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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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Nucleic Acid Structure01:25

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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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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Related Experiment Video

Updated: Jun 11, 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, Massachusetts, 02115, United States.

Biorxiv : the Preprint Server for Biology
|October 10, 2024
PubMed
Summary
This summary is machine-generated.

SEISMICgraph is a new web tool for RNA structure research, visualizing chemical probing data to reveal how RNA modifications affect structure and function. This tool aids in understanding gene regulation and RNA binding.

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Last Updated: Jun 11, 2025

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA plays crucial roles in gene regulation beyond its genetic information carrier function.
  • Chemical probing techniques have advanced, improving the identification and analysis of RNA secondary structures.
  • High-resolution and high-throughput RNA structural analyses are increasingly important for understanding biological mechanisms.

Purpose of the Study:

  • To introduce SEISMICgraph, a web-based tool for RNA structure research.
  • To provide data visualization and analysis for chemical probing data.
  • To facilitate the comparison of RNA structural data across sequences and conditions.

Main Methods:

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

Main Results:

  • SEISMICgraph enables simultaneous comparison of RNA structural data.
  • The tool visualizes adenine-dependent structural changes and the impact of pseudouridylation.
  • Demonstrated utility in investigating known and putative riboswitches.

Conclusions:

  • SEISMICgraph offers novel insights into RNA structure and modification.
  • The tool provides a user-friendly interface for RNA structure research without requiring programming expertise.
  • Establishes a roadmap for future applications in RNA structural biology.