Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study

0379074 - ÚOCHB 2013 RIV GB eng J - Journal Article
Kabeláč, Martin - Kroutil, O. - Předota, M. - Lankaš, Filip - Šíp, M.
Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study.
Physical Chemistry Chemical Physics. Roč. 14, č. 12 (2012), s. 4217-4229. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR GC204/09/J010; GA MŠMT LC512; GA AV ČR IAA400550808
Grant - others:GA ČR(CZ) GA203/08/0094; GA MŠk(CZ) LM2010005
Program: GA
Institutional research plan: CEZ:AV0Z40550506
Keywords : DNA * graphene * charge density * molecular dynamics * Amber
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.829, year: 2012

Molecular dynamics simulations of 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. A difference in the behaviour of the double stranded DNA and single stranded DNA was observed. The double stranded DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair, keeping its geometry close to the canonical B-DNA. The single stranded DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction.
Permanent Link: http://hdl.handle.net/11104/0210352