A single-stranded architecture for infinite counting
RNA serves not only as an intermediate medium for synthesizing proteins encoded on DNA but also as a primary medium for computing in vivo. An RNA is synthesized from its DNA template sequence by a molecular Xerox called polymerase nucleotide by nucleotide (A -> U, C -> G, G -> C, T -> A) sequentially; this process of RNA synthesis is called transcription and its product is called a transcript. While being thus synthesized, a transcript folds upon itself by having nucleotides form hydrogen bonds.
Recent studies revealed that this type of folding called cotranscriptional folding (CF) primarily drives various in-vivo computations. Cotranscriptional folding has turned out to be even programmable through an in-vitro implementation of an RNA transcript (or more precisely, its DNA template) which folds into a target "tile" structure cotranscriptionally (Geary, Rothemund, and Andersen, Science, 2014).
This talk aims at demonstrating how to program cotranscriptional folding for computing through our recent implementation of an infinite counter in a novel computational model "oritatami". The implementation is an extension of a fixed-bitwidth binary counter, which served as the first proof-of-concept demonstration of the model at its proposal (Geary et al., MFCS 2016).