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Related Concept Videos

RNA Structure01:23

RNA Structure

78.3K
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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RNA Structure01:19

RNA Structure

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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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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RNA-seq03:21

RNA-seq

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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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Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
Nucleic Acid Structure01:25

Nucleic Acid Structure

8.1K
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...
8.1K
Leaky Scanning02:28

Leaky Scanning

5.5K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

Updated: Dec 15, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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HiPR: High-throughput probabilistic RNA structure inference.

Pavel P Kuksa1, Fan Li2, Sampath Kannan3

  • 1Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Computational and Structural Biotechnology Journal
|July 9, 2020
PubMed
Summary
This summary is machine-generated.

HiPR enhances RNA structure prediction accuracy by integrating high-throughput probing data with a novel probabilistic folding algorithm. This method offers improved tools for researchers studying RNA structure across various RNA classes.

Keywords:
DMS-MaPseqDMS-seqHigh-throughput structure-sensitive sequencingProbabilistic modelingRNA structure inference

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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput sequencing assays have advanced RNA structure studies.
  • Computational prediction of RNA structures can be improved using experimental data.
  • Understanding RNA structure is crucial for its function.

Purpose of the Study:

  • To develop a novel method for accurate RNA structure prediction at single-nucleotide resolution.
  • To integrate high-throughput structure probing data with computational algorithms.
  • To provide researchers with enhanced tools for RNA structure analysis.

Main Methods:

  • Developed HiPR, a novel probabilistic folding algorithm.
  • Integrated high-throughput structure probing data (DMS-seq, DMS-MaPseq) with the algorithm.
  • Validated the method on diverse RNA classes.

Main Results:

  • HiPR often increases the accuracy of RNA structure prediction.
  • The method demonstrates effectiveness across various RNA classes.
  • HiPR provides a valuable new tool for RNA structure research.

Conclusions:

  • HiPR offers a significant advancement in RNA structure prediction accuracy.
  • The integration of experimental and computational approaches is effective.
  • Researchers gain a powerful new tool for exploring RNA structure and function.