·2025
Same author

Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria.

Nucleic acids research·2025
Same author

Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data.

bioRxiv : the preprint server for biology·2025
Same author

RNA polymerase II is a polar roadblock to a progressing DNA fork.

Nature communications·2025
Same author

Characterization of bacterial intrinsic transcription terminators identified with TERMITe-a novel method for comprehensive analysis of Term-seq data.

Nucleic acids research·2025
Same author

Chromatin Buffers Torsional Stress During Transcription.

bioRxiv : the preprint server for biology·2024

Related Experiment Video

Updated: Jul 8, 2026

Live-Cell Imaging of Transcriptional Activity at DNA Double-Strand Breaks
09:07

Live-Cell Imaging of Transcriptional Activity at DNA Double-Strand Breaks

Published on: September 20, 2021

DNA bubble formation in transcription initiation.

Vladimir Tchernaenko1, Herbert R Halvorson, Mikhail Kashlev

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

Biochemistry
|January 22, 2008
PubMed
Summary

Topological analysis reveals DNA bubble sizes in transcription open complexes: ~12.3 base pairs for lac UV5 and ~10.3 base pairs for lambda PR. This confirms DNA scrunching during transcription initiation.

More Related Videos

High-throughput Purification of Affinity-tagged Recombinant Proteins
07:44

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

Related Experiment Videos

Last Updated: Jul 8, 2026

Live-Cell Imaging of Transcriptional Activity at DNA Double-Strand Breaks
09:07

Live-Cell Imaging of Transcriptional Activity at DNA Double-Strand Breaks

Published on: September 20, 2021

High-throughput Purification of Affinity-tagged Recombinant Proteins
07:44

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • The transcription open complex is crucial for gene expression.
  • Understanding the DNA bubble's properties is key to deciphering transcription initiation mechanisms.

Purpose of the Study:

  • To characterize the DNA bubble in transcription open complexes using topological analysis.
  • To quantify bubble size for specific promoters and investigate factors influencing it.

Main Methods:

  • Topological analysis of DNA circles containing lac UV5 or lambda PR promoters.
  • Measuring linking number changes to quantify DNA duplex unwinding and bubble formation.
  • Utilizing multiple promoter copies per circle to enhance measurement precision.

Main Results:

  • Lac UV5 promoter bubble size estimated at 12.3 base pairs (linking number change of -1.17).
  • Lambda PR promoter bubble size estimated at 10.3 base pairs (linking number change of -0.98).
  • Magnesium ion presence had minimal effect on bubble size; bubble expands at the leading edge in abortive initiation complexes, supporting DNA scrunching.

Conclusions:

  • Topological analysis provides precise quantification of DNA bubble geometry during transcription.
  • The study resolves uncertainties regarding magnesium's effect and supports the DNA scrunching model.
  • Findings complement structural data and inform models of DNA structure in functional open complexes.