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Related Concept Videos

RNA Structure01:23

RNA Structure

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...
RNA-seq03:21

RNA-seq

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: Jul 1, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA

Ze-Hui Ren1,2,3, Hong-Xuan Chen1,2,4, Ying-Yuan Xie1,4

  • 1State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

Genomics, Proteomics & Bioinformatics
|June 29, 2026
PubMed
Summary
This summary is machine-generated.

NanoRAPID, a new CNN tool, precisely identifies RNA structural probing sites from Nanopore direct RNA sequencing data. This method enhances RNA structure analysis and reveals insights into RNA modifications and conformations.

Keywords:
Deep learningNanopore sequencingRNA structureSHAPE probingm6A

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Last Updated: Jul 1, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

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Published on: August 20, 2014

Nanopore DNA Sequencing for Metagenomic Soil Analysis
07:33

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA secondary structure is crucial for biological functions.
  • Current chemical probing methods with sequencing have limitations in direct readout and molecule averaging.
  • Accurate identification of probe-modified sites in Nanopore direct RNA sequencing (DRS) data is challenging.

Purpose of the Study:

  • To develop a novel computational framework, NanoRAPID, for precise RNA structural probe site identification using DRS data.
  • To improve the accuracy of RNA secondary structure analysis by directly interpreting raw nanopore signals.
  • To explore RNA structural features and their relationship with modifications across the transcriptome.

Main Methods:

  • Development of NanoRAPID, a convolutional neural network (CNN)-based framework.
  • Analysis of raw current signals from Nanopore DRS data.
  • Validation using DRS datasets with NAI-N3 and DEPC chemical probing treatments.

Main Results:

  • NanoRAPID achieves improved accuracy in probe-site identification by directly analyzing raw current signals.
  • Transcriptome-wide analysis reveals distinct RNA structural features, with variable mRNA structures and compact rRNAs.
  • Identification of RNA isoforms with distinct structural conformations and a correlation between m6A modification and 3' UTR accessibility.

Conclusions:

  • NanoRAPID is a precise and versatile tool for analyzing RNA structural probing signals from DRS data.
  • The framework enables deeper understanding of RNA structure, dynamics, and regulation.
  • Findings suggest RNA structural context influences m6A modification and highlight isoform-specific structural variations.