title: Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study.
abstract: Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic. martin.kabelac@uochb.cas.cz
authors.forename: M
authors.initials: M
authors.lastname: Kabeláč
authors.forename: O
authors.initials: O
authors.lastname: Kroutil
authors.forename: M
authors.initials: M
authors.lastname: Předota
authors.forename: F
authors.initials: F
authors.lastname: Lankaš
authors.forename: M
authors.initials: M
authors.lastname: Šíp
mesh_terms: D004247:DNA / Q000737:chemistry*; D006108:Graphite / Q000737:chemistry*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009841:Oligonucleotides / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D009841:Oligonucleotides; D006108:Graphite; D004247:DNA