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J Phys Chem B. 2016 Aug 25;120(33):8369-78. doi: 10.1021/acs.jpcb.6b02081. Epub 2016 May 4.

Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets.

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Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland.
Department of Biology, University of Warsaw , Miecznikowa 1, 02-096 Warsaw, Poland.
College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences , Banacha 2c, 02-097 Warsaw, Poland.


We have designed a protocol and server to aid in the search for putative binding sites in 16S rRNA that could be targeted by peptide nucleic acid oligomers. Various features of 16S rRNA were considered to score its regions as potential targets for sequence-specific binding that could result in inhibition of ribosome function. Specifically, apart from the functional importance of a particular rRNA region, we calculated its accessibility, flexibility, energetics of strand invasion by an oligomer, as well as similarity to human rRNA. To determine 16S rRNA flexibility in the ribosome context, we performed all-atom molecular dynamics simulations of the 30S subunit in explicit solvent. We proposed a few 16S RNA target sites, and one of them was tested experimentally to verify inhibition of bacterial growth by a peptide nucleic acid oligomer.

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