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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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,...
Translational Regulation01:29

Translational Regulation

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,...
Types of RNA01:23

Types of RNA

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...
Riboswitches01:56

Riboswitches

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...

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Related Experiment Video

Updated: Jun 27, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

A new role for cisplatin: probing ribosomal RNA structure.

Keshab Rijal1, Christine S Chow

  • 1Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA.

Chemical Communications (Cambridge, England)
|December 17, 2008
PubMed
Summary

Cisplatin identified accessible purine sites in E. coli 16S ribosomal RNA (rRNA). This anticancer drug revealed purine accessibility in free rRNA, 30S subunits, and 70S ribosomes, both in vitro and in vivo.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Ribosomal RNA (rRNA) is crucial for protein synthesis.
  • Understanding rRNA structure and accessibility is key to drug development.
  • Cisplatin is a platinum-based chemotherapy agent that interacts with DNA and RNA.

Purpose of the Study:

  • To investigate the accessibility of purine residues in Escherichia coli 16S rRNA.
  • To determine how cisplatin binding varies in free rRNA, 30S subunits, and 70S ribosomes.
  • To assess purine accessibility under both in vitro and in vivo conditions.

Main Methods:

  • Utilized cisplatin as a chemical probe.
  • Analyzed purine residue accessibility in 16S rRNA.
  • Compared accessibility in isolated rRNA, 30S ribosomal subunits, and complete 70S ribosomes.

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

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

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Last Updated: Jun 27, 2026

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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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

  • Conducted experiments both in vitro and in vivo.

    • Main Results:

    • Cisplatin selectively modified accessible purine residues within the 16S rRNA.
    • Differences in purine accessibility were observed depending on whether rRNA was free, part of a 30S subunit, or within a 70S ribosome.
    • In vivo studies provided insights into purine accessibility within the cellular context.

    Conclusions:

    • Cisplatin serves as an effective probe for mapping purine accessibility in bacterial rRNA.
    • Ribosomal structure significantly influences the accessibility of purine residues.
    • These findings contribute to understanding drug interactions with bacterial ribosomes.