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Related Concept Videos

RNA-seq03:21

RNA-seq

10.3K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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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
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...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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.
DNA Structure
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Updated: Aug 27, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Long-read single-molecule RNA structure sequencing using nanopore.

Teshome Tilahun Bizuayehu1,2, Kornel Labun1, Martin Jakubec3

  • 1Computational Biology Unit, Department of Informatics, University of Bergen, Norway.

Nucleic Acids Research
|September 27, 2022
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Summary
This summary is machine-generated.

Single-Molecule Structure sequencing (SMS-seq) reveals RNA structural heterogeneity and dependencies at the individual molecule level. This breakthrough overcomes population averaging limitations, offering unprecedented insights into RNA structure and function.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA secondary and tertiary structures are crucial for regulating RNA localization and function.
  • Current high-throughput sequencing methods provide population-averaged RNA structural information, limiting insights into molecular heterogeneity.
  • Existing long-read sequencing methods for RNA structure also rely on aggregate signals, obscuring individual molecule details.

Purpose of the Study:

  • To develop a method for obtaining non-amplified, structural profiles of individual RNA molecules.
  • To overcome the limitations of population averaging in RNA structure analysis.
  • To enable the discovery of dependencies and heterogeneity within individual RNA structures.

Main Methods:

  • Development of Single-Molecule Structure sequencing (SMS-seq), combining structural probing with native RNA sequencing.
  • Application of novel analysis methods, including mutual information, for single-molecule structural interrogation.
  • Probing numerous bases on each RNA molecule to capture detailed structural information.

Main Results:

  • SMS-seq provides non-amplified structural profiles of individual RNA molecules.
  • The method successfully captures RNA structural heterogeneity and dependencies within single molecules.
  • SMS-seq demonstrates capability in detecting tertiary interactions, riboswitch ligand binding dynamics, and mRNA structural features.

Conclusions:

  • SMS-seq represents a significant advancement in RNA structure analysis, enabling single-molecule resolution.
  • This technique overcomes previous limitations of population averaging, providing deeper insights into RNA structure-function relationships.
  • SMS-seq opens new avenues for studying RNA dynamics, interactions, and regulatory mechanisms at the single-molecule level.