Jove
Visualize
Contact Us

Related Concept Videos

Experimental RNAi02:15

Experimental RNAi

6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K
RNA-seq03:21

RNA-seq

10.0K
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...
10.0K
RNA Interference01:23

RNA Interference

26.1K
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.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
26.1K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

10.6K
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.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.6K
RNA Structure01:19

RNA Structure

4.8K
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...
4.8K
RNA Editing02:23

RNA Editing

9.0K
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...
9.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.

Nucleic acids research·2026
Same author

MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) regulates long-range alternative splicing in Drosophila.

Nucleic acids research·2026
Same author

Experimental identification of preQ<sub>1</sub>-binding RNAs in the pathogenic bacterium <i>Listeria monocytogenes</i>.

RSC chemical biology·2025
Same author

Sequence Design for RNA-RNA Interactions.

Methods in molecular biology (Clifton, N.J.)·2024
Same author

Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

Nucleic acids research·2024
Same author

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.

Nucleic acids research·2024
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jul 11, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.2K

Modified RNAs and predictions with the ViennaRNA Package.

Yuliia Varenyk1,2, Thomas Spicher1,3, Ivo L Hofacker1,4

  • 1Department of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria.

Bioinformatics (Oxford, England)
|November 16, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to predict RNA structures with modified bases by incorporating sparse energy data into existing algorithms. This enhances the accuracy of RNA structure prediction for modified RNA molecules.

More Related Videos

mirMachine: A One-Stop Shop for Plant miRNA Annotation
06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

2.6K
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

5.6K

Related Experiment Videos

Last Updated: Jul 11, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.2K
mirMachine: A One-Stop Shop for Plant miRNA Annotation
06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

2.6K
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

5.6K

Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Over 300 modified bases exist beyond the standard ACGU RNA alphabet.
  • Modified bases influence RNA structure and function, with some essential for tRNA folding.
  • Predicting RNA structures with modified bases is challenging due to algorithmic limitations and missing stability data.

Purpose of the Study:

  • To develop an efficient method for incorporating modified base energy parameters into RNA structure prediction.
  • To enhance the ViennaRNA Package to handle a larger RNA sequence alphabet.

Main Methods:

  • Implemented a plug-in constraint system within the ViennaRNA Package.
  • Adapted prediction algorithms at runtime to include sparse energy parameter data for modified bases.
  • Ensured computational efficiency by applying adaptations only where parameters are available.

Main Results:

  • Successfully integrated sparse energy parameter data for modified bases into RNA structure prediction.
  • The approach enhances the ViennaRNA Package without altering core algorithms.
  • Facilitates the future inclusion of more modified bases as data becomes available.

Conclusions:

  • The developed method provides a flexible and efficient way to improve RNA structure prediction accuracy for modified RNAs.
  • This advancement aids in understanding the roles of modified bases in RNA structure and function.