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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Jul 3, 2025

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

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Isoform-specific RNA structure determination using Nano-DMS-MaP.

Anne-Sophie Gribling-Burrer1, Patrick Bohn2, Redmond P Smyth3,4

  • 1Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany. anne-sophie.gribling@helmholtz-hiri.de.

Nature Protocols
|February 12, 2024
PubMed
Summary
This summary is machine-generated.

Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) determines RNA structures for specific isoforms. This method reveals hidden structural differences in long, similar RNA molecules using nanopore sequencing.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Understanding RNA structure is crucial for elucidating its biological functions.
  • Cells express diverse RNA isoforms with sequence variations due to processes like alternative splicing and differential polyadenylation.
  • Existing RNA structure determination methods often struggle with long and highly similar RNA molecules.

Purpose of the Study:

  • To describe the development and application of Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP).
  • To enable in situ, isoform-specific RNA structure determination.
  • To resolve structural differences in long and highly similar RNA molecules.

Main Methods:

  • Utilizes nanopore sequencing for long-read RNA structure analysis.
  • Employs dimethyl sulfate mutational profiling (DMS-MaP) for chemical probing of RNA structure.
  • Provides a protocol from experimental design and execution to data analysis.

Main Results:

  • Nano-DMS-MaP successfully resolves RNA structures of individual isoforms within complex mixtures.
  • The method reveals previously hidden structural variations among highly similar RNA molecules.
  • In-cell probing experiments are feasible within 3-4 days for experienced researchers.

Conclusions:

  • Nano-DMS-MaP is a powerful tool for isoform-specific RNA structure determination.
  • This method overcomes limitations of short-read sequencing for analyzing complex RNA structures.
  • The protocol facilitates the application of Nano-DMS-MaP for comprehensive RNA structure studies.