Computer research of some transcription process parameters influence on RNA secondary structure folding

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.