title: DNA tetrominoes: the construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes.
abstract: The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.
authors.affiliation: Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Hui San
authors.initials: HS
authors.lastname: Ong
authors.affiliation: School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia.
authors.forename: Mohd Syafiq
authors.initials: MS
authors.lastname: Rahim
authors.affiliation: School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia.
authors.forename: Mohd
authors.initials: M
authors.lastname: Firdaus-Raih
authors.affiliation: Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Effirul Ikhwan
authors.initials: EI
authors.lastname: Ramlan
mesh_terms: D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D004586:Electrophoresis; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA