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Related Concept Videos

Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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...

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Related Experiment Video

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop.

Ryan J Marcheschi1, David W Staple, Samuel E Butcher

  • 1Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI53706, USA.

Journal of Molecular Biology
|September 18, 2007
PubMed
Summary

Simian immunodeficiency virus (SIV) uses a stable stem-loop RNA structure to induce ribosomal pausing and frameshifting, essential for viral replication. This finding clarifies the mechanism for SIV and HIV-2 protein synthesis.

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Last Updated: Jul 11, 2026

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

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
10:27

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Area of Science:

  • Molecular Biology
  • Virology
  • Structural Biology

Background:

  • Simian immunodeficiency virus (SIV) requires a -1 translational frameshift for viral replication, similar to human immunodeficiency viruses (HIV-1, HIV-2).
  • This frameshift relies on a slippery sequence and a downstream RNA structure, which has been debated as either a stem-loop or pseudoknot in SIV.

Purpose of the Study:

  • To functionally, structurally, and thermodynamically characterize the SIV frameshift site RNA.
  • To determine the precise RNA structure involved in SIV-mediated translational frameshifting.
  • To investigate the structural similarity between SIV and HIV-2 frameshift elements.

Main Methods:

  • In vitro translational frameshift assays.
  • Nuclear Magnetic Resonance (NMR) spectroscopy for structural determination and thermodynamic studies.
  • Sequence conservation and modeling studies.

Main Results:

  • A stem-loop structure is sufficient to promote efficient frameshifting in vitro.
  • NMR and thermodynamic data confirm a stable stem-loop structure and rule out pseudoknot formation.
  • The determined SIV RNA structure features a stable, ordered loop with specific base pairings and a novel triloop turn.
  • HIV-2 RNA is predicted to form a similar structure.

Conclusions:

  • SIV utilizes a stable stem-loop RNA structure, not a pseudoknot, to induce translational frameshifting.
  • This stem-loop acts as a thermodynamic barrier, causing ribosomal pausing and facilitating frameshifting.
  • SIV and HIV-2 share a common mechanism involving stable stem-loop structures for efficient viral protein synthesis, analogous to HIV-1.