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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 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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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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RNA Stability01:53

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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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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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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Related Experiment Video

Updated: Feb 21, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Predicting RNA Structure with Vfold.

Chenhan Zhao1, Xiaojun Xu1, Shi-Jie Chen1

  • 1Department of Physics, Informatics Institute, University of Missouri, Columbia, MO 65211, USA.

Methods in Molecular Biology (Clifton, N.J.)
|October 8, 2017
PubMed
Summary

Predicting RNA 3D structures computationally is crucial for understanding biological functions. Vfold software offers a reliable, physics-based approach for accurate RNA structure prediction from sequence data.

Keywords:
Loop entropyRNA foldingTemplate assemblyVfold model

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • RNA molecules require specific three-dimensional (3D) structures for biological functions.
  • Experimental determination of RNA 3D structures is costly and time-intensive.
  • Advances in computational biology enhance the reliability of RNA structure prediction.

Purpose of the Study:

  • To introduce Vfold, a novel RNA structure prediction software.
  • To detail the Vfold model, a virtual bond-based approach for RNA folding.
  • To demonstrate the application of Vfold using a specific riboswitch example.

Main Methods:

  • Utilizing a virtual bond-based RNA folding model.
  • Employing physics-based loop free energy calculations for RNA motifs.
  • Implementing a template-based assembly method for 3D structure prediction.

Main Results:

  • Vfold provides a computational method for predicting RNA 3D structures.
  • The software integrates physics-based energy calculations and template assembly.
  • Successful application of Vfold demonstrated on the yybP-ykoY Orphan riboswitch.

Conclusions:

  • Vfold represents a significant advancement in computational RNA structure prediction.
  • The Vfold model offers a reliable alternative to experimental methods.
  • Accurate RNA 3D structure prediction from sequence is achievable with Vfold.