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Related Concept Videos

RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: Jun 8, 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

Metal ion-based RNA cleavage as a structural probe.

Marcello Forconi1, Daniel Herschlag

  • 1Department of Biochemistry, Stanford University, Stanford, California, USA.

Methods in Enzymology
|October 16, 2010
PubMed
Summary

Metal ions accelerate RNA degradation, aiding RNA structure studies. This review covers methods using metal ion-mediated cleavage to map RNA structure and conformational changes, including a general protocol.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Metal ions are known to accelerate the degradation of Ribonucleic Acid (RNA).
  • This reactivity has been leveraged to investigate RNA structure and dynamics.
  • Understanding RNA structure is crucial for various biological processes.

Purpose of the Study:

  • To review methods utilizing metal ion-mediated RNA cleavage for structural analysis.
  • To highlight the strengths and limitations of different approaches.
  • To provide a practical protocol for metal ion-induced RNA cleavage.

Main Methods:

  • Review of existing literature on metal ion-RNA interactions and cleavage.
  • Analysis of techniques for mapping metal ion binding sites on RNA.

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  • Description of methods to detect structural motifs and conformational changes using cleavage data.

    • Main Results:

    • Metal ion-mediated cleavage provides insights into RNA tertiary structure.
    • It can identify specific metal ion binding sites critical for RNA stability.
    • Conformational transitions in structured RNAs can be monitored.

    Conclusions:

    • Metal ion-mediated cleavage is a versatile tool for RNA structural biology.
    • It offers complementary information to other structural techniques.
    • The provided protocol facilitates experimental application of this method.