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Related Concept Videos

RNA Structure01:23

RNA Structure

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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
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RNA Structure01:19

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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.
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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-seq03:21

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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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Nucleic acids02:43

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Related Experiment Video

Updated: Feb 25, 2026

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

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Assaying RNA Structure Inside Living Cells with SHAPE.

Chao Feng1, Dalen Chan1, Robert C Spitale2,3

  • 1Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 3, 2017
PubMed
Summary
This summary is machine-generated.

This study details RNA Selective Hydroxyl Acylation analyzed by Primer Extension (SHAPE) for measuring RNA structure in living cells. SHAPE technology offers insights into gene regulation at the molecular level.

Keywords:
Chemical ProbingRNA structureSHAPE

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Last Updated: Feb 25, 2026

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Published on: January 30, 2019

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNA molecules play critical roles in gene regulation through complex structural folding.
  • Understanding RNA structure is essential for elucidating molecular mechanisms of gene expression.
  • Existing methods for RNA structure determination have limitations.

Purpose of the Study:

  • To describe the application of SHAPE for measuring RNA structure within living cells.
  • To highlight recent advancements in SHAPE technology for in vivo studies.
  • To provide a method for detailed analysis of cellular RNA structures.

Main Methods:

  • Utilizing RNA Selective Hydroxyl Acylation analyzed by Primer Extension (SHAPE).
  • Adapting SHAPE methodology for application within living cellular environments.
  • Employing primer extension techniques to analyze chemical modifications on RNA.

Main Results:

  • Demonstrated the feasibility of using SHAPE to probe RNA structures in real-time within cells.
  • Provided data on the structural dynamics of RNA in its native cellular context.
  • Established SHAPE as a powerful tool for in vivo RNA structure analysis.

Conclusions:

  • SHAPE is an effective method for determining RNA secondary and tertiary structures inside living cells.
  • This technique advances our understanding of RNA's role in gene regulation.
  • In vivo SHAPE analysis opens new avenues for studying RNA function and dysfunction.