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RNA Structure01:19

RNA Structure

8.3K
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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RNA Structure01:23

RNA Structure

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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

Nucleic Acid Structure

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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.
DNA Structure
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RNA-seq03:21

RNA-seq

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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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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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Related Experiment Video

Updated: Mar 29, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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Dynamics in Sequence Space for RNA Secondary Structure Design.

Marco C Matthies1, Stefan Bienert1,2, Andrew E Torda1

  • 1Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146 Hamburg, Germany.

Journal of Chemical Theory and Computation
|November 24, 2015
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for designing RNA sequences to fold into specific structures using computational dynamics. The approach efficiently generates compatible sequences, outperforming existing methods in structure prediction accuracy.

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Area of Science:

  • Computational biology
  • Molecular modeling
  • Bioinformatics

Background:

  • Designing RNA sequences with specific secondary structures is crucial for understanding RNA function.
  • Existing computational methods for RNA design have limitations in efficiency and accuracy.

Purpose of the Study:

  • To develop and implement an efficient computational method for designing RNA sequences that fold into arbitrary secondary structures.
  • To compare the performance of the new design method against existing algorithms.

Main Methods:

  • Utilized a popular RNA energy model to derive forces for Newtonian dynamics in sequence space.
  • Incorporated a negative design term and simulated annealing for rapid sequence sampling.
  • Designed sequences for 360 target secondary structures.

Main Results:

  • The implemented method successfully generated RNA sequences compatible with desired secondary structures.
  • Compared to another nucleic acid design program, the new method showed improved performance.
  • Evaluated designs using metrics like target structure probability and ensemble-weighted distance.

Conclusions:

  • The developed method provides an efficient and accurate approach for RNA secondary structure design.
  • This computational strategy holds potential for advancing RNA-based therapeutics and synthetic biology applications.