Related Experiment Video
Updated: Mar 30, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple
Tristan Cragnolini1, Yoann Laurin1, Philippe Derreumaux1,2
1Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.
Abstract:
HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study of RNA folding. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking, we show that noncanonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper, we give a full account of the model and present results on the folding, stability, and free energy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850 μs of simulation time.
Related Concept Videos
Nucleic Acid Structure
DNA Structure
DNA...
RNA Structure
RNA Structure
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 Structure
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...
Protein Folding
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding

