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 Structure01:23

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 Structure01:19

RNA Structure

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...
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...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

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

Sort by
Same author

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

PNAS nexus·2025
Same author

Complex In Silico RNA Design with MoiRNAiFold.

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

Alternative splicing events driven by altered levels of GEMIN5 undergo translation.

RNA biology·2024
Same author

ePyDGGA: automatic configuration for fitting epidemic curves.

Scientific reports·2024
Same author

Gemin5-dependent RNA association with polysomes enables selective translation of ribosomal and histone mRNAs.

Cellular and molecular life sciences : CMLS·2022
Same author

The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics".

Physics of life reviews·2022

Related Experiment Video

Updated: May 12, 2026

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

RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design.

Juan Antonio Garcia-Martin1, Peter Clote, Ivan Dotu

  • 1CNB-CSIC, Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain. ja.garcia@cnb.csic.es

Journal of Bioinformatics and Computational Biology
|April 23, 2013
PubMed
Summary

We developed RNAiFold, a novel computational approach for RNA design. It efficiently determines RNA sequences that fold into desired structures, supporting diverse design constraints for advanced synthetic biology applications.

More Related Videos

Designing a Bio-responsive Robot from DNA Origami
13:32

Designing a Bio-responsive Robot from DNA Origami

Published on: July 8, 2013

Folding and Characterization of a Bio-responsive Robot from DNA Origami
07:59

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

Related Experiment Videos

Last Updated: May 12, 2026

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

Designing a Bio-responsive Robot from DNA Origami
13:32

Designing a Bio-responsive Robot from DNA Origami

Published on: July 8, 2013

Folding and Characterization of a Bio-responsive Robot from DNA Origami
07:59

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

Area of Science:

  • Synthetic biology and nanotechnology integration.
  • Advancements in biomolecular self-assembly and genetic network synthesis.

Background:

  • Synthetic biology enables creation of novel life forms and molecular detection.
  • Existing methods for RNA design lack comprehensive constraint support.

Purpose of the Study:

  • To present a Constraint Programming (CP) approach for the RNA inverse folding problem.
  • To develop a method for designing RNA sequences that fold into specific target secondary structures.

Main Methods:

  • Utilizing Constraint Programming (CP) to solve the RNA inverse folding problem.
  • Implementing a Large Neighborhood Search (LNS) for larger instances.
  • Developing the RNAiFold software with a webserver and downloadable source code.

Main Results:

  • RNAiFold successfully determines RNA sequences for target secondary structures.
  • The approach supports a wide range of design constraints, including motifs and GC-content.
  • RNAiFold demonstrates competitive or superior performance compared to state-of-the-art methods.

Conclusions:

  • The developed CP approach is the first complete RNA inverse folding method with extensive constraint specification.
  • RNAiFold offers a unique combination of completeness, flexibility, and constraint support for RNA design.
  • The publicly available RNAiFold tool advances RNA design capabilities for synthetic biology.