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

Ribosome Profiling02:24

Ribosome Profiling

3.2K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.2K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

12.2K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
12.2K
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

3.7K
3.7K
Riboswitches01:56

Riboswitches

7.9K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
7.9K
Types of RNA01:23

Types of RNA

60.9K
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
60.9K
Translational Regulation01:29

Translational Regulation

861
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
861

You might also read

Related Articles

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

Sort by
Same author

Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease.

Biochemistry·2026
Same author

Capturing Translation in Action with Protein Synthesis Profiling.

bioRxiv : the preprint server for biology·2025
Same author

Structural evidence for metal ion catalysis in the ribosome.

bioRxiv : the preprint server for biology·2025
Same author

Sortase-Mediated Fluorescent Labeling of eIF4E for Investigating Translation Initiation Mechanisms.

Biochemistry·2025
Same author

Validating the EMCV IRES Secondary Structure with Structure-Function Analysis.

Biochemistry·2023
Same author

Interaction of the Influenza A Virus NS1 Protein with the 5'-m7G-mRNA·eIF4E·eIF4G1 Complex.

Biochemistry·2022
Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Apr 21, 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

5.4K

Modification interference analysis of the ribosome.

Simpson Joseph1

  • 1Department of Chemistry and Biochemistry, University of California at San Diego, 4102 Urey Hall, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA, sjoseph@ucsd.edu.

Methods in Molecular Biology (Clifton, N.J.)
|October 30, 2014
PubMed
Summary
This summary is machine-generated.

This study used a modification interference method to pinpoint essential bases in 16S ribosomal RNA (rRNA). These identified nucleotides are crucial for the ribosome

More Related Videos

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

8.1K
Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
10:56

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Published on: May 17, 2014

68.9K

Related Experiment Videos

Last Updated: Apr 21, 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

5.4K
RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

8.1K
Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
10:56

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Published on: May 17, 2014

68.9K

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Ribonucleic acids (RNAs) are fundamental to cellular processes, playing diverse roles in structure and function.
  • Understanding RNA function requires identifying critical nucleotides involved in its structure and interactions.
  • Biochemical methods like footprinting, cross-linking, and modification interference analysis are vital for studying RNA interactions.

Purpose of the Study:

  • To identify specific bases within 16S ribosomal RNA (rRNA) that are essential for ribosome function.
  • To investigate the role of these identified nucleotides in the translocation of messenger RNA (mRNA) and transfer RNA (tRNA) complexes.
  • To refine and apply modification interference analysis for studying RNA-protein interactions within complex molecular machinery.

Main Methods:

  • Employed a modification interference analysis technique to probe the 16S rRNA.
  • Utilized biochemical methods to map nucleotide positions critical for ribosome activity.
  • Focused on analyzing the translocation of the mRNA-tRNA complex during protein synthesis.

Main Results:

  • Successfully identified specific bases in 16S rRNA that are indispensable for its function.
  • These key nucleotides were found to be critical for facilitating the translocation of the mRNA-tRNA complex.
  • The study demonstrates the efficacy of modification interference in dissecting functional sites within rRNA.

Conclusions:

  • Specific bases within 16S rRNA are essential for the ribosome's ability to translocate mRNA-tRNA complexes.
  • Modification interference analysis is a powerful tool for elucidating the structure-function relationships of RNA molecules.
  • This research provides a deeper understanding of the molecular mechanisms underlying protein synthesis.