The theoretical analysis of the process of RNA molecule self-assembly.
The Kinetic approach to the problem of the RNA structure prediction based on the analysis of the molecule self-formation is proposed. Re-structurization that occurs during processing is described in terms of Markov processes. A new formalism designating nucleotides by complex numbers is proposed, leading to the complex unitary space of nucleic vectors. Properties of structure and transition matrices are discussed in relation to the analysis of RNA structural formation processes. The non-linear dynamic behavior of secondary structure transition is analyzed. Soliton-like oscillations of RNA and DNA tertiary structures are predicted. The Monte-Carlo simulation of the RNA structure self-formation is used to calculate the ensemble of the secondary structures of the tRNA(Ala) precursor from Bombix mori formed during processing.
Kister
A
A
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.
Magarshak
Y
Y
Malinsky
J
J
D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D007700:Kinetics; D008433:Mathematics; D008956:Models, Chemical; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics
D012313:RNA; D004247:DNA