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

Result code in 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>
Alternative codes found
RIV/60076658:12110/14:43887114
Result on the web
<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>

Result language
angličtina
Original language name
Cy3 and Cy5 Dyes Terminally Attached to 5'C End of DNA: Structure, Dynamics and Energetics
Original language 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 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
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
<a href="/en/project/GAP208%2F12%2F0622" target="_blank" >GAP208/12/0622: Interactions of organometallic antitumor compounds with nucleic acids and proteins: study of sequence and substrate selectivity</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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