About: Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/pdf/10.1021/jp311180u
Description	Guanine to inosine (G -> I) substitution has often been used to study various properties of nucleic acids. Inosine differs from guanine only by loss of the N2 amino group, while both bases have similar electrostatic potentials. Therefore, G -> I substitution appears to be optimally suited to probe structural and thermodynamics effects of single H-bonds and atomic groups. However, recent experiments have revealed substantial difference in free energy impact of G -> I substitution in the context of B-DNA and A-RNA canonical helices, suggesting that the free energy changes reflect context-dependent balance of energy contributions rather than intrinsic strength of a single Fl-bond. In the present study, we complement the experiments by free energy computations using thermodynamics integration method based on extended explicit solvent molecular dynamics simulations. Guanine to inosine (G -> I) substitution has often been used to study various properties of nucleic acids. Inosine differs from guanine only by loss of the N2 amino group, while both bases have similar electrostatic potentials. Therefore, G -> I substitution appears to be optimally suited to probe structural and thermodynamics effects of single H-bonds and atomic groups. However, recent experiments have revealed substantial difference in free energy impact of G -> I substitution in the context of B-DNA and A-RNA canonical helices, suggesting that the free energy changes reflect context-dependent balance of energy contributions rather than intrinsic strength of a single Fl-bond. In the present study, we complement the experiments by free energy computations using thermodynamics integration method based on extended explicit solvent molecular dynamics simulations. (en)
Title	Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study (en)
skos:prefLabel	Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study (en)
skos:notation	RIV/00216224:14740/13:00067680!RIV14-MSM-14740___
http://linked.open...avai/predkladatel	Středoevropský technologický institut
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GBP305/12/G034), P(GPP301/11/P558), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	6
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Šponer, Jiří
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	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	71531
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00067680
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	FREE-ENERGY CALCULATIONS; PARTICLE MESH EWALD; ACID BASE-PAIRS; NUCLEIC-ACIDS; FORCE-FIELD; BIOMOLECULAR SIMULATIONS; SECONDARY STRUCTURE; HYDROGEN-BONDS; AMINO-GROUPS; A-RNA (en)
http://linked.open.../riv/klicoveSlovo	A-RNA ACID BASE-PAIRS AMINO-GROUPS BIOMOLECULAR SIMULATIONS FREE-ENERGY CALCULATIONS HYDROGEN-BONDS PARTICLE MESH EWALD SECONDARY STRUCTURE FORCE-FIELD NUCLEIC-ACIDS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[16D69D71BD95]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF PHYSICAL CHEMISTRY B
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Centre for RNA Biology Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	117
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Krepl, Miroslav
http://linked.open...ain/vavai/riv/wos	000315181600046
http://linked.open...n/vavai/riv/zamer	Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions
issn	1520-6106
number of pages	8 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp311180u
http://localhost/t...ganizacniJednotka	14740

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