An analysis of simple computational strategies to facilitate the design of functional molecular information processors
| Autor: | Shariza Azizan, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih, Rozieffa Roslan, Yiling Lee |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Theoretical computer science Computer science RNA computing 010402 general chemistry 01 natural sciences Biochemistry 03 medical and health sciences chemistry.chemical_compound Structural Biology Simple (abstract algebra) Computer Simulation RNA Catalytic Molecular Biology Computational RNA Applied Mathematics Computational Biology Reproducibility of Results RNA Molecular computing Molecular programming humanities 0104 chemical sciences Computer Science Applications ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology chemistry Electrophoresis Polyacrylamide Gel DNA microarray Molecular logic circuit DNA Research Article Macromolecule |
| Zdroj: | BMC Bioinformatics |
| ISSN: | 1471-2105 |
| DOI: | 10.1186/s12859-016-1297-x |
| Popis: | 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. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1297-x) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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