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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 Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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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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Experimental RNAi02:15

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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Updated: May 29, 2025

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

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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 8, 2025
PubMed
Summary
This summary is machine-generated.

R2DT 2.0 enhances RNA secondary structure visualization with new features like template-free and animated modes. This software allows interactive diagram modification for reproducible RNA analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

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 visualization capabilities.

Purpose of the Study:

  • To introduce R2DT 2.0, an updated software package for RNA 2D structure visualization.
  • To highlight new features that improve RNA visualization flexibility and interactivity.
  • 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).
  • New modes include template-free visualization, constrained folding, and animated structures.
  • Interactive modification via manual input or natural language prompts is supported.
  • Performance enhancements and an expanded template library are included.

Main Results:

  • R2DT 2.0 offers versatile RNA 2D structure visualization with enhanced features.
  • Users can generate new templates and publication-quality images through interactive editing.
  • The software provides faster performance and broader applicability.
  • Integration into biological databases demonstrates its utility.

Conclusions:

  • R2DT 2.0 represents a significant advancement in RNA 2D structure visualization tools.
  • Its new features and interactive capabilities facilitate deeper understanding of RNA structure-function relationships.
  • R2DT is a valuable, accessible platform for researchers in molecular biology and bioinformatics.