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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
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...
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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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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.
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Related Experiment Video

Updated: Sep 13, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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SEISMICgraph: a web-based tool for RNA structure data visualization.

Federico Fuchs Wightman1, Grant Yang1, Yves J Martin des Taillades2

  • 1Department of Microbiology, Harvard School of Medicine, Boston, MA 02115, United States.

Nucleic Acids Research
|July 31, 2025
PubMed
Summary
This summary is machine-generated.

SEISMICgraph is a new web tool for RNA structure research. It visualizes chemical probing data, aiding the study of RNA modifications and riboswitches.

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Last Updated: Sep 13, 2025

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA plays crucial roles in gene regulation beyond genetic information transfer.
  • Chemical probing techniques have advanced RNA secondary structure identification.
  • High-resolution RNA structural analysis is critical for understanding regulatory functions.

Purpose of the Study:

  • Introduce SEISMICgraph, a web-based tool for RNA structure research.
  • Provide data visualization and analysis for chemical probing data.
  • Facilitate comparison of RNA structures across sequences and conditions.

Main Methods:

  • Development of a user-friendly, web-based platform (SEISMICgraph).
  • Integration of data visualization for chemical probing modalities.
  • Application to study riboswitches and RNA modifications like pseudouridylation.

Main Results:

  • SEISMICgraph enables simultaneous data comparison without programming.
  • Demonstrated utility in analyzing adenine-dependent structural changes.
  • Visualized the impact of pseudouridylation on RNA structural transitions.

Conclusions:

  • SEISMICgraph offers novel insights into RNA structure and function.
  • The tool supports research on RNA modifications and regulatory elements.
  • Establishes a foundation for future RNA structure analysis applications.