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Related Concept Videos

Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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
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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

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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.
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DNA has a double-helix structure. The...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Updated: Jun 6, 2026

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
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Published on: July 8, 2019

Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number.

Arne Werner1

  • 1Experimental Biomolecular Physics, Applied Physics, Royal Institute of Technology, Stockholm, SE-10691, Sweden. arne_werner@web.de

Nucleic Acids Research
|November 12, 2010
PubMed
Summary

Researchers developed a method to predict the hydrodynamic behavior of single-stranded ribonucleic acids (RNA) based on their size. This advancement aids in understanding RNA structure and function through polymer physics principles.

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Last Updated: Jun 6, 2026

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Polymer Science

Background:

  • Ribonucleic acids (RNA) are crucial for cellular functions.
  • RNA's hydrodynamic behavior significantly influences its biological roles.
  • Predicting RNA behavior is essential for understanding molecular mechanisms.

Purpose of the Study:

  • To establish a predictive model for the hydrodynamic behavior of single-stranded RNA (ssRNA).
  • To correlate RNA size with its hydrodynamic radius and diffusion coefficient.
  • To validate empirical models with experimental data for conserved and unevolved RNAs.

Main Methods:

  • Atom-level shell-modelling of high-resolution RNA structures.
  • Calculation of hydrodynamic radius (R(H)) and diffusion coefficient (D) based on nucleotide count (N).
  • Comparison of calculated parameters with experimental measurements in solution.

Main Results:

  • Established empirical laws: D = 4.56 × 10⁻¹⁰ N⁻⁰.³⁹ m²/s and R(H) = 5.00 × 10⁻¹⁰ N⁰.³⁸ m.
  • Calculated an average ratio of radius of gyration to hydrodynamic radius of 0.98 ± 0.08.
  • Demonstrated high consistency between model predictions and experimental data for conserved ssRNA.

Conclusions:

  • Empirical models accurately predict translational diffusion and molecular size of short ssRNA based on polymer size.
  • The findings provide a valuable tool for analyzing RNA structure-function relationships.
  • This approach is applicable to both evolutionarily conserved and unevolved RNA molecules.