About: Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/jp509459y
Description	Cy3 and Cy5 cyanine dyes terminally attached to the 5'C end (C1) of the DNA oligonucleotide were studied by metadynamics (MTD), molecular dynamics (MD), and density-functional methods with dispersion corrections (DFT-D). MTD simulations explored the free energy surface (FES) of the dyeDNA interactions, which included stacking and major groove binding motifs and unstacked structures. Dynamics of the stacked structures was studied by the MD simulations. All possible combinations of stacking interactions between the two indole rings of the dyes and the neighbor guanine and cytosine rings were observed. The most probable interaction included the stacking between the dyes distal indole ring and the guanine base. In similar to 10% of the structures the delocalized pi-electrons of the dyes polymethine linkers played a key role in the dyeDNA dispersion interactions. The stacked conformers of the Cy3 dye were confirmed as true minima by DFT-D full optimizations. The stacked dye decreased flexibility up to two neighbor base pairs. Cy3 and Cy5 cyanine dyes terminally attached to the 5'C end (C1) of the DNA oligonucleotide were studied by metadynamics (MTD), molecular dynamics (MD), and density-functional methods with dispersion corrections (DFT-D). MTD simulations explored the free energy surface (FES) of the dyeDNA interactions, which included stacking and major groove binding motifs and unstacked structures. Dynamics of the stacked structures was studied by the MD simulations. All possible combinations of stacking interactions between the two indole rings of the dyes and the neighbor guanine and cytosine rings were observed. The most probable interaction included the stacking between the dyes distal indole ring and the guanine base. In similar to 10% of the structures the delocalized pi-electrons of the dyes polymethine linkers played a key role in the dyeDNA dispersion interactions. The stacked conformers of the Cy3 dye were confirmed as true minima by DFT-D full optimizations. The stacked dye decreased flexibility up to two neighbor base pairs. (en)
Title	Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics (en)
skos:prefLabel	Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics (en)
skos:notation	RIV/60076658:12110/14:43887114!RIV15-GA0-12110___
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(GAP208/12/0622)
http://linked.open...iv/cisloPeriodika	47
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šíp, Miroslav Chval, Zdeněk Kroutil, Ondřej
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	Jihočeská univerzita v Českých Budějovicích / Zdravotně sociální fakulta
http://linked.open...dnocenehoVysledku	9564
http://linked.open...ai/riv/idVysledku	RIV/60076658:12110/14:43887114
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	SIMULATIONS; BINDING; FLUORESCENCE; FORCE-FIELD; NUCLEIC-ACIDS; MOLECULAR-DYNAMICS; BACK-ISOMERIZATION; PHOTOINDUCED ISOMERIZATION; DOUBLE-STRANDED DNA; RESONANCE ENERGY-TRANSFER (en)
http://linked.open.../riv/klicoveSlovo	FLUORESCENCE RESONANCE ENERGY-TRANSFER BINDING FORCE-FIELD NUCLEIC-ACIDS MOLECULAR-DYNAMICS SIMULATIONS BACK-ISOMERIZATION DOUBLE-STRANDED DNA PHOTOINDUCED ISOMERIZATION
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[C3D521299546]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
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	Interactions of organometallic antitumor compounds with nucleic acids and proteins: study of sequence and substrate selectivity
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	118
http://linked.open...iv/tvurceVysledku	Chval, Zdeněk Romancová, Ingrid Šíp, Miroslav Kroutil, Ondřej
http://linked.open...ain/vavai/riv/wos	000345722900031
issn	1520-6106
number of pages	9 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp509459y
http://localhost/t...ganizacniJednotka	12110

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