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

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	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. 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. (en)
Title	Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study (en)
skos:prefLabel	Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study (en)
skos:notation	RIV/61388963:_____/12:00379074!RIV13-AV0-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/08/0094), P(GC204/09/J010), P(IAA400550808), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	12
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Kabeláč, Martin Lankaš, Filip
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	141309
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/12:00379074
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DNA; graphene; charge density; molecular dynamics; Amber (en)
http://linked.open.../riv/klicoveSlovo	Amber DNA graphene molecular dynamics charge density
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[4F6B37BEAD9E]
http://linked.open...i/riv/nazevZdroje	Physical Chemistry Chemical Physics
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Modeling of DNA-chip hybridization in real conditions Hydration and solvation of building blocks of biopolymers Center for biomolecules and complex molecular systems Computer modeling of structural, dynamical and transport properties of fluids in nanospace
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	14
http://linked.open...iv/tvurceVysledku	Kabeláč, Martin Lankaš, Filip Kroutil, O. Předota, M. Šíp, M.
http://linked.open...ain/vavai/riv/wos	000300946600022
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	1463-9076
number of pages	13 (xsd:int)
http://bibframe.org/vocab/doi	10.1039/c2cp23540d

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