Abstract
RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene by an RNA polymerase. Oritatami is a computational model of this phenomenon, which lets its sequence of beads (abstract molecules) taken from a finite alphabet [Formula: see text] fold cotranscriptionally via interactions between beads according to its rule set. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. Self-attraction is one of the major challenges in the construction of intrinsic oritatami systems, which can simulate even the dynamics of all the oritatami systems.
Highlights
Self-assembly is the process by which relatively simple components coalesce to form intricate and complex structures
One proposed model of self-assembly is called Oritatami [8], which seeks to capture the fundamental dynamics of cotranscriptional folding
In part supported by JST Program to Disseminate Tenure Tracking System No 6F36 and JSPS KAKENHI Grant-in-Aid for Young Scientists (A) No 16H05854 † Corresponding author attaches to a DNA sequence and sequentially produces RNA nucleotides (A, C, G, U)
Summary
Self-assembly is the process by which relatively simple components coalesce to form intricate and complex structures. Supported by International Cooperation Program (2017K2A9A2A08000270) and Basic Science Research Program (2015R1D1A1A01060097) by NRF of Korea. Oritatami is a theoretical model to study the computational aspect of cotranscriptional folding It models a single strand of RNA as a “strand” of abstract molecules, or beads. The class of oritatami systems implementable in the laboratory by the cotranscriptional folding of RNA is limited by the properties of RNA. If we wanted to implement an oritatami system in this setting which had a rule specifying a bead type is attracted to itself, the self-attraction would need to be removed. We examine the removal of rules specifying that a bead type is attracted to itself, which we call self-attraction rules, from Oritatami systems. Given a system Ξ, the goal of self-attraction removal is to create another system Ξ such that Ξ behaves in the same way as Ξ, Ξ produces the same set of conformations as Ξ, and Ξ does not contain any self-attraction rules
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