  RNA interference (RNAi) is a mechanism whereby small RNAs (siRNAs) directly
control gene expression without assistance from proteins. This mechanism
consists of interactions between RNAs and small RNAs both of which may be
single or double stranded. The target of the mechanism is mRNA to be degraded
or aberrated, while the initiator is double stranded RNA (dsRNA) to be cleaved
into siRNAs. Observing the digital nature of RNAi, we represent RNAi as a
Minsky register machine such that (i) The two registers hold single and double
stranded RNAs respectively, and (ii) Machine's instructions are interpreted by
interactions of enzyme (Dicer), siRNA (with RISC com- plex) and polymerization
(RdRp) to the appropriate registers. Interpreting RNAi as a computational
structure, we can investigate the computational meaning of RNAi, especially its
complexity. Initially, the machine is configured as a Chemical Ground Form
(CGF), which generates incorrect jumps. To remedy this problem, the system is
remodeled as recursive RNAi, in which siRNA targets not only mRNA but also the
machine instructional analogues of Dicer and RISC. Finally, probabilistic
termination is investigated in the recursive RNAi system.
