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Nucleic Acids Research, 1982, Vol. 10, No. 1 265-278
© 1982

Articles

Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures

Minoru I. Kanehisa and Walter B. Goad

Theoretical Biology and Biophysics Group, University of California, Los Alamos National Laboratory Los Alamos, NM 87545, USA

Received September 15, 1981. We present a method for calculating all possible single hairpin loop secondary structures in a nucleic acid sequence by the order of N2 operations where N is the total number of bases. Each structure may contain any number of bulges and internal loops. Most natural sequences are found to be indistinguishable from random sequences in the potential of forming secondary structures, which is defined by the frequency of possible secondary structures calculated by the method. There is a strong correlation between the higher G+C content and the higher structure forming potential. Interestingly, the removal of intervening sequences in mRNAs is almost always accompanied by an increase in the G+C content, which may suggest an involvement of structural stabilization in the mRNA maturation.


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