title: An analysis of simple computational strategies to facilitate the design of functional molecular information processors.
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.
authors: Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors: Yiling
authors: Y
authors: Lee
authors: School of Biosciences & Biotechnology, Faculty of Science & Technology, and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia.
authors: Rozieffa
authors: R
authors: Roslan
authors: Bioscience Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
authors: Shariza
authors: S
authors: Azizan
authors: School of Biosciences & Biotechnology, Faculty of Science & Technology, and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia. firdaus@mfrlab.org.
authors: Mohd
authors: M
authors: Firdaus-Raih
authors: Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia. effirul@um.edu.my.|Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture, and Healthcare (CRYSTAL), University of Malaya, 50603, Kuala Lumpur, Malaysia. effirul@um.edu.my.
authors: Effirul I
authors: http://orcid.org/0000-0002-8150-4782
authors: EI
authors: Ramlan
mesh_terms: D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D003198:Computer Simulation; D004591:Electrophoresis, Polyacrylamide Gel; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D016337:RNA, Catalytic; D012313:RNA
keywords: Computational RNA; Molecular computing; Molecular logic circuit; Molecular programming; RNA computing