Ok: A Kinetic Model for Locally Reconfigurable Molecular Systems

Abstract

Oritatami is a formal model of RNA co-transcriptional folding, in which an RNA sequence (transcript) folds upon itself while being synthesized (transcribed) out of its DNA template. This model is simple enough for further extension and also strong enough to study computational aspects of this phenomenon. Some of the structural motifs designed for Turing universal computations in oritatami have been demonstrated approximately in-vitro recently. This model has yet to take a significant aspect of co-transcriptional folding into full account, that is, reconfiguration of molecules. Here we propose a kinetic extension of this model called the oritatami kinetic (Ok) model, similar to what kinetic tile assembly model (kTAM) is to abstract tile assembly model (aTAM). In this extension, local rerouting of the transcript inside a randomly chosen area of parameterized radius competes with the transcription and the folding of the nascent beads (beads are abstract monomers which are the transcription units in oritatami). We compare this extension to a simulation of oritatami in the nubot model, another reconfiguration-based molecular folding model. We show that this new extension matches better a reconfiguration model and is also faster to simulate than passing through a nubot simulation.