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Related Concept Videos

RNA Stability01:53

RNA Stability

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...
RNA Stability01:53

RNA Stability

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...
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...
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 Structure01:23

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...

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

Published on: December 9, 2022

On nucleotide solvent accessibility in RNA structure.

Yumlembam H Singh1, Munazah Andrabi, Bratati Kahali

  • 1Bio-informatics Centre, North Eastern Hill University, Shillong-22, Meghalaya, India.

Gene
|May 18, 2010
PubMed
Summary
This summary is machine-generated.

Nucleotide solvent accessibility in RNA varies by sequence and is predictable. High accessibility of key translational signals like the AUG start codon may be evolutionarily important.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Solvent accessibility is crucial for protein structure and function but understudied in nucleic acids.
  • Understanding RNA structural features is vital for deciphering gene expression regulation.

Purpose of the Study:

  • To investigate sequence-dependent nucleotide solvent accessibility in various RNA types.
  • To explore the relationship between RNA accessibility, translational signals, and codon usage bias.

Main Methods:

  • Statistical analysis of nucleotide solvent accessibility in single-stranded, double-stranded, protein-unbound, and protein-bound RNA.
  • Neighbor-dependent analysis and predictability modeling.
  • Correlation analysis with synonymous codon usage bias.

Main Results:

  • Significant variation in solvent accessibility among RNA trinucleotides was observed.
  • Key translational signals, including the initiatory AUG codon and Shine-Dalgharno site, exhibit high solvent accessibility.
  • Nucleotide accessibility is directly related to synonymous codon usage bias.

Conclusions:

  • Nucleotide solvent accessibility in RNA is sequence-dependent and predictable.
  • High accessibility of translational signals may play a role in their evolutionary selection.
  • Predicting RNA solvent accessibility offers new insights into RNA structure-function relationships.