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Related Concept Videos

RNA Structure01:23

RNA Structure

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...
RNA Structure01:19

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
RNA-seq03:21

RNA-seq

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 microarray-based...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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
DNA has a double-helix structure. The...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

Emidio Capriotti1, Marc A Marti-Renom

  • 1Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

BMC Bioinformatics
|June 17, 2010
PubMed
Summary
This summary is machine-generated.

This study quantifies the link between RNA sequence and structure conservation. It reveals that structure is more conserved than sequence, defining a

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • RNA Biology

Background:

  • Growing number of available RNA structures fuels interest in RNA biology.
  • Previous protein studies established links between sequence and structure conservation.
  • Current advancements allow for similar quantification in RNA.

Purpose of the Study:

  • To quantitatively analyze the relationship between RNA sequence and structure conservation.
  • To identify the limitations and theoretical basis for RNA 3D structure prediction.
  • To define the region for detecting RNA homology.

Main Methods:

  • All-against-all comparison of RNA sequences and 3D structures.
  • Quantitative analysis of sequence and structure conservation.
  • Evaluation of homology detection limits.

Main Results:

  • A measurable relationship between sequence and structure conservation exists.
  • This relationship weakens below 60% sequence identity.
  • RNA structure is evolutionarily more conserved than its sequence.
  • A 'twilight zone' for RNA homology detection is identified.

Conclusions:

  • The study quantitatively describes the sequence-structure relationship in RNA.
  • A specific 'twilight zone' for RNA homology detection is defined.
  • This work provides a theoretical foundation for RNA 3D structure prediction.