Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer

Polynomial time dynamic programming algorithms play a crucial role in the design, analysis and engineering of nucleic acid systems including DNA computers and DNA/RNA nanostructures. However, in complex multistranded or pseudoknotted systems, computing the minimum free energy (MFE), and partition function of nucleic acid systems is NP-hard. Despite this, multistranded and/or pseudoknotted systems represent some of the most utilised and successful systems in the field. This leaves open the tempting possibility that many of the kinds of multistranded and/or pseudoknotted systems we wish to engineer actually fall into restricted classes, that do in fact have polynomial time algorithms, but we\u27ve just not found them yet. Here, we give polynomial time algorithms for MFE and partition function calculation for a restricted kind of multistranded system called the 1D scaffolded DNA computer. This model of computation thermodynamically favours correct outputs over erroneous states, simulates finite state machines in 1D and Boolean circuits in 2D, and is amenable to DNA storage applications. In an effort to begin to ask the question of whether we can naturally compare the expressivity of nucleic acid systems based on the computational complexity of prediction of their preferred energetic states, we show our MFE problem is in logspace (the complexity class L), making it perhaps one of the simplest known, natural, nucleic acid MFE problems. Finally, we provide a stochastic kinetic simulator for the 1D scaffolded DNA computer and evaluate strategies for efficiently speeding up this thermodynamically favourable system in a constant-temperature kinetic regime