About: Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The geometries of a 13 mer of a DNA double helix (5’-GCGTACACATGCG-3’) were determined by molecular dynamics simulations using a Cornell et al. empirical force field. The bases in the central base pair were replaced by a series of hydrophobic base analogues (phenyl, biphenyl, phenylnaphathalene, phenylanthracene and phenylphenanthrene). Due to the large fluctuations of the systems, an average geometry could not be determined. The interaction energies of the Model A, which consisted of three central steps of a duplex without a sugar phosphate backbone, taken from molecular dynamics simulations, were calculated by the selfconsistent charge density functional based tight-binding (SCC-DFTB-D) method and were subsequently averaged. The higher the stability of the systems the higher the aromaticity of the base analogues. To estimate the desolvation energy of the duplex, the COSMO continuum solvent model was used and the calculations were provided on a larger model. The geometries of a 13 mer of a DNA double helix (5’-GCGTACACATGCG-3’) were determined by molecular dynamics simulations using a Cornell et al. empirical force field. The bases in the central base pair were replaced by a series of hydrophobic base analogues (phenyl, biphenyl, phenylnaphathalene, phenylanthracene and phenylphenanthrene). Due to the large fluctuations of the systems, an average geometry could not be determined. The interaction energies of the Model A, which consisted of three central steps of a duplex without a sugar phosphate backbone, taken from molecular dynamics simulations, were calculated by the selfconsistent charge density functional based tight-binding (SCC-DFTB-D) method and were subsequently averaged. The higher the stability of the systems the higher the aromaticity of the base analogues. To estimate the desolvation energy of the duplex, the COSMO continuum solvent model was used and the calculations were provided on a larger model. (en)
Title	Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues (en)
skos:prefLabel	Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues (en)
skos:notation	RIV/61388963:_____/09:00328589!RIV10-MSM-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/05/0043), P(IAA400550510), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	31
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Zendlová, Lucie Hobza, Pavel Hocek, Michal
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	346177
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/09:00328589
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DNA structures; solvent effects; stacking interactions (en)
http://linked.open.../riv/klicoveSlovo	solvent effects DNA structures stacking interactions
http://linked.open...odStatuVydavatele	DE - Spolková republika Německo
http://linked.open...ontrolniKodProRIV	[AD45D9534AA3]
http://linked.open...i/riv/nazevZdroje	Chemistry - A European Journal
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Center for biomolecules and complex molecular systems Conjugates of nucleobases with metal complexes as electroactive markers. Application of labelled oligonucleotides in electrochemical DNA sensors Accurate calculations of stabilization energies of stacking and hydrogen bonding: nucleic acid bases and proteins
http://linked.open...UplatneniVysledku	2009
http://linked.open...v/svazekPeriodika	15
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Hocek, Michal Zendlová, Lucie Řeha, D.
http://linked.open...ain/vavai/riv/wos	000268845000013
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	0947-6539
number of pages	10 (xsd:int)

Faceted Search & Find service v1.16.118 as of Jun 21 2024

Alternative Linked Data Documents: ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3240 as of Jun 21 2024, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (126 GB total memory, 38 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software