Abstract
A method is presented that enables computation of the stability of hairpin loops in an RNA chain, knowing only the amino-acid sequence translated from that chain. The method is based on a statistical decoding procedure and a thenno-dynamic evaluation of bonding in terms of free energy. The decoding takes into account all triplets of bases for each amino acid. Every possible hairpin loop formed by bonding between base pairs is examined by a computer program. Using thermodynamic criteria, it is decided which loops have a high probability of being bound. For these, a free energy of loop formation is evaluated in order to predict stability. The method is tested on 54 amino-acid sequences obtained by translating 18 different tRNA's. The loops predicted from the amino-acid sequence are compared with their actual counterparts in the original nucleotide sequence. A strong positive correlation is observed between the predicted and actual stabilities. A hairpin loop predicted to be stable from the amino-acid sequence has, on average, a probability of 0.5 of being stable, 0.3 of being metastable and 0.2 of being unstable, in the actual nucleotide sequence. Various applications of this method to obtain information about sequence and structure in messenger RNA's are discussed.
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