Evolving The Deoxyribozyme-Based Logic Gate Design Process Through MAYA-II Reconstruction

We previously described a tic-tac-toe playing molecular automaton, MAYA-II, constructed from a molecular array of deoxyribozyme-based logic gates, that uses oligonucleotides as inputs and outputs. We are now developing an ensemble modeling tool for high-throughput oligonucleotide input and logic gate designs. The modeling tool is based on exhaustive reconstruction of both intended and unintended reactions between MAYA-II gates and inputs, and seeks to directly correlate empirical observations with computational predictions. Here we describe exhaustive analysis of the MAYA-II Yes logic gates folding structures, both alone and in conjunction with the MAYA-II oligonucleotide inputs. Results indicate that in silico modeling accurately reflects experimental results, creating a predictive value and benchmark for future high-throughput oligonucleotide input and Yes gate designs. These studies serve purpose towards our goal of constructing a generalized oligonucleotide design library for expansion of molecular computation beyond hundreds, to millions of potential interactions, conferring greater functionality in terms of both reliability and complexity.