Self-assembly programming of DNA polyominoes

Hui San Ong, Mohd Syafiq-Rahim, Noor Hayaty Abu Kasim, Mohd Firdaus Mohd Raih, Effirul Ikhwan Ramlan

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)141-151
Number of pages11
JournalJournal of Biotechnology
Volume236
DOIs
Publication statusPublished - 20 Oct 2016

Fingerprint

Self assembly
DNA
Fabrication
Nanostructures
Atomic Force Microscopy
Single-Stranded DNA
Imagery (Psychotherapy)
Tile
Atomic force microscopy

Keywords

  • DNA nanofabrication
  • DNA nanotechnology
  • DNA polyominoes
  • Molecular programming
  • Self-assembly

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology

Cite this

Ong, H. S., Syafiq-Rahim, M., Kasim, N. H. A., Mohd Raih, M. F., & Ramlan, E. I. (2016). Self-assembly programming of DNA polyominoes. Journal of Biotechnology, 236, 141-151. https://doi.org/10.1016/j.jbiotec.2016.08.017

Self-assembly programming of DNA polyominoes. / Ong, Hui San; Syafiq-Rahim, Mohd; Kasim, Noor Hayaty Abu; Mohd Raih, Mohd Firdaus; Ramlan, Effirul Ikhwan.

In: Journal of Biotechnology, Vol. 236, 20.10.2016, p. 141-151.

Research output: Contribution to journalArticle

Ong, Hui San ; Syafiq-Rahim, Mohd ; Kasim, Noor Hayaty Abu ; Mohd Raih, Mohd Firdaus ; Ramlan, Effirul Ikhwan. / Self-assembly programming of DNA polyominoes. In: Journal of Biotechnology. 2016 ; Vol. 236. pp. 141-151.
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