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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 Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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...

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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

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Stacking interactions in PUF-RNA complexes.

Yvonne Yiling Koh1, Yeming Wang, Chen Qiu

  • 1Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

RNA (New York, N.Y.)
|March 5, 2011
PubMed
Summary
This summary is machine-generated.

Amino acid stacking in RNA-protein interactions is crucial for regulating messenger RNAs (mRNAs). Specific amino acid identities in PUF proteins fine-tune RNA binding affinity and specificity, impacting gene regulation.

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Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters

Published on: May 29, 2026

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • RNA-protein interactions are vital for gene regulation, often involving proteins binding to messenger RNA (mRNA) in the 3'-untranslated region (3' UTR).
  • PUF ( Pumilio family) proteins are key regulators of mRNA, known for their specific RNA-binding capabilities.

Purpose of the Study:

  • To investigate the role of amino acid-base stacking interactions in the formation and specificity of RNA-protein complexes.
  • To determine how specific amino acid residues within PUF proteins, like FBF from Caenorhabditis elegans, influence binding to their target RNAs.

Main Methods:

  • In vivo selection experiments to identify functional RNA sequences.
  • Site-directed mutagenesis to alter specific amino acid residues in the FBF protein.
  • Biochemical assays to measure binding affinity.
  • Structural analysis to visualize RNA-protein complex formation.

Main Results:

  • Stacking interactions involving every RNA base are prominent in FBF-RNA complexes.
  • The identity of amino acids involved in stacking significantly affects both the affinity and specificity of RNA binding.
  • Amino acid substitutions can either narrow or broaden the range of recognized RNA sequences.

Conclusions:

  • Amino acid stacking residues are critical for the natural specificity of PUF proteins in recognizing their target RNAs.
  • Understanding these stacking interactions is important for engineering PUF proteins with novel RNA-binding specificities and for designing targeted therapeutic agents.