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Related Concept Videos

RNA Structure01:23

RNA Structure

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RNA Structure01:23

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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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RNA Structure01:19

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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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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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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 Secondary Structure Prediction Using High-throughput SHAPE
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Secondary Structure Prediction of Single Sequences Using RNAstructure.

Zhenjiang Zech Xu1,2, David H Mathews3

  • 1Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2016
PubMed
Summary
This summary is machine-generated.

RNAstructure software predicts RNA secondary structures using folding thermodynamics. It offers tools for predicting base pairing probabilities, structures with pseudoknots, and more, with a user-friendly interface.

Keywords:
RNA folding thermodynamicsRNA statistical mechanicsRNA structure prediction

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Predicting RNA secondary structure is crucial for understanding RNA function.
  • Folding thermodynamics provide a foundation for computational RNA structure prediction.

Purpose of the Study:

  • To provide protocols for using the RNAstructure software package.
  • To detail RNAstructure's capabilities in RNA secondary structure prediction.

Main Methods:

  • Utilizing RNAstructure for RNA secondary structure prediction.
  • Employing free energy minimization for structure prediction.
  • Predicting base pairing probabilities and structures with pseudoknots.

Main Results:

  • RNAstructure enables prediction of RNA secondary structures.
  • The software includes methods for predicting base pairing probabilities.
  • RNAstructure supports the prediction of structures with pseudoknots.

Conclusions:

  • RNAstructure is a versatile software package for RNA secondary structure prediction.
  • The software offers a user-friendly graphical interface across multiple operating systems.
  • Protocols for RNAstructure usage are provided for structure prediction.