Prediction of 3D Structure (Folding) of a RNA Sequence

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RNA Structure

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 the complexity of the algorithm used in the programs.

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