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Nucleic Acids Research, 1989, Vol. 17, No. 13 5149-5162
© 1989

MOLECULAR BIOLOGY

A new method to find a set of energetically optimal RNA secondary structures

Giorgio Benedetti, Pasquale De Santis and Stefano Morosetti

Department of Chemistry, University of Rome I P.le A.Moro 5, 00185 Rome, Italy

Received February 13, 1989. Revised June 1, 1989. Accepted June 1, 1989.

We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown. In order to demonstrate the confidence of the program a test on four RNA sequences is performed. The method has computer time requirement proportional to N2, where N is the length of the sequence and retrieves a set of optimal free energy structures.


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