DNA Codon Recognition by a Cubane Wire: In Silico Approach

Authors : Mahmoud MIRZAEI, Nasser HADİPOUR, Oguz GULSEREN

Pages : 13-19

Doi:10.33435/tcandtc.828634

View : 20 | Download : 9

Publication Date : 2021-06-15

Article Type : Research Paper

Abstract :DNA codons, consisting of triplet nucleotides insert ignore into journalissuearticles values(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 insert ignore into journalissuearticles values(A);, Guanine insert ignore into journalissuearticles values(G);, Cytosine insert ignore into journalissuearticles values(C); and Thymine insert ignore into journalissuearticles values(T); NTs, 64 codons were investigated in this work regarding their complexation with a molecular cubane insert ignore into journalissuearticles values(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.
Keywords : Codon, DNA, Triplet, Cubane, In silico