BioGem Blog

The prediction of 3D RNA-RNA structure and interaction is a multi-step process involving loop-loop recognition, coaxial stacking, and metal-ion stabilization, resulting in a complex topological structure essential for biological function.Unlike DNA, which primarily exists as a double helix, RNA is single-stranded and can adopt diverse three-dimensional shapes, allowing it to perform catalytic, structural, and regulatory roles. Structural Hierarchy and Driving Forces RNA-RNA interactions are governed by a hierarchical folding process where secondary structure elements (helices, loops, and bulges) form first, followed by the arrangement of these elements into a specific tertiary structure. The primary physical forces driving these interactions include: Hydrogen Bonding: Beyond standard Watson-Crick base pairing (A-U, G-C), RNA frequently utilizes non-canonical interactions such as Wobble base pairs (G-U) and Hoogsteen pairings. Base Stacking: The hydrophobic effec...

Ribonucleic acid (RNA) is a linear polymeric molecule composed of four bases namely adenine (A), cytosine (C), guanine (G), and uracil (U). It is used for the prediction of various functions which include coding, decoding, regulation, and gene expression. The prediction of RNA–RNA interaction plays a major role in the study of structure folding and free energy of RNA complex molecule. This is a video tutorial for RNA-RNA interaction prediction using RactIP (RNA-RNA interACTion prediction using IP) and visualize inter and/or intramolecular base-pair interactions using VARNA (Visualization Applet for RNA) tools. The list of tools used is RactIP and VARNA .