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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 Structure01:23

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...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
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...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
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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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

Protein structure preference, tRNA copy number, and mRNA stem/loop content.

Liaofu Luo1, Mengwen Jia, Xiaoqin Li

  • 1Department of Physics, Inner Mongolia University, Hohhot 010021, China. lfluo@mail.imu.edu.cn

Biopolymers
|July 27, 2004
PubMed
Summary
This summary is machine-generated.

High tRNA copy number (TCN) in messenger RNA codons preferentially codes for alpha helices, while low TCN codes for coils in humans and E. coli. This codon bias impacts protein structure.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • The relationship between codon usage and protein structure is crucial for understanding gene expression.
  • Transfer RNA (tRNA) copy number (TCN) is a key factor influencing translation.
  • Previous studies have explored codon bias but lacked detailed correlation with specific protein secondary structures.

Purpose of the Study:

  • To investigate the correlation between messenger RNA (mRNA) codon usage, specifically m-codons (m=2 to 6), and protein secondary structures.
  • To determine if tRNA copy number (TCN) influences the preference for coding alpha helices, coils, or beta strands.
  • To propose a model linking codon structure preference to translational efficiency and accuracy.

Main Methods:

  • Statistical analysis of protein sequences from humans and Escherichia coli.
  • Categorization of codons based on their TCN into high, low, and intermediate regions.
  • Utilizing F distribution to test the interaction between protein secondary structure type and codon TCN.
  • Deduction of strong preference-modes of TCN for protein secondary structures.

Main Results:

  • High TCN codons (e.g., >10.5 in humans, >1.95 in E. coli) predominantly code for alpha helices.
  • Low TCN codons (e.g., <7.5 in humans, <1.7 in E. coli) predominantly code for coil structures.
  • No obvious preference or avoidance tendency was observed for beta strands based on TCN.
  • A correlation was found between codon structure preference and mRNA stem/loop content across different TCN regions.

Conclusions:

  • Codon usage, influenced by TCN, exhibits a preference for coding specific protein secondary structures.
  • The findings suggest a link between codon TCN, protein structure, and potentially translational efficiency/accuracy.
  • A phenomenological model is proposed to explain the observed structure preference of codons.