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A Bioinformatics Approach to Ribosomal Antibiotics Research Using Peptide-Peptide Nucleic Acid (PNA) Conjugates
Hyon Chang Kim1+, Seungpyo Hong1+, Hosang Jeon2, Seongjo Kim2, Dong Soon Choi3, Hyun Joo4, Churl K. Min3 and Han Jip Kim1,*
1Department of Biological Sciences, Ajou University, Suwon, Korea
2Division of Information & Computer Engineering, Ajou University, Suwon, Korea
3Department of Molecular Science & Technology, Ajou University, Suwon, Korea
4Department of Physiology and Biophysics, College of Medicine, Inje University, Busan, Korea
*Corresponding author
+These authors contributed equally to this work
  Published : October 31, 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Peptide - Peptide Nucleic Acid (PNA) conjugates are known for their antibacterial effects on several pathogens. Here we designed five PNA-peptide conjugates that consist of sequences originating from conservative sequences of 16S ribosomal RNA (rRNA) from hundreds of different bacterial species. Their antibacterial effects were tested on E. coli K12 and Klebsiella pneumoniae. The result shows the sequence-dependent antibacterial or bactericidal effects of the designed peptide-PNA conjugates. We also developed a bioinformatics tool and examined any possible off-target effects of the peptide-PNA we designed. Using this tool, we also predicted the least off-target sequences for further studies. Designing peptide-PNAs utilizing conservative 16S rRNA sequences may pave a way to developing broad-spectrum ribosomal antibiotics fighting life-threatening, drug-resistant infections.

Keyword: Peptide-Peptide Nucleic Acid , 16S rRNA , drug-resistant infections
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