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Related Concept Videos

Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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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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Updated: Jan 27, 2026

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection
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Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules.

Christopher S Eubanks, Bo Zhao, Neeraj N Patwardhan

    Journal of the American Chemical Society
    |March 13, 2019
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    Pattern Recognition of RNA by Small Molecules (PRRSM) visualizes RNA folding changes. This method accurately classifies riboswitch structures and identifies critical nucleotide positions for RNA folding.

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    Area of Science:

    • Molecular Biology
    • Biochemistry
    • Structural Biology

    Background:

    • RNA conformational changes are crucial for biological regulation but difficult to visualize.
    • Previous work established Pattern Recognition of RNA by Small Molecules (PRRSM) for clustering RNA secondary structure motifs.
    • Aminoglycoside receptor libraries were utilized in PRRSM for unbiased clustering.

    Purpose of the Study:

    • To demonstrate the utility of PRRSM for visualizing secondary structure changes in riboswitches.
    • To assess PRRSM's ability to differentiate between apo and ligand-bound states.
    • To identify nucleotide positions critical for RNA folding.

    Main Methods:

    • Labeling of three independent positions on two distinct riboswitch structures.
    • Application of the PRRSM assay to classify RNA structures.
    • Analysis of structural motif size changes and identification of folding-disrupting modifications.

    Main Results:

    • PRRSM accurately classified all apo and ligand-bound riboswitch structures.
    • The method detected changes in the size of structural motifs upon ligand binding.
    • PRRSM identified modification sites that hindered proper RNA folding or resulted in mixed states.

    Conclusions:

    • PRRSM is a powerful and robust method for assessing RNA structural dynamics.
    • The assay provides rapid insights into nucleotide positions essential for RNA folding.
    • PRRSM facilitates the visualization of RNA conformational changes at the secondary structure level.