About: Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks

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

About: Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks 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 unwinding Gibbs energy (or duplex dissociation energy) is an important measure of the thermodynamic stability of DNA oligomers. This value can be measured experimentally or predicted by empirical models parametrised on experimental data. Our previously developed model based on accurate DFT-D calculations of interaction energies between nucleic acid bases corrected for solvation contribution. This work was successfully extended to cover variable lengths of oligomers. This model was further applied to oligomers containing inosine, an unnatural base. The results, however, are not satisfactory and it is clear that the model does not take into account all variables contributing to DNA stability. The unwinding Gibbs energy (or duplex dissociation energy) is an important measure of the thermodynamic stability of DNA oligomers. This value can be measured experimentally or predicted by empirical models parametrised on experimental data. Our previously developed model based on accurate DFT-D calculations of interaction energies between nucleic acid bases corrected for solvation contribution. This work was successfully extended to cover variable lengths of oligomers. This model was further applied to oligomers containing inosine, an unnatural base. The results, however, are not satisfactory and it is clear that the model does not take into account all variables contributing to DNA stability. (en) Gibbsova energie disociace dvojšroubovice DNA je důležité měřítko stability oligomerů DNA. Tato veličina může být měřena experimntálně, k jejímu odhadu se používají i empirické modely parametrizované na experimentální data. V předchozí práci jme vyvynuli nový model založený na přesných DFT-D výpočtech intrakčních energií mezi bázemi DNA, zahrnující i opravu o solvatační volnou energii. Tato práce rozšiřuje tento model na oligomery různé délky. Model byl také aplikován na sekvence obsahující nepřírodní bázi inosin. Výsledky pro tyto sekvence nejsou uspokojivé a ukazuje se, že navržený model nezahrnuje příspěvky nutné k popisu takovýchto struktur. (cs)
Title	Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks (en) Korelace mezi termodynamickou stabilitou dvojšroubovice DNA a interakčními a solvatačními energiemi stavebních bloků DNA (cs)
skos:prefLabel	Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks (en) Korelace mezi termodynamickou stabilitou dvojšroubovice DNA a interakčními a solvatačními energiemi stavebních bloků DNA (cs)
skos:notation	RIV/61388963:_____/08:00310559!RIV09-AV0-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/05/0009), P(GD203/05/H001), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	2
http://linked.open...vai/riv/dodaniDat	2009
http://linked.open...aciTvurceVysledku	Řezáč, Jan Hobza, Pavel
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	361391
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/08:00310559
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DNA duplex; interaction energy; stability (en)
http://linked.open.../riv/klicoveSlovo	DNA duplex stability interaction energy
http://linked.open...odStatuVydavatele	CZ - Česká republika
http://linked.open...ontrolniKodProRIV	[DA170AA68F35]
http://linked.open...i/riv/nazevZdroje	Collection of Czechoslovak Chemical Communications
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...vavai/riv/projekt	Center for biomolecules and complex molecular systems Experimental Study and Computer Modeling of the Structure and Function of the Complex Molecular Systems and Bio(macro)molecules Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs
http://linked.open...UplatneniVysledku	2008
http://linked.open...v/svazekPeriodika	73
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Řezáč, Jan
http://linked.open...ain/vavai/riv/wos	000253884000003
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	0010-0765
number of pages	14 (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, 58 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software