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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.
Different Types of RNA Have the Same Basic Structure
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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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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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RNA Editing02:23

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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RNA Interference

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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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Updated: Aug 4, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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On a barrier height problem for RNA branching.

Christine Heitsch1, Chi N Y Huynh2, Greg Johnston3

  • 1School of Mathematics, Georgia Institute of Technology.

Arxiv
|March 30, 2023
PubMed
Summary
This summary is machine-generated.

Predicting RNA branching is challenging. This study uses plane trees to model RNA folding, analyzing the thermodynamic cost of structural transitions and identifying conditions for optimal folding paths.

Keywords:
05A1805C0592D20MSCRNA secondary structurebarrier heightplane tree

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Area of Science:

  • Computational Biology
  • Biophysics
  • RNA Structure Analysis

Background:

  • RNA branching is a key structural feature, crucial for function but difficult to predict accurately, especially in longer RNA sequences.
  • Understanding the energy landscape of RNA folding, particularly the barriers between different structural configurations, is essential for predicting molecular behavior.

Approach:

  • Utilizes plane trees as a combinatorial model to represent RNA folding configurations.
  • Investigates the thermodynamic cost, or barrier height, associated with transitions between these branching configurations.
  • Employs branching skew as a simplified energy approximation to analyze paths within the RNA configuration landscape.

Key Points:

  • Characterizes various paths in the discrete RNA configuration landscape using branching skew.
  • Provides sufficient conditions for identifying paths that exhibit both minimal length and minimal branching skew.
  • The analysis offers biological insights into RNA folding dynamics.

Conclusions:

  • The study highlights the potential significance of hairpin stability and domain architecture in higher-resolution analyses of RNA barrier heights.
  • Findings contribute to a better understanding of the energetic factors governing RNA structural transitions.
  • This combinatorial approach offers a novel perspective on predicting complex RNA folding patterns.