Biopolym. Cell. 1990; 6(6):31-36.
The method for RNA secondary structure construction on the basis of self-organization principles
1Gultyaev A. P., 1Monakov Yu. N.
  1. All-Union Institute of Influenza, Ministry of Public Health of the USSR
    Leningrad, USSR


The method for computer calculation of RNA secondary structure is described. The algorithm is based on successive formation of helices in the RNA self-organization process with the generation of random structure sets by the Monte-Carlo mehtod. This way permits constructing RNA secondary structures for rather long sequences (up to 5000 nucleotides) by means of the personal computer without using large memory volumes.


[1] Wada A, Suyama A. Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog Biophys Mol Biol. 1986;47(2):113-57.
[2] Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981;9(1):133-48.
[3] Jacobson AB, Good L, Simonetti J, Zuker M. Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res. 1984;12(1 Pt 1):45-52.
[4] Kolchanov NA, Solovyev VV, Zharkikh AA. Context theoretical analysis techniques of genetic macromolecules (DNA, RNA and proteins). Itogi nauki i tekhniki. Moscow, VINITI, (Ser. Molekulyarnaya biologiya, Vol. 21). 1985; 6-37.
[5] Martinez HM. An RNA folding rule. Nucleic Acids Res. 1984;12(1 Pt 1):323-34.
[6] Mironov AA, D'iakonova LP, Kister AE. Prediction of the ensembles of RNA secondary structures. Kinetic analysis of self-organization. Mol Biol (Mosk). 1984;18(6):1686-94.
[7] Nussinov R, Pieczenik G. Structural and combinatorial constraints on base pairing in large nucleotide sequences. J Theor Biol. 1984;106(3):245-59.
[8] Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986;83(24):9373-7.
[9] Mills DR, Kramer FR, Spiegelman S. Complete nucleotide sequence of a replicating RNA molecule. Science. 1973;180(4089):916-27.
[10] Eigen M, Shuster P. The Hypercycle - a principle of natural self-organization. Moscow, Mir, 1982; 270 p.
[11] Woese CR, Gutell R, Gupta R, Noller HF. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983;47(4):621-69.
[12] Williams AL Jr, Tinoco I Jr. A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res. 1986;14(1):299-315.
[13] Gutell RR, Fox GE. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 1988;16 Suppl:r175-269.