Structural and energetic basis for hybridization limits in high-density DNA monolayers
Autor: | Giacinto Scoles, Pietro Parisse, Loredana Casalis, Alessandro De Vita, Giovanni Doni, Alessandro Barducci, Maryse D. Nkoua Ngavouka, Giovanni M. Pavan |
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Přispěvatelé: | Giovanni, Doni, Maryse D., Nkoua Ngavouka, Alessandro, Barducci, Pietro, Parisse, DE VITA, Alessandro, Giacinto, Scole, Loredana, Casali, Giovanni M., Pavan |
Předmět: |
Steric effects
Molecular dynamic Surface Properties DNA Single-Stranded High density Nanotechnology 02 engineering and technology Molecular Dynamics Simulation Molecular dynamics Microscopy Atomic Force 010402 general chemistry 01 natural sciences surface science chemistry.chemical_compound Monolayer Molecule General Materials Science Nanoscopic scale Chemistry Oligonucleotide Nucleic Acid Hybridization 021001 nanoscience & nanotechnology Nanostructures 0104 chemical sciences Chemical physics Thermodynamics 0210 nano-technology DNA |
Zdroj: | Nanoscale |
Popis: | High-density monolayers (HDMs) of single-strand (ss) DNA are important nanoscale platforms for the fabrication of sensors and for mechanistic studies of enzymes on surfaces. Such systems can be used, for example, to monitor gene expression, and for the construction of more complex nanodevices via selective hybridization with the complementary oligos dissolved in solution. In this framework, controlling HDM hybridization is essential to control the final properties. Different studies demonstrate that at the typical density of approximate to 10(13) molecules per cm(2) no more than approximate to 30-40% of the HDM ssDNA is successfully hybridized. Until now, however, the origin of the HDM hybridization limit has remained unclear. In this work, molecular dynamics (MD) simulations of HDM systems with variable hybridization reveal that, independently of other experimental parameters, the effective hybridization for a HDM of this density is intrinsically limited by molecular and electrostatic crowding. A detailed structural analysis of the HDM model shows good agreement with our atomic force microscopy (AFM) experiments, and provides further insight into the steric hindrance behaviour and time-resolved surface topography of these nanostructured systems. The explicit relationship proposed between structural crowding and limited HDM hybridization offers a rationale to control the final properties of HDM-based nanodevices. |
Databáze: | OpenAIRE |
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