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Related Concept Videos

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 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 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...

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Related Experiment Video

Updated: May 15, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

mRNA secondary structure optimization using a correlated stem-loop prediction.

Paulo Gaspar1, Gabriela Moura, Manuel A S Santos

  • 1DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. paulogaspar@ua.pt

Nucleic Acids Research
|January 18, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method to optimize messenger RNA (mRNA) secondary structures without altering the protein sequence. The approach efficiently modifies mRNA to reduce structural constraints, enhancing gene expression control.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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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

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Gene Expression Regulation

Background:

  • Messenger RNA (mRNA) secondary structures significantly impact protein biosynthesis by influencing translation efficiency.
  • Strong mRNA secondary structures can impede ribosomal movement, reducing protein yield and serving as a key regulatory mechanism in gene expression.
  • Existing algorithms predict RNA structures or derive sequences for given structures, but lack methods to optimize mRNA secondary structure without changing the amino acid sequence.

Purpose of the Study:

  • To develop the first strategy for optimizing mRNA secondary structures to modulate minimum free energy.
  • To achieve modification of mRNA secondary structures while preserving the encoded amino acid sequence.
  • To provide a time-efficient method for controlling mRNA secondary structure strength.

Main Methods:

  • A novel strategy was developed to redesign mRNA sequences.
  • The method employs a simplified approximation of hairpin formation to adjust secondary structure.
  • The approach optimizes minimum free energy without altering the resulting polypeptide sequence.

Main Results:

  • The developed strategy efficiently increases the minimum free energy of nucleotide sequences by over 40%.
  • This significant increase in minimum free energy leads to a substantial reduction in the strength of mRNA secondary structures.
  • The method demonstrates time-efficient optimization of mRNA secondary structures.

Conclusions:

  • This work presents a pioneering approach for optimizing mRNA secondary structures to control gene expression.
  • The technique offers a powerful tool for applications including multi-objective gene optimization and genomic-level secondary structure manipulation.
  • The method allows for the fine-tuning of mRNA secondary structures to enhance protein production or regulate gene expression levels.