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A Phase Transition for the Minimum Free Energy of Secondary Structures of a Random RNA

✍ Scribed by Momiao Xiong; Michael S. Waterman

Publisher
Elsevier Science
Year
1997
Tongue
English
Weight
209 KB
Volume
18
Category
Article
ISSN
0196-8858

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✦ Synopsis

The free energy of a single-stranded RNA can be calculated by adding the free energies of the components: basepairs, bulges, and loops. Basepairs receive negative free energy while the unpaired bases receive positive free energy. The minimum free energy of a random RNA secondary structure with one domain has value F where the sequence length is n. Under simplifying assumptions, we show n that for ''small'' values of bulge and loop penalties F has linear growth in n, while n for ''large'' values of these parameters F has logarithmic growth in n. This phase n transition generalizes results obtained for the local-alignment score of two random sequences. The random variable F is conjectured to have a Poisson approximan tion. The multi-domain secondary structure minimum free energy E has linear n growth in n for all values of the penalty functions. Nothing more is known about the distributional properties of E . ᮊ 1997 Academic Press n Ž .

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