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

Yiling Lee, Rozieffa Roslan, Shariza Azizan, Mohd Firdaus-Raih, E. Ramlan

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Abstract

Background: Biological 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. Results: Using 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. Conclusions: By 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.

Original languageEnglish
Article number438
Pages (from-to)1-13
JournalBMC Bioinformatics
Volume17
Issue number1
DOIs
Publication statusPublished - 28 Oct 2016

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Keywords

  • Computational RNA
  • Molecular computing
  • Molecular logic circuit
  • Molecular programming
  • RNA computing

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