Investigation of structural and electronic properties of biologically important small nucleotides by molecular modeling

In eukaryotic organisms, the flow of genetic information is regulated by the transfer of information from DNA to mRNA ending with a functional protein. In addition, some proteins implicated in the transcription of a gene by binding to short DNA sequences in promoter region in order to initiate RNA synthesis. In this study, we aimed to generate 3D molecular modelling of the nucleotide (primarily mono-tetramer) structures whose specific biological functions are known and to reveal electronic properties of these structures. The Spartan'14 program was used to analysis of the conformer structures of the mono, di, tri and tetramer structures of the TATA-box sequence. The MOPAC2016 program with PM6-D3H4 method and Gaussian09 program at ωB97XD/6-311++G(d,p) level were used for optimizations and frequency calculations for each investigated conformer. Using the calculated results, the most stable structures were determined using the relative energies. Molecular structures were drawn by Discovery Studio Visualizer 2019. As a result, we found that the –H bond was formed between the –OH group of the ribose ring and -PO43 group of the nucleotide structure. In addition, we observed nucleobase conjugates (A=T) of tetranucleotide structures and CH−π bond, as non-covalent interaction.