Browsing by Subject "Cubane"

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    Cubane cluster surface for pyrimidine nucleobases relaxation: DFT approach
    (Danishgah-i Azad-i Islami, 2020-12-27) Mirzaei, M.; Hadipour, N.; Gülseren, Oğuz
    Density functional theory (DFT) approach was employed to investigate relaxation processes of each of pyrimidine nucleobases (NBs); cytosine (C), thymine (T) and uracil (U), at the Cubane Cluster Surface (CCS). The main idea was about providing a material for recognition of NBs, in which a nanostructure form of cubane (CCS) was first generated by optimization process. In the next step, relaxation processes of each of NBs at the surface were investigated to examine the function of such system for NBs recognition. The results indicated that the electronic based molecular properties could work as proper parameters for recognizing such molecular system, in which energy gap (EG) could be referred for the purpose. Measuring EG could help to recognize the complexes of CCS-C, CCS-T and CCS-U from each other. Strength of such complex formations was investigated using values of binding energy (BE); CCS-U > CCS-C > CCS-T. Total results of EG, BE and additional atomic scale properties indicated that the investigated CCS could work very well to recognize U as the characteristic NB of RNA.
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    DNA codon recognition by a cubane wire: In silico approach
    (DergiPark, 2021) Mirzaei, M.; Hadipour, N.; Gülseren, Oğuz
    DNA codons, consisting of triplet nucleotides (NTs), could play important roles for RNA transcription and protein translation in living systems. Therefore, their recognition could be seen important for diagnosis and therapy purposes. Based on triplet sequence formations of Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) NTs, 64 codons were investigated in this work regarding their complexation with a molecular cubane (CUB) wire. To achieve this aim, each of singular 64 codons and CUB were optimized to be prepared for docking processes of complex formations. Hence, 64 complexes of codon-CUB were docked to see the recognition potency of CUB wire versus each of DNA codons. Interestingly, the obtained docking scores indicated that the CUB could work specifically versus the DNA codons, in which G-rich and A-rich triples were seen to be more favorable for complexation with CUB in comparison with other C-rich and T-rich triplet codons. Moreover, the results indicated that not pure G triplet but GAG codon was the most favorable one to be recognized by the CUB wire. However, pure T triplet was the worst one for such complex formations. The results of this work remarkably indicated that the CUB wire could work for recognition process of DNA codons from each other and such recognition could be very much specified for each of G-rich and A-rich codons, in which GAG codon was the best one among all the 64 investigated codons.