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

Transcription Elongation Factors02:35

Transcription Elongation Factors

14.2K
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...
14.2K
Transcription Elongation Factors02:35

Transcription Elongation Factors

4.9K
4.9K
Bacterial Transcription01:53

Bacterial Transcription

37.1K
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:
37.1K
DNA Helicases00:55

DNA Helicases

24.4K
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
24.4K
Post-translational Translocation of Proteins to the RER01:27

Post-translational Translocation of Proteins to the RER

7.9K
A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
7.9K
The Replisome03:01

The Replisome

38.7K
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...
38.7K

You might also read

Related Articles

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

Sort by
Same author

Understanding parents' perspectives of repeated blinded continuous glucose monitoring in children with early-stage type 1 diabetes and an affected first-degree relative.

Diabetic medicine : a journal of the British Diabetic Association·2026
Same author

The Evolution of the First Code.

Genes·2026
Same author

Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry.

Journal of chemical theory and computation·2026
Same author

Balancing fidelity and flexibility: a case study presentation of an augmented dynamic adaptation process for socio-technical innovations in healthcare.

Frontiers in health services·2026
Same author

Extracellular iron and the lung microbiome in smoking and COPD.

ERJ open research·2025
Same author

Fibrosis 4 Index After Left Ventricular Assist Device Implantation: Right Congestion or Device Shear?

European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery·2025

Related Experiment Video

Updated: Feb 23, 2026

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

6.6K

Hinge action versus grip in translocation by RNA polymerase.

Yuri A Nedialkov1,2, Kristopher Opron1,3,4, Hailey L Caudill1

  • 1a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.

Transcription
|August 31, 2017
PubMed
Summary

RNA polymerase (RNAP) translocation involves a conformational mechanism, with simulations showing clamp closure and hinge-supported force generation. Biochemical assays confirm ion and RNA 3’-OH/H2 effects on RNAP sliding, supporting a sticky translocation model.

Keywords:
Bridge helix and trigger loop hingesRNA polymerase translocationRNA threading through the exit channelhyper-translocation in terminationmolecular dynamics simulationternary elongation complextrigger loop dynamics

More Related Videos

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

15.5K
Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.9K

Related Experiment Videos

Last Updated: Feb 23, 2026

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

6.6K
Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

15.5K
Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.9K

Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • RNA polymerase (RNAP) is crucial for gene transcription, involving complex translocation steps.
  • Understanding RNAP translocation mechanism is key to deciphering gene expression regulation.

Purpose of the Study:

  • To elucidate the conformational mechanism of forward translocation by RNA polymerase.
  • To investigate the role of specific protein domains and environmental factors in RNAP movement.

Main Methods:

  • Molecular dynamics simulations of RNAP ternary elongation complex.
  • Functional studies using exonuclease III assay to monitor RNAP translocation.
  • Biochemical assays monitoring the effect of ions and RNA 3'-OH/H2 on RNAP sliding.
  • Mutational analysis of the bridge helix in RNAP.

Main Results:

  • Simulations revealed clamp closure and hinge-driven force generation, enabling RNAP sliding.
  • The β flap tip helix and β' Zn finger engage RNA, guiding its exit.
  • RNAP active site is coupled to the RNA exit channel and translocation.
  • K+, Mg2+, and RNA 3'-OH/H2 significantly affect RNAP sliding, consistent with a sticky translocation mechanism.
  • Mutational analysis identified a homeostatic hinge in the bridge helix crucial for conformational dynamics.

Conclusions:

  • A conformational mechanism for RNAP forward translocation is proposed, involving coordinated movements of protein domains.
  • Environmental factors like ions and RNA structure play critical roles in regulating RNAP translocation.
  • The identified bridge helix hinge is essential for managing conformational changes during transcription.