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• W2478995280 abstract "Hybridization of surface-immobilized oligonucleotides to their complementary counterparts is central to the rational design of novel nano-devices and DNA sensors. In this study, we have adopted a unified approach of combining sensing experiments with molecular dynamics simulations to characterize the hybridization of a 23 nucleotide long single-strand probe DNA tethered to a gold surface. Experiments indicate significant conformational changes of DNA in close vicinity (∼1 nm) of the gold surface upon hybridization and also conformational heterogeneity within hybridized DNA, consistent with simulation results. Simulations show that the conformational heterogeneity on a gold surface arises due to stabilization of surface-adsorbed partial and full duplexes, resulting in impeded hybridization in comparison to what observed on a repulsive surface. Furthermore, these simulations indicate that hybridization could be improved by tuning the non-specific adsorption on a nano-patterned surface with an optimal patterning length. Simulations were performed on the probe tethered to gold nano-dots of varying (2-8 nm) diameter. An improved hybridization of the present probe sequence was only observed for the 6 nm gold dots patterned on a repulsive surface. Results reveal that the 2D nano-confinement provided by the 6 nm gold dot is optimal for reducing conformational heterogeneity for the specific sequence used in this study. Thus, improved DNA hybridization can be achieved on a gold nano-dot patterned repulsive surface, where the optimal dot diameter will depend on the probe length and sequence. In summary, this study provides mechanistic insights onto hybridization on gold and offers a unique method toward improved hybridization on a nano-patterned surface with an optimized patterning length." @default.
• W2478995280 created "2016-08-23" @default.
• W2478995280 creator A5035651665 @default.
• W2478995280 creator A5064335115 @default.
• W2478995280 date "2016-02-01" @default.
• W2478995280 modified "2023-09-28" @default.
• W2478995280 title "Mechanistic Influence of Nanometer Length-Scale Surface Chemistry on DNA Hybridization" @default.
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• W2478995280 doi "https://doi.org/10.1016/j.bpj.2015.11.2200" @default.
• W2478995280 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26051361" @default.
• W2478995280 hasPublicationYear "2016" @default.
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