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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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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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Related Experiment Video

Updated: Sep 14, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
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Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly.

Kai Sheng1,2, Xiyu Dong1,2, Sriram Aiyer3

  • 1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

Nature Communications
|July 18, 2025
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Summary

This study used anti-sense oligonucleotides (ASOs) to reveal novel RNA-protein complex (RNP) folding intermediates. The findings provide a hierarchical view of ribosome assembly, highlighting template-directed RNA docking and domain consolidation.

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Area of Science:

  • Structural biology
  • Molecular biology
  • Biochemistry

Background:

  • Investigating the folding kinetics of large RNA-protein complexes (RNPs), such as the bacterial ribosome, is challenging.
  • Previous methods relied on genetic approaches to modulate protein or factor expression.

Purpose of the Study:

  • To probe RNP assembly by generating novel folding intermediates.
  • To elucidate the hierarchical structure and dynamics of RNP assembly.

Main Methods:

  • Utilized anti-sense oligonucleotides (ASOs) to disrupt RNA/RNA and RNA/protein interactions.
  • Employed an in vitro co-transcriptional ribosome assembly assay.
  • Determined intermediate structures using cryo-electron microscopy (cryo-EM).

Main Results:

  • Identified 10 assembly inhibitor ASOs and determined 38 intermediate structures using cryo-EM.
  • Provided evidence for independent rRNA domain folding prior to interdomain docking.
  • Discovered that PNAs targeting 23S rRNA domain-I subdivide the assembly core into smaller blocks.

Conclusions:

  • Developed an assembly graph revealing template-directed RNA docking (foldons) and domain consolidation.
  • Established a hierarchical model for RNP assembly.
  • Identified potential antibiotic targets and a platform for studying RNP structure and dynamics.