An analysis of simple computational strategies to facilitate the design of functional molecular information processors

Abstract

BackgroundBiological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging.ResultsUsing three simple heuristics, we designed RNA sensors that can mimic the function of a seven-segment display (SSD). Ten independent and orthogonal sensors representing the numerals 0 to 9 are designed and constructed. Each sensor has its own unique oligonucleotide binding site region that is activated uniquely by a specific input. Each operator was subjected to a stringent in silico filtering. Random sensors were selected and functionally validated via ribozyme self cleavage assays that were visualized via electrophoresis.ConclusionsBy utilising simple permutation and randomisation in the sequence design phase, we have developed functional RNA sensors thus demonstrating that even the simplest of computational methods can greatly aid the design phase for constructing functional molecular devices.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1297-x) contains supplementary material, which is available to authorized users.

A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids

“…10 It is believed that this approach can potentially help in the analysis of the complex patterns of biological markers in biomedical applications. 11 …”