title: Self-assembly programming of DNA polyominoes.
abstract: Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously.
authors: Natural Computing Laboratory, Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors: Hui San
authors: HS
authors: Ong
authors: School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia.
authors: Mohd
authors: M
authors: Syafiq-Rahim
authors: Department of Restorative Dentistry, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
authors: Noor Hayaty Abu
authors: NH
authors: Kasim
authors: School of Biosciences and Biotechnology, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia.
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; Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture, and Healthcare (CRYSTAL), University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: effirul@um.edu.my.
authors: Effirul Ikhwan
authors: EI
authors: Ramlan
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D004587:Electrophoresis, Agar Gel; D018625:Microscopy, Atomic Force; D049329:Nanostructures / Q000737:chemistry / Q000648:ultrastructure; D036103:Nanotechnology / Q000379:methods*; D013816:Thermodynamics
chemical_list: D004247:DNA
keywords: DNA nanofabrication; DNA nanotechnology; DNA polyominoes; Molecular programming; Self-assembly