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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.

Genetic engineering field has become an imperative approach for enhancement of various bioproducts yield and productivity; and found extended applications in gene therapy, nanotechnology, as well as industrial microbiology. Modern genetic engineering tool CRISPR/Cas system, specifically the Type II system from Streptococcus pyogenes, is gaining traction in recent years and being utilized to engineer novel strains to overproduce primary fermentation product of interest. Employing this technology for non-model microorganism such as Clostridium spp is still restricted due to several limitations such as inadequate genome information, resistance against transformation, low plasmid replication, and the ability for gene expression. The prediction of CRISPR/Cas systems in microbial genomes is fundamentally the initial step towards exploitation of this technology to engineer Clostridium spp. In this study, we demonstrate a simple yet effective method to predict component of endogenous CRISPR/Cas systems, using Clostridium spp genomes as a proof-of-concept. We identified the “real” CRISPR array together with the cas gene operon consist of Type I B signature proteins in Clostridium pasteurianum which is in agreement with the previous report, implying that this strategy generates reliable CRISPR/Cas systems prediction. Thus, this provides a glimpse on how bioinformatics and biocomputational tools can be utilized to overcome barriers in genetic engineering.