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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.
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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 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 Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Using Molecular Replacement Phasing to Study the Structure and Function of RNA.

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Determining RNA structures using molecular replacement (MR) is becoming crucial. This guide details selecting models, performing MR, and refining solutions for novel RNA structure determination and functional analysis.

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Crystallography

Background:

  • Numerous RNA molecules regulating cellular processes have been discovered.
  • The increasing number of determined RNA structures necessitates efficient phasing methods for crystallography.
  • Molecular Replacement (MR) is poised to become a key technique for RNA structure determination.

Purpose of the Study:

  • To provide a comprehensive guide for RNA structure determination using molecular replacement (MR).
  • To outline protocols for selecting and preparing MR search models for nucleic acids.
  • To detail the process of performing, refining, and interpreting MR solutions for RNA crystallography.

Main Methods:

  • Selection and creation of appropriate molecular replacement search models for nucleic acids.
  • Execution of molecular replacement searches using established crystallographic software for RNA.
  • Refinement and interpretation of successful molecular replacement solutions to obtain final RNA structures.

Main Results:

  • Established protocols for utilizing molecular replacement in RNA structure determination.
  • Demonstrated methods for preparing and validating MR search models specific to nucleic acids.
  • Provided guidelines for interpreting and refining MR solutions for accurate RNA structural analysis.

Conclusions:

  • Molecular replacement is an increasingly vital method for determining novel RNA structures.
  • The described protocols facilitate the application of MR in RNA crystallography.
  • These methods aid in establishing structure-function relationships for both novel and existing RNA molecules.