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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F14%3A43887114" target="_blank" >RIV/60076658:12310/14:43887114 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12110/14:43887114

Výsledek na webu

<a href="http://pubs.acs.org/doi/abs/10.1021/jp509459y" target="_blank" >http://pubs.acs.org/doi/abs/10.1021/jp509459y</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/jp509459y" target="_blank" >10.1021/jp509459y</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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 freeenergy 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 flexib

Název v anglickém jazyce

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

Popis výsledku anglicky

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 freeenergy 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 flexib

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

<a href="/cs/project/GAP208%2F12%2F0622" target="_blank" >GAP208/12/0622: Interakce organokovových protinádorových komplexů s nukleovými kyselinami a proteiny: studium sekvenční a substrátové selektivity</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2014

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

—

Svazek periodika

118

Číslo periodika v rámci svazku

47

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

9

Strana od-do

13564-13572

Kód UT WoS článku

000345722900031

EID výsledku v databázi Scopus

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