• About
  • Policies
  • What is open access
  • Library
  • Contact
Advanced search
      View Item 
      •   BUIR Home
      • Scholarly Publications
      • Faculty of Science
      • Department of Physics
      • View Item
      •   BUIR Home
      • Scholarly Publications
      • Faculty of Science
      • Department of Physics
      • View Item
      JavaScript is disabled for your browser. Some features of this site may not work without it.

      DNA codon recognition by a cubane wire: In silico approach

      Thumbnail
      View / Download
      319.3 Kb
      Author(s)
      Mirzaei, M.
      Hadipour, N.
      Gülseren, Oğuz
      Date
      2021
      Source Title
      Turkish Computational and Theoretical Chemistry
      Electronic ISSN
      2602-3237
      Publisher
      DergiPark
      Volume
      5
      Issue
      1
      Pages
      13 - 19
      Language
      English
      Type
      Article
      Item Usage Stats
      31
      views
      45
      downloads
      Abstract
      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.
      Keywords
      Codon
      DNA
      Triplet
      Cubane
      In silico
      Permalink
      http://hdl.handle.net/11693/77208
      Published Version (Please cite this version)
      https://doi.org/10.33435/tcandtc.828634
      Collections
      • Department of Physics 2550
      Show full item record

      Browse

      All of BUIRCommunities & CollectionsTitlesAuthorsAdvisorsBy Issue DateKeywordsTypeDepartmentsCoursesThis CollectionTitlesAuthorsAdvisorsBy Issue DateKeywordsTypeDepartmentsCourses

      My Account

      Login

      Statistics

      View Usage StatisticsView Google Analytics Statistics

      Bilkent University

      If you have trouble accessing this page and need to request an alternate format, contact the site administrator. Phone: (312) 290 2976
      © Bilkent University - Library IT

      Contact Us | Send Feedback | Off-Campus Access | Admin | Privacy