About this project
The capability and strength of oligomer binding depends on multiple features of ribosomal RNA such as its function, secondary and tertiary structures, accessibility of a particular RNA fragment, and its dynamics. We have gathered and computed multiple characteristics of 16S rRNA and based on these the best target sites were chosen. The entire procedure, analyses and results are described in our publication A. Górska et al., Scanning of 16S RNA for peptide nucleic acid targets, J. Phys. Chem. B, doi:10.1021/acs.jpcb.6b2082. To calculate some of the properties we performed a full atom molecular dynamics simulation of the entire E. coli 30S ribosomal subunit (PDB code: 4v9d). From the trajectory we included the flexibility by mapping 16S rRNA with the average RMSF, number of hydrogen bonds and stacking energy. On the other hand, in order to asses the energy needed for an oligomer to bind to the targeted RNA region, we computed the opening energy of the targeted region. We used RNAEval to compute the free energy of the entire rRNA structure and subtract it from the free energy of the same structure in which the region of interest was open, i.e. the hydrogen bonds were removed. Translation inhibition may only occur if the targeted region is important for ribosome function. The region can be an antibiotic binding site, protein elongation, release, initiation factor binding site. Also, the regions participating in intersubunit bridges or A, P or E ribosomal sites where tRNA molecules interact with rRNA or the place were mRNA binds. In the Run bookmark you can provide your own sequence to be aligned to the 16S rRNA of E. coli. For the region that your oligomer sequence aligns to the characteristics will be outputted.