Introduction: Using antisense oligonucleotides for targeting essential genes is one of the new methods to control microbial infections. The aim of this study was to investigate four antisense oligonucleotides against rpoD gene of staphylococcus aurous, and to find the probable match in human genes.
Method: First, rpoD gene of staphylococcus aurous was extracted from NCBI (National Center for Biotechnology Information) database. Then, its mRNA sequence was generated and four antisense were selected according to secondary structure of mRNA and thermodynamic parameters. Finally, matching of each selected antisense and all human genome with Nblast algorithm, was evaluated.
Results: This study showed that according to secondary structure and thermodynamic parameters, antisense 1, GAAGAAGTTGGTA, was the best antisense, and had the least Overall ∆G. Matching antisense sequences showed that antisense 1, 2, and 4 had different targets at human mRNA level. But, antisense 3, GAAGCAATTAATT, was ideal and could target only rpoD gene.
Conclusion: Given to secondary structure and thermodynamic parameters, the adequate antisense could be selected for target gene, but most of these antisense targeting other genes in human cells.
