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

    Year: 2010

    Journal: Langmuir, 2010, 26 (22), pp 17339–17347, 20101201

    Authors: Singh A. †, Snyder S. †, Lee L. ‡, Johnston A.P.R ‡, Caruso F. ‡*, Yingling Y.G†*

    Last authors: Yaroslava G. Yingling

    Organizations: † 911 Partners Way, Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States ‡ Centre for Nanoscience and Nanotechnology, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia

    Country: USA, US, United States of America

    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.