COMPUTER RESEARCH OF SOME TRANSCRIPTION PROCESS PARAMETERS INFLUENCE ON RNA SECONDARY STRUCTURE FOLDING
Eneev T. M., Kozlov N. N., Kugushev E. I.
Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 125047, Moscow, Miusskaya Sq. 4, Russia
Computer simulation results of formation of RNA secondary structures
during transcription are presented. The main parameter of this process
is the ratio of the elongation molecular chain rate to the secondary structure
formation rate (T-parameter). Three RNA classes have been processed: transfer,
ribosomal and fermentative RNA. The obtained results allow us to make a
conclusion that the ratio of RNA molecular chain lengthening rate to structures'
formation rate essentially influences structure formation; also, RNA molecular
chain may be supposed to grow unevenly. The process is simulated both in
the model with permission of any rearrangements of local structure that
decrease the free energy and in the model in which such rearrangements
are prohibited. It is revealed that the structure rearrangements play an
important role in RNA secondary structure formation. The dependence of
the simulation results on the T-parameter suggests that the process of
transcription is of discontinuous nature. The dependence of the obtained
solution on the choice of the transcribed DNA chain and on the transcription
direction is studied.
This research was supported by Russian Foundation for Basic Research
Grants N 96-01-01192 and N 96-15-97229.