Jove
Visualize
Contact Us
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 Concept Videos

RNA Structure01:19

RNA Structure

5.8K
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...
5.8K
RNA Structure01:23

RNA Structure

76.4K
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...
76.4K
RNA Interference01:23

RNA Interference

26.9K
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...
26.9K
Experimental RNAi02:15

Experimental RNAi

6.7K
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...
6.7K
RNA-seq03:21

RNA-seq

10.9K
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...
10.9K
RNA Splicing01:32

RNA Splicing

58.4K
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...
58.4K

You might also read

Related Articles

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

Sort by
Same author

Low Inflammation Correlates with Protumor Tim4+TREM1+ Resident Macrophage Expansion and Limited Monocyte-Derived Macrophage Differentiation during Peritoneal Colorectal Cancer.

Cancer immunology research·2026
Same author

A transient sex-biased transcriptional program shapes early postnatal L2/3 neuron development.

Biology of sex differences·2026
Same author

Genome resequencing and custom genotyping elucidates the origin and dissemination history of an emblematic grapevine cultivar, 'Tempranillo Tinto'.

Horticulture research·2025
Same author

Detecting bias in algorithms used to disseminate information in social networks and mitigating it using multiobjective optimization.

PNAS nexus·2025
Same author

Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches.

International journal of molecular sciences·2025
Same author

Complex In Silico RNA Design with MoiRNAiFold.

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

Related Experiment Video

Updated: Nov 6, 2025

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

4.4K

MoiRNAiFold: a novel tool for complex in silico RNA design.

Gerard Minuesa1, Cristina Alsina1, Juan Antonio Garcia-Martin2,3

  • 1Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain.

Nucleic Acids Research
|May 6, 2021
PubMed
Summary

MoiRNAiFold is a new computational tool for designing synthetic RNA molecules, including riboregulators for gene expression control. This versatile software accelerates RNA design, reducing time and cost for developing new diagnostics and therapeutics.

More Related Videos

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

12.0K
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

4.7K

Related Experiment Videos

Last Updated: Nov 6, 2025

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

4.4K
A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

12.0K
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

4.7K

Area of Science:

  • Computational Biology
  • Synthetic Biology
  • Molecular Biology

Background:

  • Developing novel RNA constructs for diagnostics and therapeutics requires efficient in silico design tools.
  • Current methods for synthetic RNA design are time-consuming and costly.
  • There is a need for advanced software to handle complex RNA design constraints and improve regulatory functions.

Purpose of the Study:

  • To introduce MoiRNAiFold, a user-friendly tool for de novo synthetic RNA design.
  • To enhance the design of RNA molecules for gene expression regulation, including Translation Efficiency.
  • To provide a powerful and accessible platform for complex RNA construct development.

Main Methods:

  • MoiRNAiFold utilizes Constraint Programming with novel variable types, heuristics, and Large Neighborhood Search strategies.
  • The software incorporates advanced features for RNA regulation, such as Translation Efficiency calculation.
  • Benchmarking was performed using structural RNA puzzles from EteRNA and functional validation of designed riboregulators.

Main Results:

  • MoiRNAiFold outperforms existing software in solving structural RNA puzzles.
  • Designed RNA sequences, specifically riboregulators, demonstrate functionality in vitro and in vivo.
  • The tool successfully handles numerous design constraints and quality measures for complex RNA constructs.

Conclusions:

  • MoiRNAiFold is a powerful and versatile tool for de novo synthetic RNA design.
  • The software significantly improves the design process for RNA constructs, particularly riboregulators.
  • MoiRNAiFold is available as a free web server, facilitating advancements in RNA-based diagnostics and therapeutics.