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Related Concept Videos

RNA Structure01:23

RNA Structure

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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.
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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.
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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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RNA Interference01:23

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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.
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RNA Stability

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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: Dec 29, 2025

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

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Antisense probing of dynamic RNA structures.

Alexandra J Lukasiewicz1, Lydia M Contreras2

  • 1Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States.

Methods (San Diego, Calif.)
|January 29, 2020
PubMed
Summary
This summary is machine-generated.

A new cell-free antisense probing method reveals dynamic RNA structures and rare intermediates, offering insights into RNA regulation. This technique enhances understanding of how regulatory elements and interactions affect RNA accessibility.

Keywords:
Antisense probingRNA accessibilityRNA: Protein interactionsRibozymesSmall RNAs

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA regulation is governed by dynamic conformational changes affecting transcript accessibility.
  • Traditional chemical probing methods have limitations in detecting transient RNA structures.

Purpose of the Study:

  • To validate a novel cell-free antisense probing technique for analyzing structured RNAs.
  • To demonstrate the method's capability in identifying rare RNA intermediates and understanding RNA accessibility.

Main Methods:

  • Utilized a cell-free antisense probing approach.
  • Employed the Tetrahymena group I intron as a model structured RNA target.
  • Compared results with traditional dimethyl sulfate (DMS) footprinting experiments.

Main Results:

  • Observed signal changes that qualitatively align with established DMS footprinting data.
  • Demonstrated the method's enhanced sensitivity for detecting rare RNA intermediates.
  • Showcased the technique's ability to provide new insights into RNA structure and dynamics.

Conclusions:

  • The cell-free antisense probing method is a validated tool for studying RNA structure and dynamics.
  • This technique offers advantages over traditional methods for observing transient RNA states.
  • The approach has broad applications in understanding RNA accessibility, regulatory element effects, RNA-RNA interactions, and small molecule binding.