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 single-stranded molecule that takes part in translation to protein. The intramolecular interactions ( a.k.a. folding) of RNA base pairs (A=U and C≡G) form a secondary structure. Nussinov (or) Zuker algorithm is a dynamic programming approach used for the prediction of the secondary structure of the RNA. The dot-bracket structure with the minimum free energy is a stable secondary structure. Prediction of the three-dimensional (3D) structure of RNA using mFold and RNAComposer tools have demonstrated in this tutorial. The mFold tool predicts the dot-bracket notation format RNA folding result from the RNA sequence, while the RNAComposer tool predicts the 3D structure from the dot-bracket notation. The resources used in this tutorial are NCBI GenBank , mFold , and RNAComposer . Note: The length of RNA sequence input in mFold is limited to 4000 bases and sequence/dot-bracket notation input in RNAComposer is limited to 500 bases, due to...