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

Abstract

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.

Exploring the Molecular Basis of dsRNA Recognition by Mss116p Using Molecular Dynamics Simulations and Free-Energy Calculations

“…Detailed information would contribute to the further understanding of the essence of protein−RNA interactions and demonstrate the origin of the binding affinity. 24 To characterize the recognition and binding mechanism of the Mss116p-dsRNA interaction and identify the key residues in the interaction, 20 ns MD simulations followed by the molecular mechanics generalized Born surface area (MM-GBSA) calculation were performed on the Mss116p-dsRNA complex. Furthermore, MD simulations of mutants Q412A and D441A with dsRNA complexes were executed to illustrate the origin of the reduced binding affinity.…”

Preparation of mecA Biosensor Based On Gold Nanoparticles to Determine Methicillin Resistant Staphylococcus Aureus (MRSA) Strains from Human and Animals

“…The length of probes used was from 20 and 21 for probe 1 of mecA and probe 2 mecA, respectively. The selected length ensured optimum immobilization according to (Singh et al, 2010). In the current study different spacers were used.…”

Sensing Techniques Involving Thin Films for Studying Biomolecular Interactions and Membrane Fouling Phenomena

“…In this sense, QCM-D can also contribute to better characterize sensing applications involving DNA which can be understood as yet another type of polymer brush. Layer-by-layer DNA fi lms [11], DNA hybridization [12], Holliday junctions [13], and aptamer-protein interactions [14] have been reported where the dissipation served as a major parameter for this fi lm characterization. Using a small molecule binding aptamer as a model system, Serrano Santos et al not only determined the interaction of adenosine-5´-monophosphate (AMP) with AMP-binding aptamer fi lms using QCM-D, but also succeeded in quantifying in situ and in real-time the structural changes that occur in this particular DNA aptamer when binding to AMP [15].…”