The Ribonucleic Acid (RNA) is a nucleic acid that consists of a long chain of nucleotide units. The RNA is the genetic material used by some virus and it is also important in the production of proteins in living organisms. The study of the folding of RNA molecules is very important from a biological point of view. For example, a bad transcription of DNA into RNA causes an undesirable folding of the molecule that consequently produces a wrong folding of the protein. The result is a cellular disfunction known as amyloidosis, which causes some nasty diseases such as Alzheimer's.

We present a model that predicts the tridimensional folding of RNA molecules. RNA chains where modeled by means of three types of effective potentials: radial, angular flexion and angular torsion, which where directly obtained from experimental data using angular and radial distribution functions of the nucleotides' centroids. As a result, our method considerably reduces the computational time since it minimizes the potential functions that have to be evaluated. The simulations were performed using the Metropolis-Monte Carlo method, that allows to obtain a chain of minimum energy.

You can download the effective potentials here

We performed a Pade-like fit of 10 radial potentials. Here we show some of them.

wrau wrgc wrac

In addition, we obtained only a bending potential and 10 torsion potentials. Here we show some of them.

bth bphgc bphgg

The preliminary results show that it's possible to predict the tridimensional folding of RNA via our model. The model is able to predict the difference between two very similar molecules than differ only in one nucleotide. We show the tridimensional structures of hairpin-type RNA molecules. The first figure shows the molecule 1esh; in blue the experimental data and in cyan the simulated molecule. The second figure shows the molecule 1jzc; in blue the experimental data and in cyan the simulated molecule.

esh jzc

We are waiting to get more complicated tridimensional structures.

You can download the effective potentials here


Information: M.D. Carbajal Tinoco
e-mail: mdct@fis.cinvestav.mx