About: Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations

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About: Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The geometries of DNA hexamer (5’-GGAACC-3’) and DNA 13-mer (5’-GCGTACACATGCG-3’) have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2’-bipyridyl and 3-methylisocarbostyril. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The geometries of DNA hexamer (5’-GGAACC-3’) and DNA 13-mer (5’-GCGTACACATGCG-3’) have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2’-bipyridyl and 3-methylisocarbostyril. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. (en) Geometrie hexamerů DNA (5’-GGAACC-3’) a 13-merů (5’-GCGTACACATGCG-3’) byla určena pomocí molekulové dynamiky založené na empirických potenciálech. Centrální pár kanonických bazí byl nahrazen párem nepolárních analogů. Celková stabilizační energie neporušeného a porušeného systému byla srovnatelná s experimentálně určenou stabilitou obou duplexů. Je to způsobeno velkým stackingem párů analogů, který kompenzuje chybějící energii vodíkových vazeb nahraženého páru adenin-thymin. (cs)
Title	Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations (en) Mimořádná termodynamická stabilita DNA duplexů modifikovaných nepolárními analogy je způsobena zvýšeným stackingem a příznivou solvatací: korelované ab initio výpočty a molekulová dynamika (cs)
skos:prefLabel	Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations (en) Mimořádná termodynamická stabilita DNA duplexů modifikovaných nepolárními analogy je způsobena zvýšeným stackingem a příznivou solvatací: korelované ab initio výpočty a molekulová dynamika (cs)
skos:notation	RIV/61388963:_____/06:00040282!RIV07-AV0-61388963
http://linked.open.../vavai/riv/strany	3587;3595
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/05/0009), P(GA203/05/0043), P(LC512), Z(AV0Z4055905)
http://linked.open...iv/cisloPeriodika	13
http://linked.open...vai/riv/dodaniDat	2007
http://linked.open...aciTvurceVysledku	Řeha, David 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	474951
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/06:00040282
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	ab initio calculations; DNA structures; molecular dynmics simulations; solvent effects (en)
http://linked.open.../riv/klicoveSlovo	ab initio calculations solvent effects DNA structures molecular dynmics simulations
http://linked.open...odStatuVydavatele	DE - Spolková republika Německo
http://linked.open...ontrolniKodProRIV	[DF39929AE518]
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	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Center for biomolecules and complex molecular systems Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs Conjugates of nucleobases with metal complexes as electroactive markers. Application of labelled oligonucleotides in electrochemical DNA sensors
http://linked.open...UplatneniVysledku	2006
http://linked.open...v/svazekPeriodika	12
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Hocek, Michal Řeha, David
http://linked.open...n/vavai/riv/zamer	Chemical principles of selected biological phenomena in medicine and ecology
issn	0947-6539
number of pages	8 (xsd:int)
is http://linked.open...avai/riv/vysledek of	Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations

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