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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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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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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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Types of RNA01:23

Types of RNA

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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Ribosome Profiling02:24

Ribosome Profiling

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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: May 27, 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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R2DT: a comprehensive platform for visualizing RNA secondary structure.

Holly McCann1,2,3, Caeden D Meade1,2, Loren Dean Williams1,2

  • 1NASA Center for Integration of the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, United States.

Nucleic Acids Research
|February 19, 2025
PubMed
Summary
This summary is machine-generated.

R2DT 2.0 enhances RNA secondary structure visualization with new features like template-free mode and interactive editing. This software provides reproducible RNA 2D layouts for functional analysis.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • RNA secondary (2D) structure visualization is crucial for understanding RNA function.
  • Consistent and reproducible RNA 2D structure layouts are essential for analysis.
  • Existing tools may lack flexibility or advanced features for RNA visualization.

Purpose of the Study:

  • To introduce R2DT 2.0, an upgraded software package for RNA 2D structure visualization.
  • To highlight new features enabling enhanced visualization and user interaction.
  • To present R2DT as a comprehensive platform for RNA 2D structure analysis.

Main Methods:

  • R2DT 2.0 incorporates position-specific data display (e.g., SNPs, SHAPE reactivities).
  • Introduces a template-free mode for visualizing RNAs without predefined templates.
  • Supports constrained folding, animated visualizations, and interactive diagram modification via manual input or natural language prompts.

Main Results:

  • R2DT 2.0 offers faster performance and an expanded template library.
  • New features allow for the generation of novel templates and publication-quality images.
  • The software is integrated into multiple biological databases, demonstrating its utility.

Conclusions:

  • R2DT 2.0 significantly advances RNA 2D structure visualization capabilities.
  • The enhanced features and interactive options make it a versatile tool for researchers.
  • R2DT is a comprehensive and accessible platform for RNA 2D structure analysis and discovery.