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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 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...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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...
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...

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Updated: Jun 20, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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RNA design: update on computational frameworks and programs for inverse RNA folding.

Sumit Mukherjee1,2, Rami Zakh1,3, Alexander Churkin3

  • 1Institute for Interdisciplinary Computational Science, Ben-Gurion University, David Ben-Gurion Blvd. 1, Be'er-Sheva, 8410501, Israel.

Briefings in Bioinformatics
|June 19, 2026
PubMed
Summary
This summary is machine-generated.

This review updates computational tools for inverse RNA folding, enabling the design of RNA sequences with specific structures. It covers key software and emerging machine learning applications for RNA design.

Keywords:
RNA designinverse RNA folding

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Last Updated: Jun 20, 2026

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Molecular biology

Background:

  • Computational tools for predicting RNA folding properties are continuously evolving.
  • Inverse RNA folding designs RNA sequences for desired structures and properties.
  • A previous review was published a decade ago.

Purpose of the Study:

  • To provide an updated review of freeware programs for inverse RNA folding.
  • To highlight advancements in RNA design computational frameworks.
  • To examine emerging machine learning applications in RNA design.

Main Methods:

  • Review of widely used freeware programs for inverse RNA folding.
  • Analysis of computational frameworks like Infrared and DesiRNA.
  • Examination of updated tools including RNAstructure, NUPACK, and others.
  • Discussion of diverse strategies: Monte Carlo, constraint satisfaction, Boltzmann sampling, and machine learning.

Main Results:

  • Identified key programs and frameworks: RNAinverse, Infrared, DesiRNA, RNAstructure, NUPACK, MoiRNAiFold, MODENA, incaRNAfbinv.
  • Highlighted diverse computational approaches including machine learning.
  • Noted emerging applications in messenger RNA (mRNA) and CRISPR guide RNA (gRNA) design.
  • Covered advancements in 3D RNA design and RNA-RNA interactions.

Conclusions:

  • The field of inverse RNA folding has seen significant advancements over the past decade.
  • Machine learning is increasingly important for novel RNA design applications.
  • This review offers a timely update on essential computational tools for RNA sequence design.