Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films

DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate...

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Bibliographic Details
Published in:Langmuir 2010-11, Vol.26 (22), p.17339-17347
Main Authors: Singh, Abhishek, Snyder, Stacy, Lee, Lillian, Johnston, Angus P. R, Caruso, Frank, Yingling, Yaroslava G
Format: Article
Language:English
Subjects:
Base Sequence
Biological Interfaces: Biocolloids, Biomolecular and Biomimetic Materials
Chemistry
DNA - chemistry
DNA - genetics
Exact sciences and technology
General and physical chemistry
Gold - chemistry
Metal Nanoparticles - chemistry
Molecular Dynamics Simulation
Nanotechnology - methods
Nucleic Acid Conformation
Nucleic Acid Hybridization
Oligodeoxyribonucleotides - chemistry
Oligodeoxyribonucleotides - genetics
Poly T - chemistry
Quartz Crystal Microbalance Techniques
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Summary:DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate that short (less than 10 bases) and long (more than 30 bases) single-stranded DNAs do not exhibit optimal film growth, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization. Interestingly, the presence of a duplex attached to a single strand significantly alters the persistence length of the polyT strands. Our study suggests that restrained polyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly.
ISSN:0743-7463
1520-5827
DOI:10.1021/la102762t