DNA tetrominoes: The construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes

Hui San Ong, Mohd Syafiq Rahim, Mohd Firdaus-Raih, E. Ramlan

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

LanguageEnglish
Article numbere0134520
JournalPLoS ONE
Volume10
Issue number8
DOIs
Publication statusPublished - 10 Aug 2015

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nanomaterials
Nanostructures
DNA
Nucleic Acids
nucleic acids
Sequence Deletion
Insertional Mutagenesis
Electrophoresis
Thermodynamics
Evolutionary algorithms
Gels
thermodynamics
transposons
gel electrophoresis
Mutation
mutation

Cite this

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DNA tetrominoes : The construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes. / Ong, Hui San; Rahim, Mohd Syafiq; Firdaus-Raih, Mohd; Ramlan, E.

In: PLoS ONE, Vol. 10, No. 8, e0134520, 10.08.2015.

Research output: Contribution to journalArticle

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